---
_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:
- access_level: closed
checksum: ec453918c3bf8e6f460fd1156ef7b493
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T11:46:25Z
date_updated: 2019-08-13T11:46:25Z
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file_name: Thesis_Georg_Rieckh_w_signature_page.pdf
file_size: 2614660
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content_type: application/pdf
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: '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
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T10:50:00Z
date_updated: 2019-08-13T10:50:00Z
file_id: '6812'
file_name: MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf
file_size: 4785167
relation: main_file
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checksum: dd4136247fe472e7d47880ec68ac8de0
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:42:06Z
date_updated: 2021-02-22T11:42:06Z
file_id: '9180'
file_name: 2016_MORRI_Thesis.pdf
file_size: 4495669
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:42:06Z
has_accepted_license: '1'
language:
- 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: '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:
- access_level: closed
checksum: e3cd6b28f9c5cccb8891855565a2dade
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T10:55:35Z
date_updated: 2019-08-13T10:55:35Z
file_id: '6813'
file_name: Thesis_JSchwarz_final.pdf
file_size: 32044069
relation: main_file
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content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:43:14Z
date_updated: 2021-02-22T11:43:14Z
file_id: '9181'
file_name: 2016_Thesis_JSchwarz.pdf
file_size: 8396717
relation: main_file
success: 1
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: '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
date_updated: 2018-12-12T10:14:07Z
file_id: '5056'
file_name: IST-2017-776-v1+1_Pentina_Thesis_2016.pdf
file_size: 2140062
relation: main_file
file_date_updated: 2018-12-12T10:14:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '127'
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6234'
pubrep_id: '776'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Theoretical foundations of multi-task lifelong learning
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1397'
abstract:
- lang: eng
text: 'We study partially observable Markov decision processes (POMDPs) with objectives
used in verification and artificial intelligence. The qualitative analysis problem
given a POMDP and an objective asks whether there is a strategy (policy) to ensure
that the objective is satisfied almost surely (with probability 1), resp. with
positive probability (with probability greater than 0). For POMDPs with limit-average
payoff, where a reward value in the interval [0,1] is associated to every transition,
and the payoff of an infinite path is the long-run average of the rewards, we
consider two types of path constraints: (i) a quantitative limit-average constraint
defines the set of paths where the payoff is at least a given threshold L1 = 1.
Our main results for qualitative limit-average constraint under almost-sure winning
are as follows: (i) the problem of deciding the existence of a finite-memory controller
is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory
controller is undecidable. For quantitative limit-average constraints we show
that the problem of deciding the existence of a finite-memory controller is undecidable.
We present a prototype implementation of our EXPTIME algorithm. For POMDPs with
w-regular conditions specified as parity objectives, while the qualitative analysis
problems are known to be undecidable even for very special case of parity objectives,
we establish decidability (with optimal complexity) of the qualitative analysis
problems for POMDPs with parity objectives under finite-memory strategies. We
establish optimal (exponential) memory bounds and EXPTIME-completeness of the
qualitative analysis problems under finite-memory strategies for POMDPs with parity
objectives. Based on our theoretical algorithms we also present a practical approach,
where we design heuristics to deal with the exponential complexity, and have applied
our implementation on a number of well-known POMDP examples for robotics applications.
For POMDPs with a set of target states and an integer cost associated with every
transition, we study the optimization objective that asks to minimize the expected
total cost of reaching a state in the target set, while ensuring that the target
set is reached almost surely. We show that for general integer costs approximating
the optimal cost is undecidable. For positive costs, our results are as follows:
(i) we establish matching lower and upper bounds for the optimal cost, both double
and exponential in the POMDP state space size; (ii) we show that the problem of
approximating the optimal cost is decidable and present approximation algorithms
that extend existing algorithms for POMDPs with finite-horizon objectives. We
show experimentally that it performs well in many examples of interest. We study
more deeply the problem of almost-sure reachability, where given a set of target
states, the question is to decide whether there is a strategy to ensure that the
target set is reached almost surely. While in general the problem EXPTIME-complete,
in many practical cases strategies with a small amount of memory suffice. Moreover,
the existing solution to the problem is explicit, which first requires to construct
explicitly an exponential reduction to a belief-support MDP. We first study the
existence of observation-stationary strategies, which is NP-complete, and then
small-memory strategies. We present a symbolic algorithm by an efficient encoding
to SAT and using a SAT solver for the problem. We report experimental results
demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized
POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents
operate in an uncertain environment independently to achieve a joint objective.
In this work we consider Goal DEC-POMDPs, where given a set of target states,
the objective is to ensure that the target set is reached with minimal cost. We
consider the indefinite-horizon (infinite-horizon with either discounted-sum,
or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present
a new and novel method to solve the problem that extends methods for finite-horizon
DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present
experimental results on several examples, and show that our approach presents
promising results. In the end we present a short summary of a few other results
related to verification of MDPs and POMDPs.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chmelik M. Algorithms for partially observable markov decision processes. 2016.
apa: Chmelik, M. (2016). Algorithms for partially observable markov decision
processes. Institute of Science and Technology Austria.
chicago: Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.”
Institute of Science and Technology Austria, 2016.
ieee: M. Chmelik, “Algorithms for partially observable markov decision processes,”
Institute of Science and Technology Austria, 2016.
ista: Chmelik M. 2016. Algorithms for partially observable markov decision processes.
Institute of Science and Technology Austria.
mla: Chmelik, Martin. Algorithms for Partially Observable Markov Decision Processes.
Institute of Science and Technology Austria, 2016.
short: M. Chmelik, Algorithms for Partially Observable Markov Decision Processes,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2023-09-07T11:54:58Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '02'
oa_version: None
page: '232'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5810'
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Algorithms for partially observable markov decision processes
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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language:
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oa: 1
oa_version: Published Version
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: '1432'
abstract:
- lang: eng
text: CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory
storage and pattern completion. Whether the plasticity properties of these synapses
are consistent with their proposed network functions remains unclear. Here, we
examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3
synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs)
and action potentials (APs) induces long-term potentiation (LTP), independent
of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms).
Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear
summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs)
following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and
EPSPs summate with dendritic ADPs. In autoassociative network models, storage
and recall are more robust with symmetric than with asymmetric STDP rules. Thus,
a specialized STDP induction rule allows reliable storage and recall of information
in the hippocampal CA3 network.
acknowledgement: 'We thank Jozsef Csicsvari and Nelson Spruston for critically reading
the manuscript. We also thank A. Schlögl for programming, F. Marr for technical
assistance and E. Kramberger for manuscript editing. '
article_number: '11552'
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity
at CA3–CA3 synapses optimizes storage and recall in autoassociative networks.
Nature Communications. 2016;7. doi:10.1038/ncomms11552
apa: Mishra, R. K., Kim, S., Guzmán, J., & Jonas, P. M. (2016). Symmetric spike
timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in
autoassociative networks. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms11552
chicago: Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric
Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall
in Autoassociative Networks.” Nature Communications. Nature Publishing
Group, 2016. https://doi.org/10.1038/ncomms11552.
ieee: R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks. Nature Communications. 7, 11552.
mla: Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at
CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature
Communications, vol. 7, 11552, Nature Publishing Group, 2016, doi:10.1038/ncomms11552.
short: R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:59Z
date_published: 2016-05-13T00:00:00Z
date_updated: 2023-09-07T11:55:25Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/ncomms11552
ec_funded: 1
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checksum: 7e84d0392348c874d473b62f1042de22
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intvolume: ' 7'
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license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5766'
pubrep_id: '582'
quality_controlled: '1'
related_material:
record:
- id: '1396'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage
and recall in autoassociative networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1396'
abstract:
- lang: eng
text: CA3 pyramidal neurons are thought to pay a key role in memory storage and
pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent
excitatory synapses. To examine the induction rules of synaptic plasticity at
CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal
slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory
postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum
oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced
N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although
LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel
blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute
to LTP induction without requirement of a somatic action potential (AP). We next
examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3
synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action
potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was
symmetric and broad, with a half-width of ~150 ms. Consistent with these specific
STDP induction properties, post-presynaptic sequences led to a supralinear summation
of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage
and recall was substantially more robust with symmetric than with asymmetric STDP
rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral
synapses with distinct induction rules. LTP induced by HFS may be associated with
dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic
activity induced LTP only if EPSP-AP were temporally very close. Together, these
induction mechanisms of synaptiic plasticity may contribute to memory storage
in the CA3-CA3 microcircuit at different ranges of activity.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
citation:
ama: Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus.
2016.
apa: Mishra, R. K. (2016). Synaptic plasticity rules at CA3-CA3 recurrent synapses
in hippocampus. Institute of Science and Technology Austria.
chicago: Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus.” Institute of Science and Technology Austria, 2016.
ieee: R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus,” Institute of Science and Technology Austria, 2016.
ista: Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in
hippocampus. Institute of Science and Technology Austria.
mla: Mishra, Rajiv Kumar. Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses
in Hippocampus. Institute of Science and Technology Austria, 2016.
short: R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus,
Institute of Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:46Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-07T11:55:26Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
file:
- access_level: closed
checksum: 5a010a838faf040f7064f3cfb802f743
content_type: application/pdf
creator: dernst
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date_updated: 2020-07-14T12:44:48Z
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file_name: Thesis_Mishra_Rajiv (Final).pdf
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publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5811'
related_material:
record:
- id: '1432'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus
type: dissertation
user_id: 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: 2023-09-07T11:55:53Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
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content_type: application/pdf
creator: dernst
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content_type: application/pdf
creator: dernst
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: 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: '1093'
abstract:
- lang: eng
text: 'We introduce a general class of distances (metrics) between Markov chains,
which are based on linear behaviour. This class encompasses distances given topologically
(such as the total variation distance or trace distance) as well as by temporal
logics or automata. We investigate which of the distances can be approximated
by observing the systems, i.e. by black-box testing or simulation, and we provide
both negative and positive results. '
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF)
under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award),
by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced
Postdoc. Mobility Fellowship – grant number P300P2_161067."
alternative_title:
- LIPIcs
article_number: '20'
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov
chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear
distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency
Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2016.20'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances
between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City;
Canada, 2016, vol. 59.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between
Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.'
mla: Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol.
59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
- _id: CaGu
doi: 10.4230/LIPIcs.CONCUR.2016.20
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:39Z
date_updated: 2018-12-12T10:11:39Z
file_id: '4895'
file_name: IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf
file_size: 501827
relation: main_file
file_date_updated: 2018-12-12T10:11:39Z
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6283'
pubrep_id: '794'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Linear distances between Markov chains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1234'
abstract:
- lang: eng
text: We present a new algorithm for the statistical model checking of Markov chains
with respect to unbounded temporal properties, including full linear temporal
logic. The main idea is that we monitor each simulation run on the fly, in order
to detect quickly if a bottom strongly connected component is entered with high
probability, in which case the simulation run can be terminated early. As a result,
our simulation runs are often much shorter than required by termination bounds
that are computed a priori for a desired level of confidence on a large state
space. In comparison to previous algorithms for statistical model checking our
method is not only faster in many cases but also requires less information about
the system, namely, only the minimum transition probability that occurs in the
Markov chain. In addition, our method can be generalised to unbounded quantitative
properties such as mean-payoff bounds.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under\r\ngrant agreement 267989 (QUAREM), the Austrian Science Fund
\ (FWF) under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award),
the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh
Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility
Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation
under grant agreement P202/12/G061."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking
for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Faster
statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129).
Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/978-3-662-49674-9_7'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29.
Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical
model checking for unbounded temporal properties,” presented at the TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands,
2016, vol. 9636, pp. 112–129.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model
checking for unbounded temporal properties. TACAS: Tools and Algorithms for the
Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.'
mla: Daca, Przemyslaw, et al. Faster Statistical Model Checking for Unbounded
Temporal Properties. Vol. 9636, Springer, 2016, pp. 112–29, doi:10.1007/978-3-662-49674-9_7.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp.
112–129.
conference:
end_date: 2016-04-08
location: Eindhoven, The Netherlands
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2016-04-02
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1007/978-3-662-49674-9_7
ec_funded: 1
intvolume: ' 9636'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.05739
month: '01'
oa: 1
oa_version: Preprint
page: 112 - 129
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6099'
quality_controlled: '1'
related_material:
record:
- id: '471'
relation: later_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster statistical model checking for unbounded temporal properties
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9636
year: '2016'
...
