---
_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.
date_created: 2018-12-11T11:50:16Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2023-09-07T11:42:26Z
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'
file_name: PhDThesis_HandeAcar_1230.pdf
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content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:51:13Z
date_updated: 2021-02-22T11:51:13Z
file_id: '9184'
file_name: 2016_Thesis_HandeAcar.pdf
file_size: 3682711
relation: main_file
success: 1
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1122'
abstract:
- lang: eng
text: "Computer graphics is an extremely exciting field for two reasons. On the
one hand,\r\nthere is a healthy injection of pragmatism coming from the visual
effects industry\r\nthat want robust algorithms that work so they can produce
results at an increasingly\r\nfrantic pace. On the other hand, they must always
try to push the envelope and\r\nachieve the impossible to wow their audiences
in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism,
and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance
that it will pan into something\r\nuseful.\r\nWater simulation has been in visual
effects for decades, however it still remains\r\nextremely challenging because
of its high computational cost and difficult artdirectability.\r\nThe work in
this thesis tries to address some of these difficulties.\r\nSpecifically, we make
the following three novel contributions to the state-of-the-art\r\nin water simulation
for visual effects.\r\nFirst, we develop the first algorithm that can convert
any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art
methods at the time\r\ncould only handle surfaces with fixed connectivity, but
we are the first to be able to\r\nhandle surfaces that merge and split apart.
This is important for water simulation\r\npractitioners, because it allows them
to convert splashy water surfaces extracted\r\nfrom particles or simulated using
grid-based level sets into triangle meshes that can\r\nbe either textured and
enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm
to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions
of human performances.\r\nSecond, we formulate a surface-based energy that measures
the deviation of a\r\nwater surface froma physically valid state. Such discrepancies
arise when there is a\r\nmismatch in the degrees of freedom between the water
surface and the underlying\r\nphysics solver. This commonly happens when practitioners
use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution
grid-based surfaces\r\nare combined with low-resolution physics. Following the
direction of steepest\r\ndescent on our surface-based energy, we can either smooth
these artifacts or turn\r\nthem into high-resolution waves by interpreting the
energy as a physical potential.\r\nThird, we extend state-of-the-art techniques
in non-reflecting boundaries to handle spatially and time-varying background flows.
This allows a novel new\r\nworkflow where practitioners can re-simulate part of
an existing simulation, such\r\nas removing a solid obstacle, adding a new splash
or locally changing the resolution.\r\nSuch changes can easily lead to new waves
in the re-simulated region that would\r\nreflect off of the new simulation boundary,
effectively ruining the illusion of a\r\nseamless simulation boundary between
the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure
that such waves are absorbed."
acknowledgement: "First and foremost I would like to thank Chris. I have been incredibly
lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right
thing in all walks of\r\nlife is something I admire and aspire to. I also really
appreciate the fact that when\r\nworking with you it felt like we were equals. I
think we had a very synergetic work\r\nrelationship: I learned immensely from you,
but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would
like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working
with you. You showed me how to persevere and keep morale\r\nhigh when things were
looking the most bleak before the deadline. You are an\r\nincredible motivator and
super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker
games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing
you by asking about your guitar playing that one\r\ntime. You really are quite awesome!
Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch
researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also
like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have
learned so much. The excellent discussions we had in reading\r\ngroups and research
meetings really helped me become a better researcher!\r\nNext, I would like to thank
all the amazing people that I met during my PhD\r\nstudies, both at IST Austria,
in Vienna and elsewhere. "
alternative_title:
- ISTA Thesis
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:th_640
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:th_640
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:th_640.
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.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.
short: M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:16Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2024-02-21T13:50:48Z
day: '15'
ddc:
- '004'
- '005'
- '006'
- '532'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_640
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:02Z
date_updated: 2018-12-12T10:13:02Z
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page: '114'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6238'
related_material:
record:
- id: '5558'
relation: other
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1123'
abstract:
- lang: eng
text: "Motivated by topological Tverberg-type problems in topological combinatorics
and by classical\r\nresults about embeddings (maps without double points), we
study the question whether a finite\r\nsimplicial complex K can be mapped into
Rd without triple, quadruple, or, more generally, r-fold points (image points
with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular,
we are interested in maps f : K → Rd that have no global r -fold intersection
points, i.e., no r -fold points with preimages in r pairwise disjoint simplices
of K , and we seek necessary and sufficient conditions for the existence of such
maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results
for embeddings, in particular of the completeness of the Van Kampen obstruction
\ for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically,
we show that under suitable restrictions on the dimensions(viz., if dimK = (r
≥ 1)k and d = rk \\ for some k ≥ 3), a well-known deleted product criterion
(DPC ) is not only necessary but also sufficient for the existence of maps without
global r -fold points. Our main technical tool is a higher-multiplicity version
of the classical Whitney trick , by which pairs of isolated r -fold points of
opposite sign can be eliminated by local modiffications of the map, assuming
codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that
suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence
of equivariant maps, might yield an approach to disproving the remaining open
cases of the the long-standing topological Tverberg conjecture , i.e., to construct
maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime
power and\r\nN = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency
of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K =
σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension
3 obstacle" and\r\nto construct the first counterexamples to the topological
Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime
power, by a reduction1 to a suitable lower-dimensional skeleton, for which the
codimension 3 restriction is satisfied and maps without r -Tverberg points exist
by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present
a different construction (which does not use the constraint method) that yields
counterexamples for d ≥ 3r , r not a prime power. "
acknowledgement: "Foremost, I would like to thank Uli Wagner for introducing me to
the exciting interface between\r\ntopology and combinatorics, and for our subsequent
years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection
points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy
Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and
IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril
Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek
Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand
Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner
and Roman Karasev\r\nfor their careful reading of the present manuscript and for
the many improvements they suggested."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
citation:
ama: 'Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney
trick for the topological Tverberg conjecture. 2016.'