---
_id: '1230'
abstract:
- lang: eng
text: Concolic testing is a promising method for generating test suites for large
programs. However, it suffers from the path-explosion problem and often fails
to find tests that cover difficult-to-reach parts of programs. In contrast, model
checkers based on counterexample-guided abstraction refinement explore programs
exhaustively, while failing to scale on large programs with precision. In this
paper, we present a novel method that iteratively combines concolic testing and
model checking to find a test suite for a given coverage criterion. If concolic
testing fails to cover some test goals, then the model checker refines its program
abstraction to prove more paths infeasible, which reduces the search space for
concolic testing. We have implemented our method on top of the concolictesting
tool Crest and the model checker CpaChecker. We evaluated our tool on a collection
of programs and a category of SvComp benchmarks. In our experiments, we observed
an improvement in branch coverage compared to Crest from 48% to 63% in the best
case, and from 66% to 71% on average.
acknowledgement: "We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand
Michael Tautschnig for help with preparing the experiments. This research was supported
in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by
the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award)."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol
9583. Springer; 2016:328-347. doi:10.1007/978-3-662-49122-5_16'
apa: 'Daca, P., Gupta, A., & Henzinger, T. A. (2016). Abstraction-driven concolic
testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model
Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_16'
chicago: Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven
Concolic Testing,” 9583:328–47. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_16.
ieee: 'P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,”
presented at the VMCAI: Verification, Model Checking and Abstract Interpretation,
St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.'
ista: 'Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing.
VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583,
328–347.'
mla: Daca, Przemyslaw, et al. Abstraction-Driven Concolic Testing. Vol. 9583,
Springer, 2016, pp. 328–47, doi:10.1007/978-3-662-49122-5_16.
short: P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:50:50Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_16
ec_funded: 1
intvolume: ' 9583'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.02615
month: '01'
oa: 1
oa_version: Preprint
page: 328 - 347
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6104'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Abstraction-driven concolic testing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9583
year: '2016'
...
---
_id: '1391'
abstract:
- lang: eng
text: "We present an extension to the quantifier-free theory of integer arrays which
allows us to express counting. The properties expressible in Array Folds Logic
(AFL) include statements such as "the first array cell contains the array
length," and "the array contains equally many minimal and maximal elements."
These properties cannot be expressed in quantified fragments of the theory of
arrays, nor in the theory of concatenation. Using reduction to counter machines,
we show that the satisfiability problem of AFL is PSPACE-complete, and with a
natural restriction the complexity decreases to NP. We also show that adding either
universal quantifiers or concatenation leads to undecidability.\r\nAFL contains
terms that fold a function over an array. We demonstrate that folding, a well-known
concept from functional languages, allows us to concisely summarize loops that
count over arrays, which occurs frequently in real-life programs. We provide a
tool that can discharge proof obligations in AFL, and we demonstrate on practical
examples that our decision procedure can solve a broad range of problems in symbolic
testing and program verification."
alternative_title:
- LNCS
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Andrey
full_name: Kupriyanov, Andrey
id: 2C311BF8-F248-11E8-B48F-1D18A9856A87
last_name: Kupriyanov
citation:
ama: 'Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer;
2016:230-248. doi:10.1007/978-3-319-41540-6_13'
apa: 'Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic
(Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto,
Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13'
chicago: Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds
Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13.
ieee: 'P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented
at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp.
230–248.'
ista: 'Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer
Aided Verification, LNCS, vol. 9780, 230–248.'
mla: Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016,
pp. 230–48, doi:10.1007/978-3-319-41540-6_13.
short: P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:45Z
date_published: 2016-07-13T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-319-41540-6_13
ec_funded: 1
intvolume: ' 9780'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1603.06850
month: '07'
oa: 1
oa_version: Preprint
page: 230 - 248
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5818'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Array folds logic
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9780
year: '2016'
...
---
_id: '1243'
abstract:
- lang: eng
text: Restriction-modification (RM) systems represent a minimal and ubiquitous biological
system of self/non-self discrimination in prokaryotes [1], which protects hosts
from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase
(M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by
methylating short specific DNA sequences called restriction sites, whereas R recognizes
unmethylated restriction sites as non-self and introduces a double-stranded DNA
break [3]. Restriction sites are significantly underrepresented in prokaryotic
genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally
leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore,
RM systems can promote DNA recombination [9] and contribute to genetic variation
in microbial populations, thus facilitating adaptive evolution [10]. However,
cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has
not been directly detected, and its cause, frequency, and outcome are unknown.
We quantify self-restriction caused by two RM systems of Escherichia coli and
find that, in agreement with levels of restriction site avoidance, EcoRI, but
not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic
process, which temporarily induces the SOS response, and is followed by DNA repair,
maintaining cell viability. We find that RM systems with higher restriction efficiency
against bacteriophage infections exhibit a higher rate of self-restriction, and
that this rate can be further increased by stochastic imbalance between R and
M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic
genomes.
acknowledgement: This work was funded by an HFSP Young Investigators’ grant. M.P.
is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute
of Science and Technology Austria. R.O. and Y.W. were supported by the Platform
for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi
for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing
us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G.
and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments
on an earlier version of the manuscript. We especially thank B.R. Levin for advice
and comments, and the anonymous reviewers for significantly improving the manuscript.
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Long
full_name: Qian, Long
last_name: Qian
- first_name: Reiko
full_name: Okura, Reiko
last_name: Okura
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Yuichi
full_name: Wakamoto, Yuichi
last_name: Wakamoto
- first_name: Edo
full_name: Kussell, Edo
last_name: Kussell
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification
system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041
apa: Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E.,
& Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification
system. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.12.041
chicago: Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto,
Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2015.12.041.
ieee: M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification
system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.
ista: Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016.
Bacterial autoimmunity due to a restriction-modification system. Current Biology.
26(3), 404–409.
mla: Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification
System.” Current Biology, vol. 26, no. 3, Cell Press, 2016, pp. 404–09,
doi:10.1016/j.cub.2015.12.041.
short: M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C.
Guet, Current Biology 26 (2016) 404–409.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-08T00:00:00Z
date_updated: 2023-09-07T11:59:32Z
day: '08'
department:
- _id: CaGu
doi: 10.1016/j.cub.2015.12.041
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 404 - 409
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '6087'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Bacterial autoimmunity due to a restriction-modification system
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1071'
abstract:
- lang: eng
text: 'We consider data-structures for answering reachability and distance queries
on constant-treewidth graphs with n nodes, on the standard RAM computational model
with wordsize W=Theta(log n). Our first contribution is a data-structure that
after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time;
and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically)
optimal and is faster than DFS/BFS when answering more than a constant number
of single-source queries. The data-structure uses at all times O(n) space. Our
second contribution is a space-time tradeoff data-structure for distance queries.
For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing
time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha
is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space.
The input graph G is not considered in the space complexity. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant
(279307: Graph Games).'
alternative_title:
- LIPIcs
article_number: '28'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space
time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ESA.2016.28'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs (Vol.
57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ESA.2016.28'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant
Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik,
2016. https://doi.org/10.4230/LIPIcs.ESA.2016.28.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs,”
presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016,
vol. 57.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability
and a space time tradeoff for distance queries in constant treewidth graphs. ESA:
European Symposium on Algorithms, LIPIcs, vol. 57, 28.'
mla: Chatterjee, Krishnendu, et al. Optimal Reachability and a Space Time Tradeoff
for Distance Queries in Constant Treewidth Graphs. Vol. 57, 28, Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik, 2016.
conference:
end_date: 2016-08-24
location: Aarhus, Denmark
name: 'ESA: European Symposium on Algorithms'
start_date: 2016-08-22
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ESA.2016.28
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2018-12-12T10:14:31Z
file_id: '5084'
file_name: IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf
file_size: 579225
relation: main_file
file_date_updated: 2018-12-12T10:14:31Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
publist_id: '6312'
pubrep_id: '777'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Optimal reachability and a space time tradeoff for distance queries in constant
treewidth graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '1362'
abstract:
- lang: eng
text: We present a boundary element based method for fast simulation of brittle
fracture. By introducing simplifying assumptions that allow us to quickly estimate
stress intensities and opening displacements during crack propagation, we build
a fracture algorithm where the cost of each time step scales linearly with the
length of the crackfront. The transition from a full boundary element method to
our faster variant is possible at the beginning of any time step. This allows
us to build a hybrid method, which uses the expensive but more accurate BEM while
the number of degrees of freedom is low, and uses the fast method once that number
exceeds a given threshold as the crack geometry becomes more complicated. Furthermore,
we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body
coupling solves a Neumann boundary value problem by carefully separating translational,
rotational and deformational components of the collision forces and then applying
a Tikhonov regularizer to the resulting linear system. We show that our method
produces physically reasonable results in standard test cases and is capable of
dealing with complex scenes faster than previous finite- or boundary element approaches.
alternative_title:
- ACM Transactions on Graphics
article_number: '104'
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture
simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925902'
apa: 'Hahn, D., & Wojtan, C. (2016). Fast approximations for boundary element
based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim,
CA, USA: ACM. https://doi.org/10.1145/2897824.2925902'
chicago: Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element
Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925902.
ieee: D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle
fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol.
35, no. 4.
ista: Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle
fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.
mla: Hahn, David, and Chris Wojtan. Fast Approximations for Boundary Element
Based Brittle Fracture Simulation. Vol. 35, no. 4, 104, ACM, 2016, doi:10.1145/2897824.2925902.
short: D. Hahn, C. Wojtan, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T12:02:56Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925902
ec_funded: 1
file:
- access_level: open_access
checksum: 943712d9c9dc8bb5048d4adc561d7d38
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:04Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5121'
file_name: IST-2016-632-v1+2_a104-hahn.pdf
file_size: 12453704
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5880'
pubrep_id: '632'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
status: public
title: Fast approximations for boundary element based brittle fracture simulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1229'
abstract:
- lang: eng
text: Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme
is defined for some NP language L and lets a sender encrypt messages relative
to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L,
but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps
and give another construction [GGH+13b] using indistinguishability obfuscation
(iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently
hardly be implemented on powerful hardware and will unlikely be realizable on
constrained devices like smart cards any time soon. We construct a WE scheme where
encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions
and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs
public parameters containing an obfuscated circuit (only required for decryption),
two encryption keys and a common reference string (used for encryption). This
setup need only be run once, and the parame- ters can be used for arbitrary many
encryptions. Our scheme can also be turned into a functional WE scheme, where
a message is encrypted w.r.t. a statement and a function f, and decryption with
a witness w yields f (m, w). Our construction is inspired by the functional encryption
scheme by Garg et al. and we prove (selective) security assuming iO and statistically
simulation-sound NIZK. We give a construction of the latter in bilinear groups
and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at
a 128-bit security level and can be computed on a smart card.
acknowledgement: Research supported by the European Research Council, ERC starting grant
(259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol
9696. Springer; 2016:285-303. doi:10.1007/978-3-319-39555-5_16'
apa: 'Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Offline witness
encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography
and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_16'
chicago: Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline
Witness Encryption,” 9696:285–303. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_16.
ieee: 'H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,”
presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK,
2016, vol. 9696, pp. 285–303.'
ista: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption.
ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.'
mla: Abusalah, Hamza M., et al. Offline Witness Encryption. Vol. 9696, Springer,
2016, pp. 285–303, doi:10.1007/978-3-319-39555-5_16.
short: H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.
conference:
end_date: 2016-06-22
location: Guildford, UK
name: 'ACNS: Applied Cryptography and Network Security'
start_date: 2016-06-19
date_created: 2018-12-11T11:50:50Z
date_published: 2016-06-09T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '09'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_16
ec_funded: 1
file:
- access_level: open_access
checksum: 34fa9ce681da845a1ba945ba3dc57867
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:20Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5273'
file_name: IST-2017-765-v1+1_838.pdf
file_size: 515000
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9696'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 285 - 303
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6105'
pubrep_id: '765'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Offline witness encryption
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9696
year: '2016'
...
---
_id: '1236'
abstract:
- lang: eng
text: 'A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets
of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while
even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13
Boneh and Waters gave a construction which supports the most general set family
so far. Its keys kc are defined for sets decided by boolean circuits C and enable
evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF
input length and the size of the circuits C for which constrained keys can be
computed must be fixed beforehand during key generation. We construct a constrained
PRF that has an unbounded input length and whose constrained keys can be defined
for any set recognized by a Turing machine. The only a priori bound we make is
on the description size of the machines. We prove our construction secure assuming
publiccoin differing-input obfuscation. As applications of our constrained PRF
we build a broadcast encryption scheme where the number of potential receivers
need not be fixed at setup (in particular, the length of the keys is independent
of the number of parties) and the first identity-based non-interactive key exchange
protocol with no bound on the number of parties that can agree on a shared key.'
acknowledgement: Supported by the European Research Council, ERC Starting Grant (259668-PSPC).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs.
In: Vol 9610. Springer; 2016:413-428. doi:10.1007/978-3-319-29485-8_24'
apa: 'Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Constrained
PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics
in Cryptology, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-29485-8_24'
chicago: Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained
PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. https://doi.org/10.1007/978-3-319-29485-8_24.
ieee: 'H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for
unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco,
CA, USA, 2016, vol. 9610, pp. 413–428.'
ista: 'Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded
inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.'
mla: Abusalah, Hamza M., et al. Constrained PRFs for Unbounded Inputs. Vol.