apa: 'Mabillard, I. (2016). Eliminating higher-multiplicity intersections: an
r-fold Whitney trick for the topological Tverberg conjecture. Institute of
Science and Technology Austria.'
chicago: 'Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold
Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and
Technology Austria, 2016.'
ieee: 'I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney
trick for the topological Tverberg conjecture,” Institute of Science and Technology
Austria, 2016.'
ista: 'Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold
Whitney trick for the topological Tverberg conjecture. Institute of Science and
Technology Austria.'
mla: 'Mabillard, Isaac. Eliminating Higher-Multiplicity Intersections: An r-Fold
Whitney Trick for the Topological Tverberg Conjecture. Institute of Science
and Technology Austria, 2016.'
short: 'I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney
Trick for the Topological Tverberg Conjecture, Institute of Science and Technology
Austria, 2016.'
date_created: 2018-12-11T11:50:16Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:56:28Z
day: '01'
ddc:
- '500'
degree_awarded: PhD
department:
- _id: UlWa
file:
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checksum: 2d140cc924cd1b764544906fc22684ef
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creator: dernst
date_created: 2019-08-13T08:45:27Z
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oa: 1
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page: '55'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6237'
related_material:
record:
- id: '2159'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: 'Eliminating higher-multiplicity intersections: an r-fold Whitney trick for
the topological Tverberg conjecture'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1124'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maurizio
full_name: Morri, Maurizio
id: 4863116E-F248-11E8-B48F-1D18A9856A87
last_name: Morri
citation:
ama: Morri M. Optical functionalization of human class A orphan G-protein coupled
receptors. 2016.
apa: Morri, M. (2016). Optical functionalization of human class A orphan G-protein
coupled receptors. Institute of Science and Technology Austria.
chicago: Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein
Coupled Receptors.” Institute of Science and Technology Austria, 2016.
ieee: M. Morri, “Optical functionalization of human class A orphan G-protein coupled
receptors,” Institute of Science and Technology Austria, 2016.
ista: Morri M. 2016. Optical functionalization of human class A orphan G-protein
coupled receptors. Institute of Science and Technology Austria.
mla: Morri, Maurizio. Optical Functionalization of Human Class A Orphan G-Protein
Coupled Receptors. Institute of Science and Technology Austria, 2016.
short: M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled
Receptors, Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-07T11:43:03Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: HaJa
file:
- access_level: closed
checksum: b439803ac0827cdddd56562a54e3b53b
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- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '129'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6236'
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Optical functionalization of human class A orphan G-protein coupled receptors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_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.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-05-28T11:57:05Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
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publication_identifier:
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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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_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.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-09-07T11:52:03Z
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
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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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1128'
abstract:
- lang: eng
text: "The process of gene expression is central to the modern understanding of
how cellular systems\r\nfunction. In this process, a special kind of regulatory
proteins, called transcription factors,\r\nare important to determine how much
protein is produced from a given gene. As biological\r\ninformation is transmitted
from transcription factor concentration to mRNA levels to amounts of\r\nprotein,
various sources of noise arise and pose limits to the fidelity of intracellular
signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene
expression: (i) the mathematical\r\ndescription of complex promoters responsible
for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information
processing the cell faces due to the interference from multiple\r\nfluctuating
signals, (iii) how the presence of gene expression noise influences the evolution\r\nof
regulatory sequences, (iv) and tools for the experimental study of origins and
consequences\r\nof cell-cell heterogeneity, including an application to bacterial
stress response systems."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
citation:
ama: Rieckh G. Studying the complexities of transcriptional regulation. 2016.
apa: Rieckh, G. (2016). Studying the complexities of transcriptional regulation.
Institute of Science and Technology Austria.
chicago: Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.”
Institute of Science and Technology Austria, 2016.
ieee: G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute
of Science and Technology Austria, 2016.
ista: Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute
of Science and Technology Austria.
mla: Rieckh, Georg. Studying the Complexities of Transcriptional Regulation.
Institute of Science and Technology Austria, 2016.
short: G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute
of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:18Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:44:34Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GaTk
file:
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checksum: ec453918c3bf8e6f460fd1156ef7b493
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creator: dernst
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creator: dernst
date_created: 2020-09-21T11:30:40Z
date_updated: 2020-09-21T11:30:40Z
file_id: '8542'
file_name: Thesis_Georg_Rieckh.pdf
file_size: 6096178
relation: main_file
success: 1
file_date_updated: 2020-09-21T11:30:40Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '114'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6232'
status: public
supervisor:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
title: Studying the complexities of transcriptional regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1129'
abstract:
- lang: eng
text: "Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms.
Despite its importance, basic questions regarding force transduction\r\nor directional
sensing are still heavily investigated. Directed migration of cells\r\nguided
by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as
embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al.,
2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise
adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009),
or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton
et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment
sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic
migration by inducing adhesion to adhesive ligands and directional\r\nguidance
(Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the
cellular response to immobilized guidance cues requires in vitro assays\r\nthat
foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular
scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration
of haptotactic cell migration through design and employment of such\r\nassays
represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes,
which after encountering danger\r\nsignals such as pathogens in peripheral organs
instruct naïve T-cells and\r\nconsequently the adaptive immune response in the
lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery,
DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber
et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients
have not yet been addressed. The main reason for this is the lack of\r\nan assay
that offers diverse haptotactic environments, hence allowing the study\r\nof DC
migration as a response to different signals of immobilized guidance cue.\r\nIn
this work, we developed an in vitro assay that enables us to\r\nquantitatively
assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning
with physically confining migration conditions. With this tool at hand, we studied
the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis.
We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration
in combination with the local\r\nsteepness of the gradient. Our analysis suggests
that the directionality of\r\nmigrating DCs is governed by the signal-to-noise
ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21
gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic
guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also
able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To
this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which
is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization
(Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial
for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm
those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic
guidance cues\r\noften coincide and compete with soluble chemotactic guidance
cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive
cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating
DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing
chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess
these complex coinciding immobilized and soluble\r\nguidance cues, we implemented
our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing
for chemotactic gradient generation. To validate\r\nthe assay, we observed DC
migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis
has been studied intensively over the\r\nlast century. However, quantitative studies
leading to conceptual models are\r\nlargely missing, again due to the lack of
a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro
assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished
by stable passivation of the surface. In\r\naddition, controlled adhesion must
be sustainable, quantifiable and dose\r\ndependent in order to create homogenous
gradients. Therefore, we developed a novel covalent photo-patterning technique
satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol
(PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to
direct cell migration. This\r\napproach allowed us to characterize the haptotactic
migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined
patterns of adhesive cue\r\nallowed us to control for cell shape and growth on
a subcellular scale."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
acknowledgement: "First, I would like to thank Michael Sixt for being a great supervisor,
mentor and\r\nscientist. I highly appreciate his guidance and continued support.
Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to
pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe
sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel
Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice
and encouragement during our regular progress meetings.\r\nI also want to thank
the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for
amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant
factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere
as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank
my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries,
Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf,
Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz,
Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing
time with many\r\nlegendary evenings and events. Along these lines I want to thank
the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions.
I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank
the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches.
In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens,
Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny,
Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful
after-lunch matches.\r\nI would not have been able to analyze the thousands of cell
trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration
with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings,
discussions and graphs and of course for proofreading and\r\nadvice for this thesis.
For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like
to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing
me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS
coated coverslips and help with anything\r\nmicro-fabrication related. And Maria
Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her
it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva,
Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility
as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for
excellent technical support. At this\r\npoint I especially want to thank Robert
for countless image analyses and\r\ntechnical ideas. Always interested and creative
he played an essential role in all\r\nof my projects.\r\nAdditionally I want to
thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for
scientific and especially mental support in all\r\nthose years, countless coffee
sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
citation:
ama: Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.
apa: Schwarz, J. (2016). Quantitative analysis of haptotactic cell migration.
Institute of Science and Technology Austria.
chicago: Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute
of Science and Technology Austria, 2016.
ieee: J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute
of Science and Technology Austria, 2016.
ista: Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute
of Science and Technology Austria.
mla: Schwarz, Jan. Quantitative Analysis of Haptotactic Cell Migration. Institute
of Science and Technology Austria, 2016.
short: J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute
of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:18Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:54:33Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
file:
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creator: dernst
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creator: dernst
date_created: 2021-02-22T11:43:14Z
date_updated: 2021-02-22T11:43:14Z
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file_date_updated: 2021-02-22T11:43:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '178'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6231'
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: Quantitative analysis of haptotactic cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_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.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-07T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1130
ec_funded: 1
file:
- access_level: open_access
checksum: 319a506831650327e85376db41fc1094
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:39:32Z
date_updated: 2021-02-22T11:39:32Z
file_id: '9179'
file_name: 2016_Tarrach_Thesis.pdf
file_size: 1523935
relation: main_file
success: 1
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checksum: 39efcd789f0ad859ff15652cb7afc412
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:14:38Z
date_updated: 2021-11-17T13:46:55Z
file_id: '10296'
file_name: 2016_Tarrach_Thesispdfa.pdf
file_size: 1306068
relation: main_file
file_date_updated: 2021-11-17T13:46:55Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf
month: '07'
oa: 1
oa_version: Published Version
page: '151'
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: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6230'
related_material:
record:
- id: '1729'
relation: part_of_dissertation
status: public
- id: '2218'
relation: part_of_dissertation
status: public
- id: '2445'
relation: part_of_dissertation
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_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.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 66cb61a59943e4fb7447c6a86be5ef51
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:53:52Z
date_updated: 2019-08-13T08:53:52Z
file_id: '6810'
file_name: Tugrul_thesis_w_signature_page.pdf
file_size: 3695257
relation: main_file
- access_level: open_access
checksum: 293e388d70563760f6b24c3e66283dda
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:45:20Z
date_updated: 2021-02-22T11:45:20Z
file_id: '9182'
file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:45:20Z
has_accepted_license: '1'
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:
record:
- id: '5554'
relation: research_data
status: public
- id: '1666'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1134'
abstract:
- lang: eng
text: 'Hybrid systems have both continuous and discrete dynamics and are useful
for modeling a variety of control systems, from air traffic control protocols
to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools
for analyzing hybrid systems have emerged. Several of these tools implement automated
formal methods for mathematically proving a system meets a specification. This
tutorial session will present three recent hybrid systems tools: C2E2, HyST, and
TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses
validated numerical solvers and bloating of simulation traces to verify systems
meet specifications. HyST is a hybrid systems model transformation and translation
tool, and uses a canonical intermediate representation to support most of the
recent verification tools, as well as automated sound abstractions that simplify
verification of a given hybrid system. TuLiP is a controller synthesis tool for
hybrid systems, where given a temporal logic specification to be satisfied for
a system (plant) model, TuLiP will find a controller that meets a given specification.
© 2016 IEEE.'
article_number: '7587948'
author:
- first_name: Parasara
full_name: Duggirala, Parasara
last_name: Duggirala
- first_name: Chuchu
full_name: Fan, Chuchu
last_name: Fan
- first_name: Matthew
full_name: Potok, Matthew
last_name: Potok
- first_name: Bolun
full_name: Qi, Bolun
last_name: Qi
- first_name: Sayan
full_name: Mitra, Sayan
last_name: Mitra
- first_name: Mahesh
full_name: Viswanathan, Mahesh
last_name: Viswanathan
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
- first_name: Luan
full_name: Nguyen, Luan
last_name: Nguyen
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Andrew
full_name: Sogokon, Andrew
last_name: Sogokon
- first_name: Hoang
full_name: Tran, Hoang
last_name: Tran
- first_name: Weiming
full_name: Xiang, Weiming
last_name: Xiang
citation:
ama: 'Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems
verification transformation and synthesis C2E2 HyST and TuLiP. In: 2016 IEEE
Conference on Control Applications. IEEE; 2016. doi:10.1109/CCA.2016.7587948'
apa: 'Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang,
W. (2016). Tutorial: Software tools for hybrid systems verification transformation
and synthesis C2E2 HyST and TuLiP. In 2016 IEEE Conference on Control Applications.