9610, Springer, 2016, pp. 413–28, doi:10.1007/978-3-319-29485-8_24.
short: H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.
conference:
end_date: 2016-03-04
location: San Francisco, CA, USA
name: 'CT-RSA: Topics in Cryptology'
start_date: 2016-02-29
date_created: 2018-12-11T11:50:52Z
date_published: 2016-02-02T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '02'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.1007/978-3-319-29485-8_24
ec_funded: 1
file:
- access_level: open_access
checksum: 3851cee49933ae13b1272e516f213e13
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:05Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4664'
file_name: IST-2017-764-v1+1_279.pdf
file_size: 495176
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 9610'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 413 - 428
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '6097'
pubrep_id: '764'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9610
year: '2016'
...
---
_id: '1235'
abstract:
- lang: eng
text: 'A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets
of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute
a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈
S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah
et al. recently constructed the first constrained PRF for inputs of arbitrary
length whose sets S are decided by Turing machines. They use their CPRF to build
broadcast encryption and the first ID-based non-interactive key exchange for an
unbounded number of users. Their constrained keys are obfuscated circuits and
are therefore large. In this work we drastically reduce the key size and define
a constrained key for a Turing machine M as a short signature on M. For this,
we introduce a new signature primitive with constrained signing keys that let
one only sign certain messages, while forging a signature on others is hard even
when knowing the coins for key generation.'
acknowledgement: H. Abusalah—Research supported by the European Research Council,
ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
citation:
ama: 'Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short
keys. In: Vol 9696. Springer; 2016:445-463. doi:10.1007/978-3-319-39555-5_24'
apa: 'Abusalah, H. M., & Fuchsbauer, G. (2016). Constrained PRFs for unbounded
inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied
Cryptography and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_24'
chicago: Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded
Inputs with Short Keys,” 9696:445–63. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_24.
ieee: 'H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs
with short keys,” presented at the ACNS: Applied Cryptography and Network Security,
Guildford, UK, 2016, vol. 9696, pp. 445–463.'
ista: 'Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with
short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696,
445–463.'
mla: Abusalah, Hamza M., and Georg Fuchsbauer. Constrained PRFs for Unbounded
Inputs with Short Keys. Vol. 9696, Springer, 2016, pp. 445–63, doi:10.1007/978-3-319-39555-5_24.
short: H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.
conference:
end_date: 2016-06-22
location: Guildford, UK
name: 'ACNS: Applied Cryptography and Network Security'
start_date: 2016-06-19
date_created: 2018-12-11T11:50:52Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-39555-5_24
ec_funded: 1
intvolume: ' 9696'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/279.pdf
month: '01'
oa: 1
oa_version: Submitted Version
page: 445 - 463
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6098'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Constrained PRFs for unbounded inputs with short keys
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9696
year: '2016'
...
---
_id: '1441'
abstract:
- lang: eng
text: 'Optogenetics and photopharmacology enable the spatio-temporal control of
cell and animal behavior by light. Although red light offers deep-tissue penetration
and minimal phototoxicity, very few red-light-sensitive optogenetic methods are
currently available. We have now developed a red-light-induced homodimerization
domain. We first showed that an optimized sensory domain of the cyanobacterial
phytochrome 1 can be expressed robustly and without cytotoxicity in human cells.
We then applied this domain to induce the dimerization of two receptor tyrosine
kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor
trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway
non-invasively in mammalian tissue and in multicolor cell-signaling experiments.
The light-controlled dimerizer and red-light-activated receptor tyrosine kinases
will prove useful to regulate a variety of cellular processes with light. Go deep
with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was
repurposed to induce the homodimerization of proteins in living cells by red light.
By using this domain, light-activated protein kinases were engineered that can
be activated orthogonally from many fluorescent proteins and through mammalian
tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.'
acknowledgement: 'A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by
the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and
a FemTech fellowship (Austrian Research Promotion Agency: 3580812).'
author:
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736
apa: Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &
Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation
by red light. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.201601736
chicago: Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy,
Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits
Receptor Activation by Red Light.” Angewandte Chemie - International Edition.
Wiley, 2016. https://doi.org/10.1002/anie.201601736.
ieee: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H.
L. Janovjak, “A phytochrome sensory domain permits receptor activation by red
light,” Angewandte Chemie - International Edition, vol. 55, no. 21. Wiley,
pp. 6339–6342, 2016.
ista: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 55(21), 6339–6342.
mla: Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor
Activation by Red Light.” Angewandte Chemie - International Edition, vol.
55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736.
short: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L.
Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.
date_created: 2018-12-11T11:52:02Z
date_published: 2016-05-17T00:00:00Z
date_updated: 2023-09-07T12:49:08Z
day: '17'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1002/anie.201601736
ec_funded: 1
file:
- access_level: open_access
checksum: 26da07960e57ac4750b54179197ce57f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:03Z
date_updated: 2020-07-14T12:44:55Z
file_id: '5255'
file_name: IST-2017-840-v1+1_reichhart.pdf
file_size: 1268662
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 6339 - 6342
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley
publist_id: '5755'
pubrep_id: '840'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A phytochrome sensory domain permits receptor activation by red light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1358'
abstract:
- lang: eng
text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA
interactions. Limited specificity may lead to crosstalk: a regulatory state in
which a gene is either incorrectly activated due to noncognate TF–DNA interactions
or remains erroneously inactive. As each TF can have numerous interactions with
noncognate cis-regulatory elements, crosstalk is inherently a global problem,
yet has previously not been studied as such. We construct a theoretical framework
to analyse the effects of global crosstalk on gene regulation. We find that crosstalk
presents a significant challenge for organisms with low-specificity TFs, such
as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting
at equilibrium, including variants of cooperativity and combinatorial regulation.
Our results suggest that crosstalk imposes a previously unexplored global constraint
on the functioning and evolution of regulatory networks, which is qualitatively
distinct from the known constraints that act at the level of individual gene regulatory
elements.'
article_number: '12307'
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to
gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016).
Intrinsic limits to gene regulation by global crosstalk. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms12307
chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and
Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature
Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic
limits to gene regulation by global crosstalk,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits
to gene regulation by global crosstalk. Nature Communications. 7, 12307.
mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”
Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2023-09-07T12:53:49Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
file:
- access_level: open_access
checksum: fe3f3a1526d180b29fe691ab11435b78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4919'
file_name: IST-2016-627-v1+1_ncomms12307.pdf
file_size: 861805
relation: main_file
- access_level: open_access
checksum: 164864a1a675f3ad80e9917c27aba07f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:02Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4920'
file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf
file_size: 1084703
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5887'
pubrep_id: '627'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Intrinsic limits to gene regulation by global crosstalk
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1346'
abstract:
- lang: eng
text: ATP production requires the establishment of an electrochemical proton gradient
across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this
proton gradient and disrupt numerous cellular processes, including vesicular trafficking,
mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial
uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different
systems and that ES9 induces inhibition of CME not because of its effect on cellular
ATP, but rather due to its protonophore activity that leads to cytoplasm acidification.
We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely
used to block CME, displays similar properties, thus questioning its use as a
specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine
motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification
dramatically affects the dynamics and recruitment of clathrin and associated adaptors,
and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma
membrane.
acknowledgement: "We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi
Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen
Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing
S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys
for literature searches, VIB Bio Imaging Core for help with imaging conditions and
Martine De Cock for help in preparing the article. This work was supported by the
Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship
to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish
government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for
Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.);
the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.);
a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the
Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.),
the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated
by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet
grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral
fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R."
article_number: '11710'
author:
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Sabine
full_name: Kuenen, Sabine
last_name: Kuenen
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: Olivier
full_name: Keech, Olivier
last_name: Keech
- first_name: Corrado
full_name: Viotti, Corrado
last_name: Viotti
- first_name: Jef
full_name: Swerts, Jef
last_name: Swerts
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Fausto
full_name: Ortiz Morea, Fausto
last_name: Ortiz Morea
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Simon
full_name: Delang, Simon
last_name: Delang
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Xavier
full_name: Zarza, Xavier
last_name: Zarza
- first_name: Mareike
full_name: Heilmann, Mareike
last_name: Heilmann
- first_name: Jiorgos
full_name: Kourelis, Jiorgos
last_name: Kourelis
- first_name: Jaroslaw
full_name: Kasprowicz, Jaroslaw
last_name: Kasprowicz
- first_name: Le
full_name: Nguyen, Le
last_name: Nguyen
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Anna
full_name: Szatmári, Anna
last_name: Szatmári
- first_name: Mateusz
full_name: Majda, Mateusz
last_name: Majda
- first_name: Gary
full_name: Baisa, Gary
last_name: Baisa
- first_name: Sebastian
full_name: Bednarek, Sebastian
last_name: Bednarek
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Dominique
full_name: Audenaert, Dominique
last_name: Audenaert
- first_name: Christa
full_name: Testerink, Christa
last_name: Testerink
- first_name: Teun
full_name: Munnik, Teun
last_name: Munnik
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Patrik
full_name: Verstreken, Patrik
last_name: Verstreken
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated
endocytosis largely through cytoplasmic acidification. Nature Communications.
2016;7. doi:10.1038/ncomms11710
apa: Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C.,
… Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis
largely through cytoplasmic acidification. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms11710
chicago: Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech,
Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated
Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications.
Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710.
ieee: W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated
endocytosis largely through cytoplasmic acidification,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych
M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis
J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa
G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann
I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial
uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification.
Nature Communications. 7, 11710.
mla: Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis
Largely through Cytoplasmic Acidification.” Nature Communications, vol.
7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710.
short: W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J.
Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza,
M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte,
A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink,
T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken,
E. Russinova, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:30Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2023-09-07T12:54:35Z
day: '08'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1038/ncomms11710
ec_funded: 1
file:
- access_level: open_access
checksum: e8dc81b3e44db5a7718d7f1501ce1aa7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:47Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5369'
file_name: IST-2016-653-v1+1_ncomms11710_1_.pdf
file_size: 3532505
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5906'
pubrep_id: '653'
quality_controlled: '1'
related_material:
record:
- id: '7172'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through
cytoplasmic acidification
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1096'
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings
of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024
apa: Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P.
J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024
chicago: Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and
Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024.
ieee: C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg,
“Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press,
pp. 493–506, 2016.
ista: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin
rings of power. Developmental Cell. 37(6), 493–506.
mla: Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell,
vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.
short: C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental
Cell 37 (2016) 493–506.
date_created: 2018-12-11T11:50:07Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2023-09-07T12:56:41Z
day: '20'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2016.05.024
intvolume: ' 37'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 493 - 506
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6279'
quality_controlled: '1'
related_material:
record:
- id: '7186'
relation: part_of_dissertation
status: public
scopus_import: 1
status: public
title: Actin rings of power
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2016'
...
---
_id: '1328'
abstract:
- lang: eng
text: Hole spins have gained considerable interest in the past few years due to
their potential for fast electrically controlled qubits. Here, we study holes
confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature
magnetotransport measurements reveal a large anisotropy between the in-plane and
out-of-plane g-factors of up to 18. Numerical simulations verify that this large
anisotropy originates from a confined wave function of heavy-hole character. A
light-hole admixture of less than 1% is estimated for the states of lowest energy,
leading to a surprisingly large reduction of the out-of-plane g-factors compared
with those for pure heavy holes. Given this tiny light-hole contribution, the
spin lifetimes are expected to be very long, even in isotopically nonpurified
samples.
acknowledgement: 'The work was supported by the EC FP7 ICT project SiSPIN no. 323841,
the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20
project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions
related to the hut wire growth and for giving us access to the molecular beam epitaxy
system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko
for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous
support. '
author:
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Marta
full_name: Rossell, Marta
last_name: Rossell
- first_name: Violetta
full_name: Sessi, Violetta
last_name: Sessi
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Raimund
full_name: Kirchschlager, Raimund
last_name: Kirchschlager
- first_name: Elisabeth
full_name: Lausecker, Elisabeth
id: 33662F76-F248-11E8-B48F-1D18A9856A87
last_name: Lausecker
- first_name: Alisha
full_name: Truhlar, Alisha
id: 49CBC780-F248-11E8-B48F-1D18A9856A87
last_name: Truhlar
- first_name: Martin
full_name: Glaser, Martin
last_name: Glaser
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Andreas
full_name: Fuhrer, Andreas
last_name: Fuhrer
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut
wires. Nano Letters. 2016;16(11):6879-6885. doi:10.1021/acs.nanolett.6b02715
apa: Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka,
J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.6b02715
chicago: Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta
Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium
Hut Wires.” Nano Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.nanolett.6b02715.
ieee: H. Watzinger et al., “Heavy-hole states in germanium hut wires,” Nano
Letters, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016.
ista: Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager
R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G.