Buenos Aires, Argentina : IEEE. https://doi.org/10.1109/CCA.2016.7587948'
chicago: 'Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra,
Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems
Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In 2016 IEEE
Conference on Control Applications. IEEE, 2016. https://doi.org/10.1109/CCA.2016.7587948.'
ieee: 'P. Duggirala et al., “Tutorial: Software tools for hybrid systems
verification transformation and synthesis C2E2 HyST and TuLiP,” in 2016 IEEE
Conference on Control Applications, Buenos Aires, Argentina , 2016.'
ista: 'Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov
S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial:
Software tools for hybrid systems verification transformation and synthesis C2E2
HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications
, 7587948.'
mla: 'Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification
Transformation and Synthesis C2E2 HyST and TuLiP.” 2016 IEEE Conference on
Control Applications, 7587948, IEEE, 2016, doi:10.1109/CCA.2016.7587948.'
short: P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak,
S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang,
in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.
conference:
end_date: 2016-09-22
location: 'Buenos Aires, Argentina '
name: 'CCA: Control Applications '
start_date: 2016-09-19
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-10T00:00:00Z
date_updated: 2021-01-12T06:48:32Z
day: '10'
department:
- _id: ToHe
doi: 10.1109/CCA.2016.7587948
language:
- iso: eng
month: '10'
oa_version: None
publication: 2016 IEEE Conference on Control Applications
publication_status: published
publisher: IEEE
publist_id: '6224'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Tutorial: Software tools for hybrid systems verification transformation and
synthesis C2E2 HyST and TuLiP'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1135'
abstract:
- lang: eng
text: 'Time-triggered (TT) switched networks are a deterministic communication infrastructure
used by real-time distributed embedded systems. These networks rely on the notion
of globally discretized time (i.e. time slots) and a static TT schedule that prescribes
which message is sent through which link at every time slot, such that all messages
reach their destination before a global timeout. These schedules are generated
offline, assuming a static network with fault-free links, and entrusting all error-handling
functions to the end user. Assuming the network is static is an over-optimistic
view, and indeed links tend to fail in practice. We study synthesis of TT schedules
on a network in which links fail over time and we assume the switches run a very
simple error-recovery protocol once they detect a crashed link. We address the
problem of finding a pk; qresistant schedule; namely, one that, assuming the switches
run a fixed error-recovery protocol, guarantees that the number of messages that
arrive at their destination by the timeout is at least no matter what sequence
of at most k links fail. Thus, we maintain the simplicity of the switches while
giving a guarantee on the number of messages that meet the timeout. We show how
a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a
schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing
fault sequence to generate a constraint that is added to the program. The newly
added constraint disallows the schedule to be regenerated in a future iteration
while also eliminating several other schedules that are not pk; q-resistant. We
illustrate the applicability of our approach using an SMT-based implementation.
© 2016 ACM.'
article_number: '26'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Guillermo
full_name: Rodríguez Navas, Guillermo
last_name: Rodríguez Navas
citation:
ama: 'Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for
switched networks with faulty links. In: Proceedings of the 13th International
Conference on Embedded Software . ACM; 2016. doi:10.1145/2968478.2968499'
apa: 'Avni, G., Guha, S., & Rodríguez Navas, G. (2016). Synthesizing time triggered
schedules for switched networks with faulty links. In Proceedings of the 13th
International Conference on Embedded Software . Pittsburgh, PA, USA: ACM.
https://doi.org/10.1145/2968478.2968499'
chicago: Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing
Time Triggered Schedules for Switched Networks with Faulty Links.” In Proceedings
of the 13th International Conference on Embedded Software . ACM, 2016. https://doi.org/10.1145/2968478.2968499.
ieee: G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules
for switched networks with faulty links,” in Proceedings of the 13th International
Conference on Embedded Software , Pittsburgh, PA, USA, 2016.
ista: 'Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules
for switched networks with faulty links. Proceedings of the 13th International
Conference on Embedded Software . EMSOFT: Embedded Software , 26.'
mla: Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks
with Faulty Links.” Proceedings of the 13th International Conference on Embedded
Software , 26, ACM, 2016, doi:10.1145/2968478.2968499.
short: G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International
Conference on Embedded Software , ACM, 2016.
conference:
end_date: 2016-10-07
location: Pittsburgh, PA, USA
name: 'EMSOFT: Embedded Software '
start_date: 2016-10-01
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:48:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/2968478.2968499
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:31Z
date_updated: 2018-12-12T10:09:31Z
file_id: '4755'
file_name: IST-2016-644-v1+1_emsoft-no-format.pdf
file_size: 279240
relation: main_file
file_date_updated: 2018-12-12T10:09:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted 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: The Wittgenstein Prize
publication: 'Proceedings of the 13th International Conference on Embedded Software '
publication_status: published
publisher: ACM
publist_id: '6223'
pubrep_id: '644'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synthesizing time triggered schedules for switched networks with faulty links
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1136'
abstract:
- lang: eng
text: We propose an interactive sculpting system for seamlessly editing pre-computed
animations of liquid, without the need for any resimulation. The input is a sequence
of meshes without correspondences representing the liquid surface over time. Our
method enables the efficient selection of consistent space-time parts of this
animation, such as moving waves or droplets, which we call space-time features.
Once selected, a feature can be copied, edited, or duplicated and then pasted
back anywhere in space and time in the same or in another liquid animation sequence.
Our method circumvents tedious user interactions by automatically computing the
spatial and temporal ranges of the selected feature. We also provide space-time
shape editing tools for non-uniform scaling, rotation, trajectory changes, and
temporal editing to locally speed up or slow down motion. Using our tools, the
user can edit and progressively refine any input simulation result, possibly using
a library of precomputed space-time features extracted from other animations.
In contrast to the trial-and-error loop usually required to edit animation results
through the tuning of indirect simulation parameters, our method gives the user
full control over the edited space-time behaviors. © 2016 Copyright held by the
owner/author(s).
acknowledgement: This work was partly supported by the starting grant BigSplash, as
well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG
638176 , and ERC-2011-ADG 20110209).
article_number: '2994261'
article_processing_charge: No
author:
- first_name: Pierre
full_name: Manteaux, Pierre
last_name: Manteaux
- first_name: Ulysse
full_name: Vimont, Ulysse
last_name: Vimont
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Damien
full_name: Rohmer, Damien
last_name: Rohmer
- first_name: Marie
full_name: Cani, Marie
last_name: Cani
citation:
ama: 'Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of
liquid animation. In: Proceedings of the 9th International Conference on Motion
in Games . ACM; 2016. doi:10.1145/2994258.2994261'
apa: 'Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., & Cani, M. (2016). Space-time
sculpting of liquid animation. In Proceedings of the 9th International Conference
on Motion in Games . San Francisco, CA, USA: ACM. https://doi.org/10.1145/2994258.2994261'
chicago: Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie
Cani. “Space-Time Sculpting of Liquid Animation.” In Proceedings of the 9th
International Conference on Motion in Games . ACM, 2016. https://doi.org/10.1145/2994258.2994261.
ieee: P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting
of liquid animation,” in Proceedings of the 9th International Conference on
Motion in Games , San Francisco, CA, USA, 2016.
ista: 'Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting
of liquid animation. Proceedings of the 9th International Conference on Motion
in Games . MIG: Motion in Games, 2994261.'
mla: Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” Proceedings
of the 9th International Conference on Motion in Games , 2994261, ACM, 2016,
doi:10.1145/2994258.2994261.
short: P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of
the 9th International Conference on Motion in Games , ACM, 2016.
conference:
end_date: 2016-10-12
location: San Francisco, CA, USA
name: 'MIG: Motion in Games'
start_date: 2016-10-10
date_created: 2018-12-11T11:50:20Z
date_published: 2016-10-10T00:00:00Z
date_updated: 2023-02-21T09:49:49Z
day: '10'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.1145/2994258.2994261
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-01367181
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: 'Proceedings of the 9th International Conference on Motion in Games '
publication_status: published
publisher: ACM
publist_id: '6222'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Space-time sculpting of liquid animation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1137'
abstract:
- lang: eng
text: RASGRP1 is an important guanine nucleotide exchange factor and activator of
the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences
of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial
and viral infections, born to healthy consanguineous parents, we used homozygosity
mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1.
This variant segregated perfectly with the disease and has not been reported in
genetic databases. RASGRP1 deficiency was associated in T cells and B cells with
decreased phosphorylation of the extracellular-signal-regulated serine kinase
ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency
also resulted in defective proliferation, activation and motility of T cells and
B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity
with defective granule convergence and actin accumulation. Interaction proteomics
identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links
RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation
of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed
the migration and activation defects of RASGRP1-deficient lymphocytes.
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Deniz
full_name: Çaǧdaş, Deniz
last_name: Çaǧdaş
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Emily
full_name: Mace, Emily
last_name: Mace
- first_name: Wojciech
full_name: Garncarz, Wojciech
last_name: Garncarz
- first_name: Oezlem
full_name: Petronczki, Oezlem
last_name: Petronczki
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Laurène
full_name: Pfajfer, Laurène
last_name: Pfajfer
- first_name: Ivan
full_name: Bilic, Ivan
last_name: Bilic
- first_name: Sol
full_name: Ban, Sol
last_name: Ban
- first_name: Katharina
full_name: Willmann, Katharina
last_name: Willmann
- first_name: Malini
full_name: Mukherjee, Malini
last_name: Mukherjee
- first_name: Verena
full_name: Supper, Verena
last_name: Supper
- first_name: Hsiangting
full_name: Hsu, Hsiangting
last_name: Hsu
- first_name: Pinaki
full_name: Banerjee, Pinaki
last_name: Banerjee
- first_name: Papiya
full_name: Sinha, Papiya
last_name: Sinha
- first_name: Fabienne
full_name: Mcclanahan, Fabienne
last_name: Mcclanahan
- first_name: Gerhard
full_name: Zlabinger, Gerhard
last_name: Zlabinger
- first_name: Winfried
full_name: Pickl, Winfried
last_name: Pickl
- first_name: John
full_name: Gribben, John
last_name: Gribben
- first_name: Hannes
full_name: Stockinger, Hannes
last_name: Stockinger
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Johannes
full_name: Huppa, Johannes
last_name: Huppa
- first_name: Loï̈C
full_name: Dupré, Loï̈C
last_name: Dupré
- first_name: Özden
full_name: Sanal, Özden
last_name: Sanal
- first_name: Ulrich
full_name: Jäger, Ulrich
last_name: Jäger
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Ilhan
full_name: Tezcan, Ilhan
last_name: Tezcan
- first_name: Jordan
full_name: Orange, Jordan
last_name: Orange
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency
with impaired cytoskeletal dynamics. Nature Immunology. 2016;17(12):1352-1360.
doi:10.1038/ni.3575
apa: Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., …
Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal
dynamics. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3575
chicago: Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz,
Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency
with Impaired Cytoskeletal Dynamics.” Nature Immunology. Nature Publishing
Group, 2016. https://doi.org/10.1038/ni.3575.
ieee: E. Salzer et al., “RASGRP1 deficiency causes immunodeficiency with
impaired cytoskeletal dynamics,” Nature Immunology, vol. 17, no. 12. Nature
Publishing Group, pp. 1352–1360, 2016.
ista: Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer
L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha
P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa
J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1
deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature
Immunology. 17(12), 1352–1360.
mla: Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with
Impaired Cytoskeletal Dynamics.” Nature Immunology, vol. 17, no. 12, Nature
Publishing Group, 2016, pp. 1352–60, doi:10.1038/ni.3575.
short: E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer,
L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P.
Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger,
K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange,
K. Boztug, Nature Immunology 17 (2016) 1352–1360.
date_created: 2018-12-11T11:50:21Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:33Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/ni.3575
external_id:
pmid:
- '27776107'
intvolume: ' 17'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263
month: '12'
oa: 1
oa_version: Submitted Version
page: 1352 - 1360
pmid: 1
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6221'
quality_controlled: '1'
scopus_import: 1
status: public
title: RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1138'
abstract:
- lang: eng
text: Automata with monitor counters, where the transitions do not depend on counter
values, and nested weighted automata are two expressive automata-theoretic frameworks
for quantitative properties. For a well-studied and wide class of quantitative
functions, we establish that automata with monitor counters and nested weighted
automata are equivalent. We study for the first time such quantitative automata
under probabilistic semantics. We show that several problems that are undecidable
for the classical questions of emptiness and universality become decidable under
the probabilistic semantics. We present a complete picture of decidability for
such automata, and even an almost-complete picture of computational complexity,
for the probabilistic questions we consider. © 2016 ACM.
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499-
N23, FWF NFN Grant No S114
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic
semantics. In: Proceedings of the 31st Annual ACM/IEEE Symposium. IEEE;
2016:76-85. doi:10.1145/2933575.2933588'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative automata
under probabilistic semantics. In Proceedings of the 31st Annual ACM/IEEE Symposium
(pp. 76–85). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2933588'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative
Automata under Probabilistic Semantics.” In Proceedings of the 31st Annual
ACM/IEEE Symposium, 76–85. IEEE, 2016. https://doi.org/10.1145/2933575.2933588.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under
probabilistic semantics,” in Proceedings of the 31st Annual ACM/IEEE Symposium,
New York, NY, USA, 2016, pp. 76–85.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic
semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer
Science, 76–85.'
mla: Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.”
Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85,
doi:10.1145/2933575.2933588.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual
ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:50:21Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:48:34Z
day: '05'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/2933575.2933588
ec_funded: 1
external_id:
arxiv:
- '1604.06764'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06764
month: '07'
oa: 1
oa_version: Preprint
page: 76 - 85
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: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st Annual ACM/IEEE Symposium
publication_status: published
publisher: IEEE
publist_id: '6220'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative automata under probabilistic semantics
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1139'
abstract:
- lang: eng
text: Microtubules switch stochastically between phases of growth and shrinkage.
The molecular mechanism responsible for the end of a growth phase, an event called
catastrophe, is still not understood. The probability for a catastrophe to occur
increases with microtubule age, putting constraints on the possible molecular
mechanism of catastrophe induction. Here we used microfluidics-Assisted fast tubulin
washout experiments to induce microtubule depolymerization in a controlled manner
at different times after the start of growth. We found that aging can also be
observed in this assay, providing valuable new constraints against which theoretical
models of catastrophe induction can be tested. We found that the data can be quantitatively
well explained by a simple kinetic threshold model that assumes an age-dependent
broadening of the protective cap at the microtubule end as a result of an evolving
tapered end structure; this leads to a decrease of the cap density and its stability.
This analysis suggests an intuitive picture of the role of morphological changes
of the protective cap for the age dependence of microtubule stability.
article_processing_charge: No
author:
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Nicholas
full_name: Cade, Nicholas
last_name: Cade
- first_name: Thomas
full_name: Surrey, Thomas
last_name: Surrey
citation:
ama: Düllberg CF, Cade N, Surrey T. Microtubule aging probed by microfluidics assisted
tubulin washout. Molecular Biology and Evolution. 2016;27(22):3563-3573.
doi:10.1091/mbc.E16-07-0548
apa: Düllberg, C. F., Cade, N., & Surrey, T. (2016). Microtubule aging probed
by microfluidics assisted tubulin washout. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1091/mbc.E16-07-0548
chicago: Düllberg, Christian F, Nicholas Cade, and Thomas Surrey. “Microtubule Aging
Probed by Microfluidics Assisted Tubulin Washout.” Molecular Biology and Evolution.
Oxford University Press, 2016. https://doi.org/10.1091/mbc.E16-07-0548.
ieee: C. F. Düllberg, N. Cade, and T. Surrey, “Microtubule aging probed by microfluidics
assisted tubulin washout,” Molecular Biology and Evolution, vol. 27, no.
22. Oxford University Press, pp. 3563–3573, 2016.
ista: Düllberg CF, Cade N, Surrey T. 2016. Microtubule aging probed by microfluidics
assisted tubulin washout. Molecular Biology and Evolution. 27(22), 3563–3573.
mla: Düllberg, Christian F., et al. “Microtubule Aging Probed by Microfluidics Assisted
Tubulin Washout.” Molecular Biology and Evolution, vol. 27, no. 22, Oxford
University Press, 2016, pp. 3563–73, doi:10.1091/mbc.E16-07-0548.
short: C.F. Düllberg, N. Cade, T. Surrey, Molecular Biology and Evolution 27 (2016)
3563–3573.
date_created: 2018-12-11T11:50:21Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2021-01-12T06:48:34Z
day: '07'
doi: 10.1091/mbc.E16-07-0548
extern: '1'
intvolume: ' 27'
issue: '22'
language:
- iso: eng
month: '11'
oa_version: None
page: 3563 - 3573
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6218'
status: public
title: Microtubule aging probed by microfluidics assisted tubulin washout
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2016'
...
---
_id: '1140'
abstract:
- lang: eng
text: 'Given a model of a system and an objective, the model-checking question asks
whether the model satisfies the objective. We study polynomial-time problems in
two classical models, graphs and Markov Decision Processes (MDPs), with respect
to several fundamental -regular objectives, e.g., Rabin and Streett objectives.