2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.
mla: Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano
Letters, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:10.1021/acs.nanolett.6b02715.
short: H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka,
R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer,
D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.
date_created: 2018-12-11T11:51:24Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2023-09-07T13:15:02Z
day: '22'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.6b02715
ec_funded: 1
file:
- access_level: open_access
checksum: b63feece90d7b620ece49ca632e34ff3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:04Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5053'
file_name: IST-2016-664-v1+1_acs.nanolett.6b02715.pdf
file_size: 535121
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '11'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 6879 - 6885
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5941'
pubrep_id: '664'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
status: for_moderation
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Heavy-hole states in germanium hut wires
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1205'
abstract:
- lang: eng
text: In this paper, we present a formal model-driven engineering approach to establishing
a safety-assured implementation of Multifunction vehicle bus controller (MVBC)
based on the generic reference models and requirements described in the International
Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models
described in IEC-61375 are translated into a network of timed automata, and some
safety requirements tested in IEC-61375 are formalized as timed computation tree
logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the
timed automata satisfy the formulas or not. Within this step, several logic inconsistencies
in the original standard are detected and corrected. Then, we apply the tool Times
to generate C code from the verified model, which was later synthesized into a
real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify
some safety requirements at the implementation level. We set up a real platform
with worldwide mostly used MVBC D113, and verify the correctness and the scalability
of the synthesized MVBC chip more comprehensively. The errors in the standard
has been confirmed and the resulted MVBC has been deployed in real train communication
network.
acknowledgement: "This research is sponsored in part by NSFC Program (No. 91218302,
No. 61527812), National Science and Technology Major Project (No. 2016ZX01038101),
Tsinghua University Initiative Scientific Research Program (20131089331), MIIT IT
funds (Research and application of TCN key technologies) of China, and the National
Key Technology R&D Program (No. 2015BAG14B01-02), Austrian Science Fund (FWF) under
grants S11402-N23 (RiSE/SHiNE) and Z211-N23.\r\n"
alternative_title:
- LNCS
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Houbing
full_name: Song, Houbing
last_name: Song
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ming
full_name: Gu, Ming
last_name: Gu
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Liu H, Song H, et al. Safety assured formal model driven design of
the multifunction vehicle bus controller. In: Vol 9995. Springer; 2016:757-763.
doi:10.1007/978-3-319-48989-6_47'
apa: 'Jiang, Y., Liu, H., Song, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016).
Safety assured formal model driven design of the multifunction vehicle bus controller
(Vol. 9995, pp. 757–763). Presented at the FM: International Symposium on Formal
Methods, Limassol, Cyprus: Springer. https://doi.org/10.1007/978-3-319-48989-6_47'
chicago: Jiang, Yu, Han Liu, Houbing Song, Hui Kong, Ming Gu, Jiaguang Sun, and
Lui Sha. “Safety Assured Formal Model Driven Design of the Multifunction Vehicle
Bus Controller,” 9995:757–63. Springer, 2016. https://doi.org/10.1007/978-3-319-48989-6_47.
ieee: 'Y. Jiang et al., “Safety assured formal model driven design of the
multifunction vehicle bus controller,” presented at the FM: International Symposium
on Formal Methods, Limassol, Cyprus, 2016, vol. 9995, pp. 757–763.'
ista: 'Jiang Y, Liu H, Song H, Kong H, Gu M, Sun J, Sha L. 2016. Safety assured
formal model driven design of the multifunction vehicle bus controller. FM: International
Symposium on Formal Methods, LNCS, vol. 9995, 757–763.'
mla: Jiang, Yu, et al. Safety Assured Formal Model Driven Design of the Multifunction
Vehicle Bus Controller. Vol. 9995, Springer, 2016, pp. 757–63, doi:10.1007/978-3-319-48989-6_47.
short: Y. Jiang, H. Liu, H. Song, H. Kong, M. Gu, J. Sun, L. Sha, in:, Springer,
2016, pp. 757–763.
conference:
end_date: 2016-11-11
location: Limassol, Cyprus
name: 'FM: International Symposium on Formal Methods'
start_date: 2016-11-09
date_created: 2018-12-11T11:50:42Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2023-09-18T08:12:48Z
day: '08'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1007/978-3-319-48989-6_47
file:
- access_level: open_access
checksum: fea0b3fae9a2a42e8bfec59840e30d8c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:13Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4673'
file_name: IST-2017-783-v1+1_FM-Safety-Assured-Development-of-MVBC.pdf
file_size: 281501
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9995'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 757 - 763
project:
- _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_status: published
publisher: Springer
publist_id: '6144'
pubrep_id: '783'
quality_controlled: '1'
related_material:
record:
- id: '434'
relation: later_version
status: public
scopus_import: 1
status: public
title: Safety assured formal model driven design of the multifunction vehicle bus
controller
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9995
year: '2016'
...
---
_id: '1193'
abstract:
- lang: eng
text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1],
[2] for finding objects that avoid "bad features", or "flaws".
It extends the Moser-Tardos resampling algorithm [3] to more general discrete
spaces. At each step the method picks a flaw present in the current state and
"resamples" it using a "resampling oracle" provided by the
user. However, it is less flexible than the Moser-Tardos method since [1], [2]
require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and
thus can potentially be implemented more efficiently). We formulate a new "commutativity"
condition, and prove that it is sufficient for an arbitrary rule to work. It also
enables an efficient parallelization under an additional assumption. We then show
that existing resampling oracles for perfect matchings and permutations do satisfy
this condition. Finally, we generalize the precondition in [2] (in the case of
symmetric potential causality graphs). This unifies special cases that previously
were treated separately.
acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160
article_number: '7782993'
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings
- Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December.
IEEE; 2016. doi:10.1109/FOCS.2016.88'
apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma.
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science
(Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88'
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings
- Annual IEEE Symposium on Foundations of Computer Science, New Brunswick,
NJ, USA , 2016, vol. 2016–December.
ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma.
Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS:
Foundations of Computer Science vol. 2016–December, 7782993.'
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.
short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of
Computer Science, IEEE, 2016.
conference:
end_date: 2016-09-11
location: 'New Brunswick, NJ, USA '
name: 'FOCS: Foundations of Computer Science'
start_date: 2016-09-09
date_created: 2018-12-11T11:50:38Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2023-09-19T14:24:57Z
day: '15'
department:
- _id: VlKo
doi: 10.1109/FOCS.2016.88
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547v7
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science
publication_status: published
publisher: IEEE
publist_id: '6158'
quality_controlled: '1'
related_material:
record:
- id: '5975'
relation: later_version
status: public
scopus_import: 1
status: public
title: Commutativity in the algorithmic Lovasz local lemma
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-December
year: '2016'
...
---
_id: '1438'
abstract:
- lang: eng
text: 'In this paper, we consider termination of probabilistic programs with real-valued
variables. The questions concerned are: (a) qualitative ones that ask (i) whether
the program terminates with probability 1 (almost-sure termination) and (ii) whether
the expected termination time is finite (finite termination); (b) quantitative
ones that ask (i) to approximate the expected termination time (expectation problem)
and (ii) to compute a bound B such that the probability to terminate after B steps
decreases exponentially (concentration problem). To solve these questions, we
utilize the notion of ranking supermartingales which is a powerful approach for
proving termination of probabilistic programs. In detail, we focus on algorithmic
synthesis of linear ranking-supermartingales over affine probabilistic programs
(APP''s) with both angelic and demonic non-determinism. An important subclass
of APP''s is LRAPP which is defined as the class of all APP''s over which a linear
ranking-supermartingale exists. Our main contributions are as follows. Firstly,
we show that the membership problem of LRAPP (i) can be decided in polynomial
time for APP''s with at most demonic non-determinism, and (ii) is NP-hard and
in PSPACE for APP''s with angelic non-determinism; moreover, the NP-hardness result
holds already for APP''s without probability and demonic non-determinism. Secondly,
we show that the concentration problem over LRAPP can be solved in the same complexity
as for the membership problem of LRAPP. Finally, we show that the expectation
problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP''s
without probability and non-determinism (i.e., deterministic programs). Our experimental
results demonstrate the effectiveness of our approach to answer the qualitative
and quantitative questions over APP''s with at most demonic non-determinism.'
acknowledgement: 'Supported by the Natural Science Foundation of China (NSFC) under
Grant No. 61532019 '
alternative_title:
- POPL
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Rouzbeh
full_name: Hasheminezhad, Rouzbeh
last_name: Hasheminezhad
citation:
ama: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative
and quantitative termination problems for affine probabilistic programs. In: Vol
20-22. ACM; 2016:327-342. doi:10.1145/2837614.2837639'
apa: 'Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2016). Algorithmic
analysis of qualitative and quantitative termination problems for affine probabilistic
programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming
Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837639'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad.
“Algorithmic Analysis of Qualitative and Quantitative Termination Problems for
Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. https://doi.org/10.1145/2837614.2837639.
ieee: 'K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg,
FL, USA, 2016, vol. 20–22, pp. 327–342.'
ista: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.'
mla: Chatterjee, Krishnendu, et al. Algorithmic Analysis of Qualitative and Quantitative
Termination Problems for Affine Probabilistic Programs. Vol. 20–22, ACM, 2016,
pp. 327–42, doi:10.1145/2837614.2837639.
short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2023-09-19T14:38:41Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/2837614.2837639
ec_funded: 1
external_id:
arxiv:
- '1510.08517'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.08517
month: '01'
oa: 1
oa_version: Preprint
page: 327 - 342
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: ACM
publist_id: '5760'
quality_controlled: '1'
related_material:
record:
- id: '5993'
relation: later_version
status: public
scopus_import: 1
status: public
title: Algorithmic analysis of qualitative and quantitative termination problems for
affine probabilistic programs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2023-09-20T11:56:33Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1165'
abstract:
- lang: eng
text: We show that c-planarity is solvable in quadratic time for flat clustered
graphs with three clusters if the combinatorial embedding of the underlying graph
is fixed. In simpler graph-theoretical terms our result can be viewed as follows.
Given a graph G with the vertex set partitioned into three parts embedded on a
2-sphere, our algorithm decides if we can augment G by adding edges without creating
an edge-crossing so that in the resulting spherical graph the vertices of each
part induce a connected sub-graph. We proceed by a reduction to the problem of
testing the existence of a perfect matching in planar bipartite graphs. We formulate
our result in a slightly more general setting of cyclic clustered graphs, i.e.,
the simple graph obtained by contracting each cluster, where we disregard loops
and multi-edges, is a cycle.
acknowledgement: "R. Fulek—The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI
would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions
that helped to improve the presentation of the result."
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer;
2016:94-106. doi:10.1007/978-3-319-50106-2_8'
apa: 'Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp.
94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens,
Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8'
chicago: Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106.
Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.
ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD:
Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp.
94–106.'
ista: 'Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing
and Network Visualization, LNCS, vol. 9801, 94–106.'
mla: Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801,
Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8.
short: R. Fulek, in:, Springer, 2016, pp. 94–106.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-09-27T12:14:48Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_8
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.01346
month: '12'
oa: 1
oa_version: Preprint
page: 94 - 106
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6192'
quality_controlled: '1'
related_material:
record:
- id: '794'
relation: later_version
status: public
scopus_import: 1
status: public
title: C-planarity of embedded cyclic c-graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '9801 '
year: '2016'
...
---
_id: '1378'
abstract:
- lang: eng
text: 'We give a detailed and easily accessible proof of Gromov''s Topological Overlap
Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral
cell complex of dimension d. Informally, the theorem states that if X has sufficiently
strong higher-dimensional expansion properties (which generalize edge expansion
of graphs and are defined in terms of cellular cochains of X) then X has the following
topological overlap property: for every continuous map X → ℝd there exists a point
p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of
X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional
piecewise-linear (PL) manifold M, with a constant μ that depends only on d and
on the expansion properties of X, but not on M.'
alternative_title:
- LIPIcs
author:
- first_name: Dominic
full_name: Dotterrer, Dominic
last_name: Dotterrer
- first_name: Tali
full_name: Kaufman, Tali
last_name: Kaufman
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In:
Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:35.1-35.10. doi:10.4230/LIPIcs.SoCG.2016.35'
apa: 'Dotterrer, D., Kaufman, T., & Wagner, U. (2016). On expansion and topological
overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational
Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.35'
chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH,
Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.35.
ieee: 'D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA,
2016, vol. 51, p. 35.1-35.10.'
ista: 'Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.'
mla: Dotterrer, Dominic, et al. On Expansion and Topological Overlap. Vol.
51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 35.1-35.10, doi:10.4230/LIPIcs.SoCG.2016.35.
short: D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-09-27T12:29:56Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.35
file:
- access_level: open_access
checksum: cee65b0e722d50f9d1cc70c90ec1d59b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:38Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4699'
file_name: IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf
file_size: 536923
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 35.1 - 35.10
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5833'
pubrep_id: '623'
quality_controlled: '1'
related_material:
record:
- id: '742'
relation: later_version
status: public
scopus_import: 1
status: public
title: On expansion and topological overlap
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1616'
abstract:
- lang: eng
text: The hippocampus plays a key role in learning and memory. Previous studies
suggested that the main types of principal neurons, dentate gyrus granule cells
(GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity
pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal
neurons. It has been assumed but never shown that such different activity may
be caused by differential synaptic excitation. To test this hypothesis, we performed
high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo.
In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired
action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were
silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine
the underlying mechanisms, we quantitatively assessed the frequency of spontaneous
excitatory synaptic input, the passive membrane properties, and the active membrane
characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3
and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition.
Thus, differential synaptic excitation is not responsible for differences in firing.
Moreover, the three types of hippocampal neurons markedly differed in their passive
properties. While GCs showed the most negative membrane potential, CA3 pyramidal
neurons had the highest input resistance and the slowest membrane time constant.