For many of these problems the best-known upper bounds are quadratic or cubic,
yet no super-linear lower bounds are known. In this work our contributions are
two-fold: First, we present several improved algorithms, and second, we present
the first conditional super-linear lower bounds based on widely believed assumptions
about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication.
A separation result for two models with respect to an objective means a conditional
lower bound for one model that is strictly higher than the existing upper bound
for the other model, and similarly for two objectives with respect to a model.
Our results establish the following separation results: (1) A separation of models
(graphs and MDPs) for disjunctive queries of reachability and Büchi objectives.
(2) Two kinds of separations of objectives, both for graphs and MDPs, namely,
(2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b)
the separation of conjunction and disjunction of multiple objectives of the same
type such as safety, Büchi, and coBüchi. In summary, our results establish the
first model and objective separation results for graphs and MDPs for various classical
-regular objectives. Quite strikingly, we establish conditional lower bounds for
the disjunction of objectives that are strictly higher than the existing upper
bounds for the conjunction of the same objectives. © 2016 ACM.'
acknowledgement: "K. C., M. H., and W. D. are partially supported by the
\ Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK.
C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23
(RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H.,
and V. L. the research\r\nleading to these results has received funding from the
European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme
(FP/2007-2013) / ERC Grant Agreement no. 340506."
alternative_title:
- Proceedings Symposium on Logic in Computer Science
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvoák, Wolfgang
last_name: Dvoák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation
with conditional lower bounds: disjunction is harder than conjunction. In: Proceedings
of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE;
2016:197-206. doi:10.1145/2933575.2935304'
apa: 'Chatterjee, K., Dvoák, W., Henzinger, M. H., & Loitzenbauer, V. (2016).
Model and objective separation with conditional lower bounds: disjunction is harder
than conjunction. In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic
in Computer Science (pp. 197–206). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2935304'
chicago: 'Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika
Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction
Is Harder than Conjunction.” In Proceedings of the 31st Annual ACM/IEEE Symposium
on Logic in Computer Science, 197–206. IEEE, 2016. https://doi.org/10.1145/2933575.2935304.'
ieee: 'K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and
objective separation with conditional lower bounds: disjunction is harder than
conjunction,” in Proceedings of the 31st Annual ACM/IEEE Symposium on Logic
in Computer Science, New York, NY, USA, 2016, pp. 197–206.'
ista: 'Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective
separation with conditional lower bounds: disjunction is harder than conjunction.
Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science.
LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science,
, 197–206.'
mla: 'Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional
Lower Bounds: Disjunction Is Harder than Conjunction.” Proceedings of the 31st
Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206,
doi:10.1145/2933575.2935304.'
short: K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings
of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016,
pp. 197–206.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:50:22Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2025-06-02T08:53:44Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2935304
external_id:
arxiv:
- '1602.02670'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02670
month: '07'
oa: 1
oa_version: Preprint
page: 197 - 206
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_status: published
publisher: IEEE
publist_id: '6219'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Model and objective separation with conditional lower bounds: disjunction
is harder than conjunction'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1141'
abstract:
- lang: eng
text: In this paper we introduce the Multiobjective Optimization Hierarchic Genetic
Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary
optimization in a hierarchy of populations. The maturing mechanism improves growth
and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art
multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark
problems and their modifications for which single fitness evaluation time depends
on the solution accuracy. We compare the proposed algorithm with the Island Model
Genetic Algorithm as well as with single-deme methods, and discuss the impact
of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.
acknowledgement: The work presented in this paper was partially supported by Polish
National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393.
Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.
author:
- first_name: Radosław
full_name: Łazarz, Radosław
last_name: Łazarz
- first_name: Michał
full_name: Idzik, Michał
last_name: Idzik
- first_name: Konrad
full_name: Gądek, Konrad
last_name: Gądek
- first_name: Ewa P
full_name: Gajda-Zagorska, Ewa P
id: 47794CF0-F248-11E8-B48F-1D18A9856A87
last_name: Gajda-Zagorska
citation:
ama: Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy
with maturing as a generic tool for multiobjective optimization. Journal of
Computational Science. 2016;17(1):249-260. doi:10.1016/j.jocs.2016.03.004
apa: Łazarz, R., Idzik, M., Gądek, K., & Gajda-Zagorska, E. P. (2016). Hierarchic
genetic strategy with maturing as a generic tool for multiobjective optimization.
Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.03.004
chicago: Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska.
“Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective
Optimization.” Journal of Computational Science. Elsevier, 2016. https://doi.org/10.1016/j.jocs.2016.03.004.
ieee: R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic
strategy with maturing as a generic tool for multiobjective optimization,” Journal
of Computational Science, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.
ista: Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy
with maturing as a generic tool for multiobjective optimization. Journal of Computational
Science. 17(1), 249–260.
mla: Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic
Tool for Multiobjective Optimization.” Journal of Computational Science,
vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:10.1016/j.jocs.2016.03.004.
short: R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational
Science 17 (2016) 249–260.
date_created: 2018-12-11T11:50:22Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:48:35Z
day: '01'
department:
- _id: ChWo
doi: 10.1016/j.jocs.2016.03.004
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 249 - 260
publication: Journal of Computational Science
publication_status: published
publisher: Elsevier
publist_id: '6217'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hierarchic genetic strategy with maturing as a generic tool for multiobjective
optimization
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1142'
abstract:
- lang: eng
text: Hemolysis drives susceptibility to bacterial infections and predicts poor
outcome from sepsis. These detrimental effects are commonly considered to be a
consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative
sepsis model and found that elevated heme levels impaired the control of bacterial
proliferation independently of heme-iron acquisition by pathogens. Heme strongly
inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting
actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein
Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach
revealed that quinine effectively prevented heme effects on the cytoskeleton,
restored phagocytosis and improved survival in sepsis. These mechanistic insights
provide potential therapeutic targets for patients with sepsis or hemolytic disorders.