The three types of neurons also differed in the active membrane characteristics.
GCs showed the highest action potential threshold, but displayed the largest gain
of the input-output curves. In conclusion, our results reveal that differential
firing of the three main types of hippocampal principal neurons in vivo is not
primarily caused by differences in the characteristics of the synaptic input,
but by the distinct properties of synaptic integration and input-output transformation.
acknowledgement: "The authors thank Jose Guzman for critically reading prior versions
of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices,
A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger
for manuscript editing."
article_processing_charge: No
author:
- first_name: Janina
full_name: Kowalski, Janina
id: 3F3CA136-F248-11E8-B48F-1D18A9856A87
last_name: Kowalski
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
citation:
ama: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties
determine hippocampal differential firing pattern in vivo in anesthetized rats.
Hippocampus. 2016;26(5):668-682. doi:10.1002/hipo.22550
apa: Kowalski, J., Gan, J., Jonas, P. M., & Pernia-Andrade, A. (2016). Intrinsic
membrane properties determine hippocampal differential firing pattern in vivo
in anesthetized rats. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22550
chicago: Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade.
“Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern
in Vivo in Anesthetized Rats.” Hippocampus. Wiley, 2016. https://doi.org/10.1002/hipo.22550.
ieee: J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane
properties determine hippocampal differential firing pattern in vivo in anesthetized
rats,” Hippocampus, vol. 26, no. 5. Wiley, pp. 668–682, 2016.
ista: Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties
determine hippocampal differential firing pattern in vivo in anesthetized rats.
Hippocampus. 26(5), 668–682.
mla: Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal
Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus,
vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:10.1002/hipo.22550.
short: J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016)
668–682.
date_created: 2018-12-11T11:53:03Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-10-17T10:02:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/hipo.22550
file:
- access_level: open_access
checksum: 284b72b12fbe15474833ed3d4549f86b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:47Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5033'
file_name: IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf
file_size: 905348
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 668 - 682
publication: Hippocampus
publication_identifier:
eissn:
- 1098-1063
issn:
- 1050-9631
publication_status: published
publisher: Wiley
publist_id: '5550'
pubrep_id: '469'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intrinsic membrane properties determine hippocampal differential firing pattern
in vivo in anesthetized rats
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1794'
abstract:
- lang: eng
text: We consider Conditional random fields (CRFs) with pattern-based potentials
defined on a chain. In this model the energy of a string (labeling) (Formula presented.)
is the sum of terms over intervals [i, j] where each term is non-zero only if
the substring (Formula presented.) equals a prespecified pattern w. Such CRFs
can be naturally applied to many sequence tagging problems. We present efficient
algorithms for the three standard inference tasks in a CRF, namely computing (i)
the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities
are respectively (Formula presented.), (Formula presented.) and (Formula presented.)
where L is the combined length of input patterns, (Formula presented.) is the
maximum length of a pattern, and D is the input alphabet. This improves on the
previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively
(Formula presented.), (Formula presented.) and (Formula presented.), where (Formula
presented.) is the number of input patterns. In addition, we give an efficient
algorithm for sampling, and revisit the case of MAP with non-positive weights.
acknowledgement: This work has been partially supported by the European Research Council
under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no. 616160.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Rustem
full_name: Takhanov, Rustem
id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87
last_name: Takhanov
citation:
ama: Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence
data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7
apa: Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based
CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7
chicago: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7.
ieee: V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs
on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016.
ista: Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs
on sequence data. Algorithmica. 76(1), 17–46.
mla: Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based
CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp.
17–46, doi:10.1007/s00453-015-0017-7.
short: V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.
date_created: 2018-12-11T11:54:02Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-10-17T09:51:31Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00453-015-0017-7
ec_funded: 1
external_id:
arxiv:
- '1210.0508'
intvolume: ' 76'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1210.0508
month: '09'
oa: 1
oa_version: Preprint
page: 17 - 46
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '5316'
quality_controlled: '1'
related_material:
record:
- id: '2272'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Inference algorithms for pattern-based CRFs on sequence data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2016'
...
---
_id: '510'
abstract:
- lang: eng
text: 'The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted
signaling peptides that are primarily involved in the regulation of stem cell
homeostasis in different plant meristems. Particularly, the characterization of
the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on
the potential roles of CLE peptides in vascular development and wood formation.
Nevertheless, our knowledge on this gene family in a tree species is limited.
In a recent study, we reported on a systematically investigation of the CLE gene
family in Populus trichocarpa . The potential roles of PtCLE genes were studied
by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members,
many PtCLE proteins share identical CLE motifs or contain the same CLE motif as
that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression
patterns comparing to their Arabidopsis counterparts. These fi ndings indicate
the existence of both functional conservation and functional divergence between
PtCLEs and their AtCLE orthologues. Our results provide valuable resources for
future functional investigations of these critical signaling molecules in woody
plants. '
acknowledgement: 'We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement
des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading
of the article. Work in our group is supported by the National Natural Science Foundation
of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ
ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of
Higher Education from the Ministry of Education of China (20120202120009), the Scientific
Research Foundation for the Returned Overseas Chinese Scholars, State Education
Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China
(2014JM3064). '
article_number: e1191734
article_processing_charge: No
author:
- first_name: Zhijun
full_name: Liu, Zhijun
last_name: Liu
- first_name: 'Nan'
full_name: Yang, Nan
last_name: Yang
- first_name: Yanting
full_name: Lv, Yanting
last_name: Lv
- first_name: Lixia
full_name: Pan, Lixia
last_name: Pan
- first_name: Shuo
full_name: Lv, Shuo
last_name: Lv
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Guodong
full_name: Wang, Guodong
last_name: Wang
citation:
ama: Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant
Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734
apa: Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016).
The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior.
Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734
chicago: Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and
Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling
& Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.
ieee: Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant
Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.
ista: Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family
in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.
mla: Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant
Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis,
2016, doi:10.1080/15592324.2016.1191734.
short: Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &
Behavior 11 (2016).
date_created: 2018-12-11T11:46:53Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2023-10-17T11:13:40Z
day: '02'
department:
- _id: JiFr
doi: 10.1080/15592324.2016.1191734
intvolume: ' 11'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/
month: '06'
oa: 1
oa_version: Submitted Version
publication: Plant Signaling & Behavior
publication_status: published
publisher: Taylor & Francis
publist_id: '7308'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The CLE gene family in Populus trichocarpa
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1263'
abstract:
- lang: eng
text: Linking classical microwave electrical circuits to the optical telecommunication
band is at the core of modern communication. Future quantum information networks
will require coherent microwave-to-optical conversion to link electronic quantum
processors and memories via low-loss optical telecommunication networks. Efficient
conversion can be achieved with electro-optical modulators operating at the single
microwave photon level. In the standard electro-optic modulation scheme, this
is impossible because both up- and down-converted sidebands are necessarily present.
Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant
whispering gallery mode resonator by explicitly addressing modes with asymmetric
free spectral range. Compared to previous experiments, we show a 3 orders of magnitude
improvement of the electro-optical conversion efficiency, reaching 0.1% photon
number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power.
The presented scheme is fully compatible with existing superconducting 3D circuit
quantum electrodynamics technology and can be used for nonclassical state conversion
and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally
limited.
acknowledgement: Alexander von Humboldt Foundation; Studienstiftung des Deutschen
Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert
and Alessandro Pitanti.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Rueda, Alfredo
last_name: Rueda
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Michele
full_name: Collodo, Michele
last_name: Collodo
- first_name: Ulrich
full_name: Vogl, Ulrich
last_name: Vogl
- first_name: Birgit
full_name: Stiller, Birgit
last_name: Stiller
- first_name: Gerhard
full_name: Schunk, Gerhard
last_name: Schunk
- first_name: Dmitry
full_name: Strekalov, Dmitry
last_name: Strekalov
- first_name: Christoph
full_name: Marquardt, Christoph
last_name: Marquardt
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald
full_name: Schwefel, Harald
last_name: Schwefel
citation:
ama: 'Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon
conversion: An electro-optical realization. Optica. 2016;3(6):597-604.
doi:10.1364/OPTICA.3.000597'
apa: 'Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., …
Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical
realization. Optica. Optica Publishing Group. https://doi.org/10.1364/OPTICA.3.000597'
chicago: 'Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit
Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical
Photon Conversion: An Electro-Optical Realization.” Optica. Optica Publishing
Group, 2016. https://doi.org/10.1364/OPTICA.3.000597.'
ieee: 'A. Rueda et al., “Efficient microwave to optical photon conversion:
An electro-optical realization,” Optica, vol. 3, no. 6. Optica Publishing
Group, pp. 597–604, 2016.'
ista: 'Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D,
Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave
to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.'
mla: 'Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion:
An Electro-Optical Realization.” Optica, vol. 3, no. 6, Optica Publishing
Group, 2016, pp. 597–604, doi:10.1364/OPTICA.3.000597.'
short: A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov,
C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.
date_created: 2018-12-11T11:51:01Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2023-10-17T12:17:15Z
day: '20'
department:
- _id: JoFi
doi: 10.1364/OPTICA.3.000597
intvolume: ' 3'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1364/OPTICA.3.000597
month: '06'
oa: 1
oa_version: Published Version
page: 597 - 604
publication: Optica
publication_status: published
publisher: Optica Publishing Group
publist_id: '6061'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Efficient microwave to optical photon conversion: An electro-optical realization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2016'
...
---
_id: '1287'
abstract:
- lang: eng
text: A planar waveguide with an impedance boundary, composed of nonperfect metallic
plates, and with passive or active dielectric filling, is considered. We show
the possibility of selective mode guiding and amplification when a homogeneous
pump is added to the dielectric and analyze differences in TE and TM mode propagation.
Such a non-conservative system is also shown to feature exceptional points for
specific and experimentally tunable parameters, which are described for a particular
case of transparent dielectric.
acknowledgement: The research of B.M. is supported by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant No. [291734].
article_processing_charge: No
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: Midya B, Konotop V. Modes and exceptional points in waveguides with impedance
boundary conditions. Optics Letters. 2016;41(20):4621-4624. doi:10.1364/OL.41.004621
apa: Midya, B., & Konotop, V. (2016). Modes and exceptional points in waveguides
with impedance boundary conditions. Optics Letters. Optica Publishing Group.
https://doi.org/10.1364/OL.41.004621
chicago: Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points
in Waveguides with Impedance Boundary Conditions.” Optics Letters. Optica
Publishing Group, 2016. https://doi.org/10.1364/OL.41.004621.
ieee: B. Midya and V. Konotop, “Modes and exceptional points in waveguides with
impedance boundary conditions,” Optics Letters, vol. 41, no. 20. Optica
Publishing Group, pp. 4621–4624, 2016.
ista: Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with
impedance boundary conditions. Optics Letters. 41(20), 4621–4624.
mla: Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides
with Impedance Boundary Conditions.” Optics Letters, vol. 41, no. 20, Optica
Publishing Group, 2016, pp. 4621–24, doi:10.1364/OL.41.004621.
short: B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.
date_created: 2018-12-11T11:51:09Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2023-10-17T12:16:24Z
day: '15'
department:
- _id: MiLe
doi: 10.1364/OL.41.004621
ec_funded: 1
intvolume: ' 41'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.02863
month: '10'
oa: 1
oa_version: Preprint
page: 4621 - 4624
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Optics Letters
publication_status: published
publisher: Optica Publishing Group
publist_id: '6029'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modes and exceptional points in waveguides with impedance boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2016'
...
---
_id: '482'
abstract:
- lang: eng
text: Nonlinear electro-optical conversion of microwave radiation into the optical
telecommunication band is achieved within a crystalline whispering gallery mode
resonator, reaching 0.1% photon number conversion efficiency with MHz bandwidth.
alternative_title:
- Optics InfoBase Conference Papers
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Rueda, Alfredo
last_name: Rueda
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Michele
full_name: Collodo, Michele
last_name: Collodo
- first_name: Ulrich
full_name: Vogl, Ulrich
last_name: Vogl
- first_name: Birgit
full_name: Stiller, Birgit
last_name: Stiller
- first_name: Gerhard
full_name: Schunk, Gerhard
last_name: Schunk
- first_name: Dmitry
full_name: Strekalov, Dmitry
last_name: Strekalov
- first_name: Christoph
full_name: Marquardt, Christoph
last_name: Marquardt
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald
full_name: Schwefel, Harald
last_name: Schwefel
citation:
ama: 'Rueda A, Sedlmeir F, Collodo M, et al. Nonlinear single sideband microwave
to optical conversion using an electro-optic WGM-resonator. In: Optica Publishing
Group; 2016. doi:10.1364/NP.2016.NTh3A.6'
apa: 'Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., …
Schwefel, H. (2016). Nonlinear single sideband microwave to optical conversion
using an electro-optic WGM-resonator. Presented at the NP: Nonlinear Photonics,
Sydney, Australia: Optica Publishing Group. https://doi.org/10.1364/NP.2016.NTh3A.6'
chicago: Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit
Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Nonlinear Single Sideband Microwave
to Optical Conversion Using an Electro-Optic WGM-Resonator.” Optica Publishing
Group, 2016. https://doi.org/10.1364/NP.2016.NTh3A.6.
ieee: 'A. Rueda et al., “Nonlinear single sideband microwave to optical conversion
using an electro-optic WGM-resonator,” presented at the NP: Nonlinear Photonics,
Sydney, Australia, 2016.'
ista: 'Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D,
Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Nonlinear single
sideband microwave to optical conversion using an electro-optic WGM-resonator.