acknowledgement: 'Y. Fukui (Medical Institute of Bioregulation, Kyushu University)
and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for
providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children''s
Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct.
pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of
Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns
Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding
retrovirus was kindly provided by A. Leithner (Institute of Science and Technology
Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research,
National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent
technical support (Core imaging facility, Medical University of Vienna). We thank
D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was
supported by the Austrian Academy of Sciences, the Science Fund of the Austrian
National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA
framework (to S.Knapp).'
author:
- first_name: Rui
full_name: Martins, Rui
last_name: Martins
- first_name: Julia
full_name: Maier, Julia
last_name: Maier
- first_name: Anna
full_name: Gorki, Anna
last_name: Gorki
- first_name: Kilian
full_name: Huber, Kilian
last_name: Huber
- first_name: Omar
full_name: Sharif, Omar
last_name: Sharif
- first_name: Philipp
full_name: Starkl, Philipp
last_name: Starkl
- first_name: Simona
full_name: Saluzzo, Simona
last_name: Saluzzo
- first_name: Federica
full_name: Quattrone, Federica
last_name: Quattrone
- first_name: Riem
full_name: Gawish, Riem
last_name: Gawish
- first_name: Karin
full_name: Lakovits, Karin
last_name: Lakovits
- first_name: Michael
full_name: Aichinger, Michael
last_name: Aichinger
- first_name: Branka
full_name: Radic Sarikas, Branka
last_name: Radic Sarikas
- first_name: Charles
full_name: Lardeau, Charles
last_name: Lardeau
- first_name: Anastasiya
full_name: Hladik, Anastasiya
last_name: Hladik
- first_name: Ana
full_name: Korosec, Ana
last_name: Korosec
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Michelle
full_name: Duggan, Michelle
id: 2EDEA62C-F248-11E8-B48F-1D18A9856A87
last_name: Duggan
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Harald
full_name: Esterbauer, Harald
last_name: Esterbauer
- first_name: Jacques
full_name: Colinge, Jacques
last_name: Colinge
- first_name: Stephanie
full_name: Eisenbarth, Stephanie
last_name: Eisenbarth
- first_name: Thomas
full_name: Decker, Thomas
last_name: Decker
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Stefan
full_name: Kubicek, Stefan
last_name: Kubicek
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Giulio
full_name: Superti Furga, Giulio
last_name: Superti Furga
- first_name: Sylvia
full_name: Knapp, Sylvia
last_name: Knapp
citation:
ama: Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility
to infection via disruption of phagocyte functions. Nature Immunology.
2016;17(12):1361-1372. doi:10.1038/ni.3590
apa: Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp,
S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption
of phagocyte functions. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3590
chicago: Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp
Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to
Infection via Disruption of Phagocyte Functions.” Nature Immunology. Nature
Publishing Group, 2016. https://doi.org/10.1038/ni.3590.
ieee: R. Martins et al., “Heme drives hemolysis-induced susceptibility to
infection via disruption of phagocyte functions,” Nature Immunology, vol.
17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.
ista: Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone
F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec
A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth
S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme
drives hemolysis-induced susceptibility to infection via disruption of phagocyte
functions. Nature Immunology. 17(12), 1361–1372.
mla: Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection
via Disruption of Phagocyte Functions.” Nature Immunology, vol. 17, no.
12, Nature Publishing Group, 2016, pp. 1361–72, doi:10.1038/ni.3590.
short: R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo,
F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau,
A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer,
J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti
Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.
date_created: 2018-12-11T11:50:22Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:36Z
day: '01'
department:
- _id: MiSi
- _id: PeJo
doi: 10.1038/ni.3590
intvolume: ' 17'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d
month: '12'
oa: 1
oa_version: Submitted Version
page: 1361 - 1372
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6216'
quality_controlled: '1'
scopus_import: 1
status: public
title: Heme drives hemolysis-induced susceptibility to infection via disruption of
phagocyte functions
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1143'
abstract:
- lang: eng
text: We study the ground state of a dilute Bose gas in a scaling limit where the
Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger
functional whose quartic term is proportional to the scattering length of the
interparticle interaction potential. We propose a new derivation of this limit
problem, with a method that bypasses some of the technical difficulties that previous
derivations had to face. The new method is based on a combination of Dyson\'s
lemma, the quantum de Finetti theorem and a second moment estimate for ground
states of the effective Dyson Hamiltonian. It applies equally well to the case
where magnetic fields or rotation are present.
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Nicolas
full_name: Rougerie, Nicolas
last_name: Rougerie
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The
gross Pitaevskii limit revisited. Analysis and PDE. 2016;9(2):459-485.
doi:10.2140/apde.2016.9.459'
apa: 'Nam, P., Rougerie, N., & Seiringer, R. (2016). Ground states of large
bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE.
Mathematical Sciences Publishers. https://doi.org/10.2140/apde.2016.9.459'
chicago: 'Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large
Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE.
Mathematical Sciences Publishers, 2016. https://doi.org/10.2140/apde.2016.9.459.'
ieee: 'P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems:
The gross Pitaevskii limit revisited,” Analysis and PDE, vol. 9, no. 2.
Mathematical Sciences Publishers, pp. 459–485, 2016.'
ista: 'Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems:
The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.'
mla: 'Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii
Limit Revisited.” Analysis and PDE, vol. 9, no. 2, Mathematical Sciences
Publishers, 2016, pp. 459–85, doi:10.2140/apde.2016.9.459.'
short: P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.
date_created: 2018-12-11T11:50:23Z
date_published: 2016-03-24T00:00:00Z
date_updated: 2021-01-12T06:48:36Z
day: '24'
department:
- _id: RoSe
doi: 10.2140/apde.2016.9.459
ec_funded: 1
intvolume: ' 9'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1503.07061
month: '03'
oa: 1
oa_version: Preprint
page: 459 - 485
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Analysis and PDE
publication_status: published
publisher: Mathematical Sciences Publishers
publist_id: '6215'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Ground states of large bosonic systems: The gross Pitaevskii limit revisited'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...