NP: Nonlinear Photonics, Optics InfoBase Conference Papers, .'
mla: Rueda, Alfredo, et al. Nonlinear Single Sideband Microwave to Optical Conversion
Using an Electro-Optic WGM-Resonator. Optica Publishing Group, 2016, doi:10.1364/NP.2016.NTh3A.6.
short: A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov,
C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, Optica Publishing
Group, 2016.
conference:
end_date: 2016-09-08
location: Sydney, Australia
name: 'NP: Nonlinear Photonics'
start_date: 2016-09-05
date_created: 2018-12-11T11:46:43Z
date_published: 2016-08-29T00:00:00Z
date_updated: 2023-10-17T12:16:43Z
day: '29'
department:
- _id: JoFi
doi: 10.1364/NP.2016.NTh3A.6
language:
- iso: eng
month: '08'
oa_version: None
publication_status: published
publisher: Optica Publishing Group
publist_id: '7339'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonlinear single sideband microwave to optical conversion using an electro-optic
WGM-resonator
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1274'
abstract:
- lang: eng
text: Synchronized tissue polarization during regeneration or de novo vascular tissue
formation is a plant-specific example of intercellular communication and coordinated
development. According to the canalization hypothesis, the plant hormone auxin
serves as polarizing signal that mediates directional channel formation underlying
the spatio-temporal vasculature patterning. A necessary part of canalization is
a positive feedback between auxin signaling and polarity of the intercellular
auxin flow. The cellular and molecular mechanisms of this process are still poorly
understood, not the least, because of a lack of a suitable model system. We show
that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used
to study the canalization during vascular cambium regeneration and new vasculature
formation. We monitored localized auxin responses, directional auxin-transport
channels formation, and establishment of new vascular cambium polarity during
regenerative processes after stem wounding. The increased auxin response above
and around the wound preceded the formation of PIN1 auxin transporter-marked channels
from the primarily homogenous tissue and the transient, gradual changes in PIN1
localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis
is a useful model for studies of coordinated tissue polarization and vasculature
formation after wounding allowing for genetic and mechanistic dissection of the
canalization hypothesis.
acknowledgement: We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work
and valuable advices. We thank Martine De Cock for help in preparing the manuscript.
This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP),
the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation
GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the
European Regional Development Fund (project “CEITEC, Central European Institute
of Technology”, CZ.1.05/1.1.00/02.0068).
article_number: '33754'
article_processing_charge: No
author:
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation
in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6.
doi:10.1038/srep33754
apa: Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration
and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific
Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754
chicago: Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration
and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.
ieee: E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel
formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel
formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6,
33754.
mla: Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded
Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754,
Nature Publishing Group, 2016, doi:10.1038/srep33754.
short: E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:51:05Z
date_published: 2016-09-21T00:00:00Z
date_updated: 2024-02-12T12:03:42Z
day: '21'
ddc:
- '581'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/srep33754
external_id:
pmid:
- '27649687'
file:
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checksum: ee371fbc9124ad93157a95829264e4fe
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creator: system
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date_updated: 2020-07-14T12:44:42Z
file_id: '5008'
file_name: IST-2016-692-v1+1_srep33754.pdf
file_size: 2895147
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6042'
pubrep_id: '692'
quality_controlled: '1'
related_material:
record:
- id: '545'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Vascular cambium regeneration and vessel formation in wounded inflorescence
stems of Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1253'
abstract:
- lang: eng
text: This article provides an introduction to the role of microRNAs in the nervous
system and outlines their potential involvement in the pathophysiology of schizophrenia,
which is hypothesized to arise owing to environmental factors and genetic predisposition.
article_processing_charge: No
author:
- first_name: Lihuei
full_name: Tsai, Lihuei
last_name: Tsai
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. JAMA
Psychiatry. 2016;73(4):409-410. doi:10.1001/jamapsychiatry.2015.3144
apa: Tsai, L., & Siegert, S. (2016). How MicroRNAs Are involved in splitting
the mind. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2015.3144
chicago: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
the Mind.” JAMA Psychiatry. American Medical Association, 2016. https://doi.org/10.1001/jamapsychiatry.2015.3144.
ieee: L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,”
JAMA Psychiatry, vol. 73, no. 4. American Medical Association, pp. 409–410,
2016.
ista: Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind.
JAMA Psychiatry. 73(4), 409–410.
mla: Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting
the Mind.” JAMA Psychiatry, vol. 73, no. 4, American Medical Association,
2016, pp. 409–10, doi:10.1001/jamapsychiatry.2015.3144.
short: L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2024-02-14T12:07:22Z
day: '01'
ddc:
- '576'
- '610'
department:
- _id: SaSi
doi: 10.1001/jamapsychiatry.2015.3144
external_id:
pmid:
- '26963490'
file:
- access_level: open_access
checksum: 649aee381f30f7ef7e9efa912d41c2e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:24Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5278'
file_name: IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf
file_size: 601679
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 73'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 409 - 410
pmid: 1
publication: JAMA Psychiatry
publication_identifier:
issn:
- 2168-622X
publication_status: published
publisher: American Medical Association
publist_id: '6074'
pubrep_id: '981'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How MicroRNAs Are involved in splitting the mind
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2016'
...
---
_id: '5452'
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers
of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-728-v2-1
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily
strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-728-v2-1
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria,
2016. https://doi.org/10.15479/AT:IST-2017-728-v2-1.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong
amplifiers of natural selection. IST Austria, 2016.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong
amplifiers of natural selection, IST Austria, 32p.
mla: Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection.
IST Austria, 2016, doi:10.15479/AT:IST-2017-728-v2-1.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong
Amplifiers of Natural Selection, IST Austria, 2016.
date_created: 2018-12-12T11:39:25Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2024-02-21T13:48:42Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-728-v2-1
ec_funded: 1
file:
- access_level: open_access
checksum: 58e895f26c82f560c0f0989bf8b08599
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:52:59Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5460'
file_name: IST-2017-728-v2+1_main.pdf
file_size: 811558
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '32'
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '750'
related_material:
record:
- id: '5453'
relation: later_version
status: public
- id: '5559'
relation: popular_science
status: public
status: public
title: Arbitrarily strong amplifiers of natural selection
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1382'
abstract:
- lang: eng
text: Background and aims Angiosperms display remarkable diversity in flower colour,
implying that transitions between pigmentation phenotypes must have been common.
Despite progress in understanding transitions between anthocyanin (blue, purple,
pink or red) and unpigmented (white) flowers, little is known about the evolutionary
patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented
flowers. This study investigates the relative rates of evolutionary transitions
between different combinations of yellow- and anthocyanin-pigmentation phenotypes
in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on
anthocyanin and yellow floral pigmentation for 369 species across the tribe. We
then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative
methods to estimate transition rates among pigmentation phenotypes across the
phylogeny. Key Results In contrast to previous studies we found a bias towards
transitions involving a gain in pigmentation, although transitions to phenotypes
with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite
the dominance of yellow and anthocyanin-pigmented taxa, transitions between these
phenotypes are constrained to move through a white intermediate stage, whereas
transitions to double-pigmentation are very rare. The most abundant transitions
are between anthocyanin-pigmented and unpigmented flowers, and similarly the most
abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented
flowers. Conclusions Our findings show that pigment evolution is limited by the
presence of other floral pigments. This interaction between anthocyanin and yellow
pigments constrains the breadth of potential floral diversity observed in nature.
In particular, they suggest that selection has repeatedly acted to promote the
spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore,
the correlation between transition rates and polymorphism suggests that the forces
causing and maintaining variance in the short term reflect evolutionary processes
on longer time scales.
acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous
reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for
her efforts in tracking down the more obscure references.
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in
flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140.
doi:10.1093/aob/mcw043
apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin
pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany.
Oxford University Press. https://doi.org/10.1093/aob/mcw043
chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin
Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany.
Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.
ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae,” Annals of Botany, vol.
117, no. 7. Oxford University Press, pp. 1133–1140, 2016.
ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.
mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation
in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol.
117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.
short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.
date_created: 2018-12-11T11:51:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-02-21T13:49:53Z
day: '1'
department:
- _id: NiBa
doi: 10.1093/aob/mcw043
intvolume: ' 117'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 1133 - 1140
publication: Annals of Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5828'
quality_controlled: '1'
related_material:
record:
- id: '5550'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions
in the Antirrhineae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...
---
_id: '5550'
abstract:
- lang: eng
text: "We collected flower colour information on species in the tribe Antirrhineae
from taxonomic literature. We also retreived molecular data from GenBank for as
many of these species as possible to estimate phylogenetic relationships among
these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary
transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor
full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in
yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”,
Annals of Botany (in press)"
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34
apa: Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS)
files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34
chicago: Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS)
Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.
ieee: T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:34.
mla: Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS)
Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34.
short: T. Ellis, D. Field, (2016).
datarep_id: '34'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:49:54Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:34
file:
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content_type: application/zip
creator: system
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date_updated: 2020-07-14T12:47:00Z
file_id: '5594'
file_name: IST-2016-34-v1+1_tellis_flower_colour_data.zip
file_size: 4468543
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '5828'
related_material:
record:
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relation: research_paper
status: public
status: public
title: Flower colour data and phylogeny (NEXUS) files
tmp:
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year: '2016'
...
---
_id: '5555'
abstract:
- lang: eng
text: This FIJI script calculates the population average of the migration speed
as a function of time of all cells from wide field microscopy movies.
article_processing_charge: No
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. Fiji script to determine average speed and direction of migration
of cells. 2016. doi:10.15479/AT:ISTA:44
apa: Hauschild, R. (2016). Fiji script to determine average speed and direction
of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44
chicago: Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction
of Migration of Cells.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:44.
ieee: R. Hauschild, “Fiji script to determine average speed and direction of migration
of cells.” Institute of Science and Technology Austria, 2016.
ista: Hauschild R. 2016. Fiji script to determine average speed and direction of
migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.
mla: Hauschild, Robert. Fiji Script to Determine Average Speed and Direction
of Migration of Cells. Institute of Science and Technology Austria, 2016,
doi:10.15479/AT:ISTA:44.
short: R. Hauschild, (2016).
datarep_id: '44'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-07-08T00:00:00Z
date_updated: 2024-02-21T13:50:06Z
day: '08'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:44
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checksum: 9f96cddbcd4ed689f48712ffe234d5e5
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date_updated: 2020-07-14T12:47:02Z
file_id: '5621'
file_name: IST-2016-44-v1+1_migrationAnalyzer.zip
file_size: 20692
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- cell migration
- wide field microscopy
- FIJI
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Fiji script to determine average speed and direction of migration of cells
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5557'
abstract:
- lang: eng
text: "Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and
256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
citation:
ama: Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46
apa: Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:46
chicago: Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science
and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.
ieee: P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science
and Technology Austria, 2016.
ista: Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:46.
mla: Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of
Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46.
short: P. Swoboda, (2016).
contributor:
- contributor_type: data_collector
first_name: Jan
last_name: Kuske
datarep_id: '46'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-20T00:00:00Z
date_updated: 2024-02-21T13:50:21Z
day: '20'
ddc:
- '006'
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:46
file:
- access_level: open_access
checksum: aa5a16a0dc888da7186fb8fc45e88439
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:19Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5645'
file_name: IST-2016-46-v1+1_discrete_tomography_synthetic.zip
file_size: 36058401
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- discrete tomography
month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Synthetic discrete tomography problems
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
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type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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:
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creator: system
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date_updated: 2018-12-12T10:13:02Z
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language:
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month: '07'
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: '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: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2024-02-21T13:51:39Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: '10.15479/AT:ISTA:TH_526 '
file:
- access_level: open_access
checksum: a89b17ff27cf92c9a15f6b3d46bd7e53
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:51Z
date_updated: 2020-07-14T12:44:48Z
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issn:
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publication_status: published
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publist_id: '5809'
pubrep_id: '526'
related_material:
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relation: popular_science
status: public
- id: '5551'
relation: popular_science
status: public
- id: '5552'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: 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: 2024-02-21T13:50:34Z
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
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creator: dernst
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date_updated: 2021-02-22T11:45:20Z
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file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
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oa: 1
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publication_identifier:
issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
record:
- id: '1666'
relation: part_of_dissertation
status: public
- id: '5554'
relation: research_data
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: '5553'
abstract:
- lang: eng
text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
1127 open-pollinated progeny from a natural hybrid zone, collected as part of
Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
removed from this dataset.\r\n\r\nOther data were retreived from an online database
of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37
apa: Field, D., & Ellis, T. (2016). Inference of mating patterns among wild
snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:37
chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.
ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
2016.
ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
10.15479/AT:ISTA:37.
mla: Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology
Austria, 2016, doi:10.15479/AT:ISTA:37.
short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:14Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
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date_updated: 2020-07-14T12:47:01Z
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file_size: 132808
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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status: public
title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
in 2012
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type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5551'
abstract:
- lang: eng
text: "Data from array experiments investigating pollinator behaviour on snapdragons
in controlled conditions, and their effect on plant mating. Data were collected
as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a
total of 36 plants in a grid inside a closed organza tent, with a single hive
of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered
Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus,
at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn
how to deal with snapdragons, I observed pollinators foraging on plants, and recorded
the transitions between plants. Thereafter seeds on plants were allowed to develops.
A sample of these were grown to maturity when their flower colour could be determined,
and they were scored as yellow, magenta, or hybrid."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35
apa: Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35
chicago: Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.
ieee: T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:35.
mla: Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '35'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:27Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:35
file:
- access_level: open_access
checksum: aa3eb85d52b110cd192aa23147c4d4f3
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:12Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5640'
file_name: IST-2016-35-v1+1_array_data.zip
file_size: 32775
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Data on pollinator observations and offpsring phenotypes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5552'
abstract:
- lang: eng
text: "Data on pollinator visitation to wild snapdragons in a natural hybrid zone,
collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon
flowers have a mouth-like structure which pollinators must open to access nectar.
We placed 5mm cellophane tags in these mouths, which are held in place by the
pressure of the flower until a pollinator visits. When she opens the flower, the
tag drops out, and one can infer a visit. We surveyed plants over multiple days
in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic
variables which may be explanatory variables for pollinator visitation."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36
apa: Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:36
chicago: Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data.” Institute of Science and Technology Austria,
2016. https://doi.org/10.15479/AT:ISTA:36.
ieee: T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data., Institute of Science and Technology Austria,
10.15479/AT:ISTA:36.
mla: Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data. Institute of Science and Technology Austria,
2016, doi:10.15479/AT:ISTA:36.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '36'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:40Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:36
file:
- access_level: open_access
checksum: cbc61b523d4d475a04a737d50dc470ef
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:07Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5625'
file_name: IST-2016-36-v1+1_tag_assay_archive.zip
file_size: 44905
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic
and frequency data.
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5554'
abstract:
- lang: eng
text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which
is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena
Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments
and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student
in Jon Bollback's group at IST Austria) performed the experiments and created
the data on lac promoter evolution."
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.
2016. doi:10.15479/AT:ISTA:43
apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43
chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.
ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA
Polymerase.” Institute of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.
mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.
short: M. Tugrul, (2016).
contributor:
- contributor_type: researcher
first_name: Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
- contributor_type: researcher
first_name: Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
datarep_id: '43'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-05-12T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.15479/AT:ISTA:43
file:
- access_level: open_access
checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:08Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5626'
file_name: IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip
file_size: 1123495
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- RNAP binding
- de novo promoter evolution
- lac promoter
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1131'
relation: used_in_publication
status: public
status: public
title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5558'
abstract:
- lang: eng
text: PhD thesis LaTeX source code
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016.
doi:10.15479/AT:ISTA:48
apa: Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.
ieee: M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.
short: M. Bojsen-Hansen, (2016).
datarep_id: '48'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2024-02-21T13:50:48Z
day: '23'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:48
file:
- access_level: open_access
checksum: 5b1b256ad796fbddb4b7729f5e45e444
content_type: application/x-bzip2
creator: system
date_created: 2018-12-12T13:02:18Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5589'
file_name: IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2
file_size: 55237885
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '6238'
pubrep_id: '640'
related_material:
record:
- id: '1122'
relation: other
status: public
status: public
title: Tracking, Correcting and Absorbing Water Surface Waves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5556'
abstract:
- lang: eng
text: "MATLAB code and processed datasets available for reproducing the results
in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.\r\n*equal contributions"
article_processing_charge: No
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for
“Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional
Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:45
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code
for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both
Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and
Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.
ista: Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.
mla: Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.
short: M. Lukacisin, M. Landon, R. Jajoo, (2016).
datarep_id: '45'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-08-25T00:00:00Z
date_updated: 2024-02-21T13:51:53Z
day: '25'
ddc:
- '571'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:45
file:
- access_level: open_access
checksum: ee697f2b1ade4dc14d6ac0334dd832ab
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:58Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5616'
file_name: IST-2016-45-v1+1_PaperCode.zip
file_size: 296722548
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- transcription
- pausing
- backtracking
- polymerase
- RNA
- NET-seq
- nucleosome
- basepairing
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8431'
relation: used_in_publication
status: deleted
- id: '1029'
relation: research_paper
status: public
status: public
title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1183'
abstract:
- lang: eng
text: Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping
with other neurological conditions. We previously described abnormalities in the
branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we
show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid
transporter localized at the blood brain barrier (BBB), has an essential role
in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from
the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal
mRNA translation, and severe neurological abnormalities. Furthermore, we identified
several patients with autistic traits and motor delay carrying deleterious homozygous
mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular
administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate
a neurological syndrome defined by SLC7A5 mutations and support an essential role
for the BCAA in human brain function.
acknowledgement: "This work was supported by NICHD (P01HD070494) and SFARI (grant
275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu,
and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron
Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide
SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900
to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.),
the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction
University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This
work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and
FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility"
article_processing_charge: No
article_type: original
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Majdi
full_name: Kara, Majdi
last_name: Kara
- first_name: Philipp
full_name: Janiesch, Philipp
last_name: Janiesch
- first_name: Mariafrancesca
full_name: Scalise, Mariafrancesca
last_name: Scalise
- first_name: Michele
full_name: Galluccio, Michele
last_name: Galluccio
- first_name: Mateja
full_name: Tesulov, Mateja
last_name: Tesulov
- first_name: Emanuela
full_name: Morelli, Emanuela
id: 3F4D1282-F248-11E8-B48F-1D18A9856A87
last_name: Morelli
- first_name: Fatma
full_name: Sönmez, Fatma
last_name: Sönmez
- first_name: Kaya
full_name: Bilgüvar, Kaya
last_name: Bilgüvar
- first_name: Ryuichi
full_name: Ohgaki, Ryuichi
last_name: Ohgaki
- first_name: Yoshikatsu
full_name: Kanai, Yoshikatsu
last_name: Kanai
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Seham
full_name: Esharif, Seham
last_name: Esharif
- first_name: Tawfeg
full_name: Ben Omran, Tawfeg
last_name: Ben Omran
- first_name: Meral
full_name: Topcu, Meral
last_name: Topcu
- first_name: Avner
full_name: Schlessinger, Avner
last_name: Schlessinger
- first_name: Cesare
full_name: Indiveri, Cesare
last_name: Indiveri
- first_name: Kent
full_name: Duncan, Kent
last_name: Duncan
- first_name: Ahmet
full_name: Caglayan, Ahmet
last_name: Caglayan
- first_name: Murat
full_name: Günel, Murat
last_name: Günel
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at
the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494.
doi:10.1016/j.cell.2016.11.013
apa: Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise,
M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier
is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013
chicago: Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp
Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid
Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.”
Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013.
ieee: D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood
brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167,
no. 6. Cell Press, pp. 1481–1494, 2016.
ista: Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio
M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A,
Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan
A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the
blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.
mla: Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood
Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167,
no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.
short: D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise,
M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai,
A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri,
K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2024-03-28T23:30:12Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1016/j.cell.2016.11.013
file:
- access_level: open_access
checksum: 7fe01ab12a6610d3db421e0136db2f77
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:44Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5030'
file_name: IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf
file_size: 73907957
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 167'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 1481 - 1494
project:
- _id: 25473368-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F03523
name: Transmembrane Transporters in Health and Disease
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '6170'
pubrep_id: '771'
quality_controlled: '1'
related_material:
record:
- id: '395'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Impaired amino acid transport at the blood brain barrier is a cause of autism
spectrum disorder
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 167
year: '2016'
...
---
_id: '1321'
abstract:
- lang: eng
text: Most migrating cells extrude their front by the force of actin polymerization.
Polymerization requires an initial nucleation step, which is mediated by factors
establishing either parallel filaments in the case of filopodia or branched filaments
that form the branched lamellipodial network. Branches are considered essential
for regular cell motility and are initiated by the Arp2/3 complex, which in turn
is activated by nucleation-promoting factors of the WASP and WAVE families. Here
we employed rapid amoeboid crawling leukocytes and found that deletion of the
WAVE complex eliminated actin branching and thus lamellipodia formation. The cells
were left with parallel filaments at the leading edge, which translated, depending
on the differentiation status of the cell, into a unipolar pointed cell shape
or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased
speed and enormous directional persistence, while they were unable to turn towards
chemotactic gradients. Cells with multiple filopodia retained chemotactic activity
but their migration was progressively impaired with increasing geometrical complexity
of the extracellular environment. These findings establish that diversified leading
edge protrusions serve as explorative structures while they slow down actual locomotion.
acknowledged_ssus:
- _id: SSU
acknowledgement: "This work was supported by the German Research Foundation (DFG)
Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC
GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria
for excellent technical support."
article_processing_charge: No
article_type: original
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Alexander
full_name: Eichner, Alexander
id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87
last_name: Eichner
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: David
full_name: De Gorter, David
last_name: De Gorter
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Jonathan
full_name: Bayerl, Jonathan
last_name: Bayerl
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Frank
full_name: Lai, Frank
last_name: Lai
- first_name: Markus
full_name: Moser, Markus
last_name: Moser
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Victor
full_name: Small, Victor
last_name: Small
- first_name: Theresia
full_name: Stradal, Theresia
last_name: Stradal
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote
environmental exploration but are dispensable for locomotion of leukocytes. Nature
Cell Biology. 2016;18:1253-1259. doi:10.1038/ncb3426
apa: Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz,
J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental
exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/ncb3426
chicago: Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus
Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote
Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature
Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/ncb3426.
ieee: A. F. Leithner et al., “Diversified actin protrusions promote environmental
exploration but are dispensable for locomotion of leukocytes,” Nature Cell
Biology, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.
ista: Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J,
De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser
M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin
protrusions promote environmental exploration but are dispensable for locomotion
of leukocytes. Nature Cell Biology. 18, 1253–1259.
mla: Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental
Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell
Biology, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:10.1038/ncb3426.
short: A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz,
J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild,
F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt,
Nature Cell Biology 18 (2016) 1253–1259.
date_created: 2018-12-11T11:51:21Z
date_published: 2016-10-24T00:00:00Z
date_updated: 2024-03-28T23:30:16Z
day: '24'
ddc:
- '570'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/ncb3426
ec_funded: 1
file:
- access_level: open_access
checksum: e1411cb7c99a2d9089c178a6abef25e7
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:33:46Z
date_updated: 2020-07-14T12:44:43Z
file_id: '7844'
file_name: 2018_NatureCell_Leithner.pdf
file_size: 4433280
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 18'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '10'
oa: 1
oa_version: Submitted Version
page: 1253 - 1259
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5949'
quality_controlled: '1'
related_material:
record:
- id: '323'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Diversified actin protrusions promote environmental exploration but are dispensable
for locomotion of leukocytes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '1100'
abstract:
- lang: eng
text: During metazoan development, the temporal pattern of morphogen signaling is
critical for organizing cell fates in space and time. Yet, tools for temporally
controlling morphogen signaling within the embryo are still scarce. Here, we developed
a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal
signaling affects cell fate specification during zebrafish gastrulation. By using
this receptor to manipulate the duration of Nodal signaling in vivo by light,
we show that extended Nodal signaling within the organizer promotes prechordal
plate specification and suppresses endoderm differentiation. Endoderm differentiation
is suppressed by extended Nodal signaling inducing expression of the transcriptional
repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains
Nodal signaling from upregulating the endoderm differentiation gene sox17 within
these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical
role of Nodal signaling duration for organizer cell fate specification during
gastrulation.
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We are grateful to members of the C.-P.H. and H.J. labs for discussions,
R. Hauschild and the different Scientific Service Units at IST Austria for technical
help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier
version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce,
and L. Solnica-Krezel for sending plasmids. This work was supported by grants from
the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H.,
and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon
Areces fellowship.'
author:
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Saurabh
full_name: Pradhan, Saurabh
last_name: Pradhan
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Patrick
full_name: Mueller, Patrick
last_name: Mueller
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Sanjeev
full_name: Galande, Sanjeev
last_name: Galande
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling
reveals a temporal pattern of nodal signaling regulating cell fate specification
during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036
apa: Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht,
V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals
a temporal pattern of nodal signaling regulating cell fate specification during
gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036
chicago: Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick
Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and
Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal
Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.”
Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036.
ieee: K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal
pattern of nodal signaling regulating cell fate specification during gastrulation,”
Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.
ista: Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek
D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal
signaling reveals a temporal pattern of nodal signaling regulating cell fate specification
during gastrulation. Cell Reports. 16(3), 866–877.
mla: Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal
Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.”
Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036.
short: K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht,
D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016)
866–877.
date_created: 2018-12-11T11:50:08Z
date_published: 2016-07-19T00:00:00Z
date_updated: 2024-03-28T23:30:26Z
day: '19'
ddc:
- '570'
- '576'
department:
- _id: CaHe
- _id: HaJa
doi: 10.1016/j.celrep.2016.06.036
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:04Z
date_updated: 2018-12-12T10:11:04Z
file_id: '4857'
file_name: IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf
file_size: 3921947
relation: main_file
file_date_updated: 2018-12-12T10:11:04Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 866 - 877
project:
- _id: 2529486C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T 560-B17
name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation
- _id: 2527D5CC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 812-B12
name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '6275'
pubrep_id: '754'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '50'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Optogenetic control of nodal signaling reveals a temporal pattern of nodal
signaling regulating cell fate specification during gastrulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1437'
abstract:
- lang: eng
text: We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural problems that arise
in program analysis. We consider that each component of the concurrent system
is a graph with constant treewidth, a property satisfied by the controlflow graphs
of most programs. We allow for multiple possible queries, which arise naturally
in demand driven dataflow analysis. The study of multiple queries allows us to
consider the tradeoff between the resource usage of the one-time preprocessing
and for each individual query. The traditional approach constructs the product
graph of all components and applies the best-known graph algorithm on the product.
In this approach, even the answer to a single query requires the transitive closure
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time. Our main contributions are algorithms that
significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
each subsequent query can be answered in at most linear time, and even the transitive
closure can be computed in almost quartic time. Furthermore, we establish conditional
optimality results showing that the worst-case running time of our algorithms
cannot be improved without achieving major breakthroughs in graph algorithms (i.e.,
improving the worst-case bound for the shortest path problem in general graphs).
Preliminary experimental results show that our algorithms perform favorably on
several benchmarks.
alternative_title:
- POPL
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for
algebraic path properties in concurrent systems of constant treewidth components.
In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624'
apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A.
(2016). Algorithms for algebraic path properties in concurrent systems of constant
treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles
of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen,
and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624.
ieee: 'K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms
for algebraic path properties in concurrent systems of constant treewidth components,”
presented at the POPL: Principles of Programming Languages, St. Petersburg, FL,
USA, 2016, vol. 20–22, pp. 733–747.'
ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties
in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016,
pp. 733–47, doi:10.1145/2837614.2837624.
short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM,
2016, pp. 733–747.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2024-03-28T23:30:33Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/2837614.2837624
ec_funded: 1
external_id:
arxiv:
- '1510.07565'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.07565
month: '01'
oa: 1
oa_version: Preprint
page: 733 - 747
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: ACM
publist_id: '5761'
quality_controlled: '1'
related_material:
record:
- id: '5441'
relation: earlier_version
status: public
- id: '5442'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
- id: '6009'
relation: later_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '1386'
abstract:
- lang: eng
text: We consider nondeterministic probabilistic programs with the most basic liveness
property of termination. We present efficient methods for termination analysis
of nondeterministic probabilistic programs with polynomial guards and assignments.
Our approach is through synthesis of polynomial ranking supermartingales, that
on one hand significantly generalizes linear ranking supermartingales and on the
other hand is a counterpart of polynomial ranking-functions for proving termination
of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales
through Positivstellensatz's, yielding an efficient method which is not only sound,
but also semi-complete over a large subclass of programs. We show experimental
results to demonstrate that our approach can handle several classical programs
with complex polynomial guards and assignments, and can synthesize efficient quadratic
ranking-supermartingales when a linear one does not exist even for simple affine
programs.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs
through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1'
apa: 'Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis
of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22).
Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer.
https://doi.org/10.1007/978-3-319-41528-4_1'
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination
Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer,
2016. https://doi.org/10.1007/978-3-319-41528-4_1.
ieee: 'K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic
programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification,
Toronto, Canada, 2016, vol. 9779, pp. 3–22.'
ista: 'Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic
programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS,
vol. 9779, 3–22.'
mla: Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs
through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1.
short: K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.
conference:
end_date: 2016-07-23
location: Toronto, Canada
name: 'CAV: Computer Aided Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:51:43Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-03-28T23:30:33Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-41528-4_1
ec_funded: 1
intvolume: ' 9779'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1604.07169
month: '07'
oa: 1
oa_version: Preprint
page: 3 - 22
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '5824'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Termination analysis of probabilistic programs through Positivstellensatz's
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9779
year: '2016'
...
---
_id: '10794'
abstract:
- lang: eng
text: Mathematical models are of fundamental importance in the understanding of
complex population dynamics. For instance, they can be used to predict the population
evolution starting from different initial conditions or to test how a system responds
to external perturbations. For this analysis to be meaningful in real applications,
however, it is of paramount importance to choose an appropriate model structure
and to infer the model parameters from measured data. While many parameter inference
methods are available for models based on deterministic ordinary differential
equations, the same does not hold for more detailed individual-based models. Here
we consider, in particular, stochastic models in which the time evolution of the
species abundances is described by a continuous-time Markov chain. These models
are governed by a master equation that is typically difficult to solve. Consequently,
traditional inference methods that rely on iterative evaluation of parameter likelihoods
are computationally intractable. The aim of this paper is to present recent advances
in parameter inference for continuous-time Markov chain models, based on a moment
closure approximation of the parameter likelihood, and to investigate how these
results can help in understanding, and ultimately controlling, complex systems
in ecology. Specifically, we illustrate through an agricultural pest case study
how parameters of a stochastic individual-based model can be identified from measured
data and how the resulting model can be used to solve an optimal control problem
in a stochastic setting. In particular, we show how the matter of determining
the optimal combination of two different pest control methods can be formulated
as a chance constrained optimization problem where the control action is modeled
as a state reset, leading to a hybrid system formulation.
acknowledgement: "The authors would like to acknowledge contributions from Baptiste
Mottet who performed preliminary analysis regarding parameter inference for the
considered case study in a student project (Mottet, 2014/2015).\r\nThe research
leading to these results has received funding from the People Programme (Marie Curie
Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement No. [291734] and from SystemsX under the project SignalX."
article_number: '42'
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in
Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042'
apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic
individual-based models of ecological systems: a pest control simulation study.
Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042'
chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference
for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation
Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.'
ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study,” Frontiers in
Environmental Science, vol. 3. Frontiers, 2015.'
ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in Environmental
Science. 3, 42.'
mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based
Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in
Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.'
short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
date_created: 2022-02-25T11:42:25Z
date_published: 2015-06-10T00:00:00Z
date_updated: 2022-02-25T11:59:23Z
day: '10'
ddc:
- '000'
- '570'
department:
- _id: ToHe
- _id: GaTk
doi: 10.3389/fenvs.2015.00042
ec_funded: 1
file:
- access_level: open_access
checksum: 26c222487564e1be02a11d688d6f769d
content_type: application/pdf
creator: dernst
date_created: 2022-02-25T11:55:26Z
date_updated: 2022-02-25T11:55:26Z
file_id: '10795'
file_name: 2015_FrontiersEnvironmScience_Parise.pdf
file_size: 1371201
relation: main_file
success: 1
file_date_updated: 2022-02-25T11:55:26Z
has_accepted_license: '1'
intvolume: ' 3'
keyword:
- General Environmental Science
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Environmental Science
publication_identifier:
issn:
- 2296-665X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bayesian inference for stochastic individual-based models of ecological systems:
a pest control simulation study'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2015'
...
---
_id: '10796'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
acknowledgement: "The research was partly supported by FWF Grant No P 23499-N23, FWF
NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies
for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029.
doi:10.1137/1.9781611973730.69'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029).
San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings
of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29.
SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.
ieee: K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory
strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States,
2015, vol. 2015, no. 1, pp. 1018–1029.
ista: 'Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms
vol. 2015, 1018–1029.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of
the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015,
no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.
conference:
end_date: 2015-01-06
location: San Diego, CA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2015-01-04
date_created: 2022-02-25T12:18:43Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-02-25T12:33:32Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973730.69
ec_funded: 1
external_id:
arxiv:
- '1409.6690'
intvolume: ' 2015'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 1018-1029
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete
Algorithms
publication_identifier:
isbn:
- 978-161197374-7
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: The value 1 problem under finite-memory strategies for concurrent mean-payoff
games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
(det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
impairing secretion and recycling of the brassinosteroid receptor and the cellulose
synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
Thus, our results provide strong evidence that acidification of the TGN/EE, but
not of the vacuole, is indispensable for functional secretion and recycling in
plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
full_name: Yu, Luo
last_name: Yu
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Anett
full_name: Doering, Anett
last_name: Doering
- first_name: Zhang
full_name: Yi, Zhang
last_name: Yi
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Lutz
full_name: Neumetzler, Lutz
last_name: Neumetzler
- first_name: Praveen
full_name: Krishnamoorthy, Praveen
last_name: Krishnamoorthy
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Volker
full_name: Bischoff, Volker
last_name: Bischoff
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7).
doi:10.1038/nplants.2015.94
apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94
chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2015. https://doi.org/10.1038/nplants.2015.94.
ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis
and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing
Group, 2015.
ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
15094.
mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature
Publishing Group, 2015, doi:10.1038/nplants.2015.94.
short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
pmid:
- '27250258'
intvolume: ' 1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1425'
abstract:
- lang: eng
text: 'In this work we aim at extending the theoretical foundations of lifelong
learning. Previous work analyzing this scenario is based on the assumption that
learning tasks are sampled i.i.d. from a task environment or limited to strongly
constrained data distributions. Instead, we study two scenarios when lifelong
learning is possible, even though the observed tasks do not form an i.i.d. sample:
first, when they are sampled from the same environment, but possibly with dependencies,
and second, when the task environment is allowed to change over time in a consistent
way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct
generalization of the analogous previous result for the i.i.d. case. For the second
scenario we propose to learn an inductive bias in form of a transfer procedure.
We present a generalization bound and show on a toy example how it can be used
to identify a beneficial transfer algorithm.'
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015.
Neural Information Processing Systems; 2015:1540-1548.'
apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks
(Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada: Neural Information Processing Systems.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d.
Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.
ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol.
2015, pp. 1540–1548.'
ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 2015, 1540–1548.'
mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d.
Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.
short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015,
pp. 1540–1548.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:57Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
intvolume: ' 2015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks
month: '01'
oa: 1
oa_version: None
page: 1540 - 1548
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5781'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lifelong learning with non-i.i.d. tasks
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1424'
abstract:
- lang: eng
text: We consider the problem of statistical computations with persistence diagrams,
a summary representation of topological features in data. These diagrams encode
persistent homology, a widely used invariant in topological data analysis. While
several avenues towards a statistical treatment of the diagrams have been explored
recently, we follow an alternative route that is motivated by the success of methods
based on the embedding of probability measures into reproducing kernel Hilbert
spaces. In fact, a positive definite kernel on persistence diagrams has recently
been proposed, connecting persistent homology to popular kernel-based learning
techniques such as support vector machines. However, important properties of that
kernel enabling a principled use in the context of probability measure embeddings
remain to be explored. Our contribution is to close this gap by proving universality
of a variant of the original kernel, and to demonstrate its effective use in twosample
hypothesis testing on synthetic as well as real-world data.
acknowledgement: This work was partially supported by the Austrian Science FUnd, project
no. KLI 00012.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Marc
full_name: Niethammer, Marc
last_name: Niethammer
- first_name: Weili
full_name: Lin, Weili
last_name: Lin
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
citation:
ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data
analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems;
2015:3070-3078.'
apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical
topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information
Processing Systems.'
chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer.
“Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural
Information Processing Systems, 2015.
ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological
data analysis-A kernel perspective,” presented at the NIPS: Neural Information
Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.'
ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological
data analysis-A kernel perspective. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 28, 3070–3078.'
mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective.
Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.
short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information
Processing Systems, 2015, pp. 3070–3078.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:56Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '01'
department:
- _id: HeEd
intvolume: ' 28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective
month: '12'
oa: 1
oa_version: Submitted Version
page: 3070 - 3078
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5782'
quality_controlled: '1'
status: public
title: Statistical topological data analysis-A kernel perspective
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '1430'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse their runtime on many illustrative
problems. Here we apply this theory to a simple model of natural evolution. In
the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (1+1)
EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing
fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking
advantage of information on the fitness gradient.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: 1
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1474'
abstract:
- lang: eng
text: Cryptographic access control offers selective access to encrypted data via
a combination of key management and functionality-rich cryptographic schemes,
such as attribute-based encryption. Using this approach, publicly available meta-data
may inadvertently leak information on the access policy that is enforced by cryptography,
which renders cryptographic access control unusable in settings where this information
is highly sensitive. We begin to address this problem by presenting rigorous definitions
for policy privacy in cryptographic access control. For concreteness we set our
results in the model of Role-Based Access Control (RBAC), where we identify and
formalize several different flavors of privacy, however, our framework should
serve as inspiration for other models of access control. Based on our insights
we propose a new system which significantly improves on the privacy properties
of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving
attribute-based encryption, which we introduce and show how to instantiate. We
present our results in the context of a cryptographic RBAC system by Ferrara et
al. (CSF'13), which uses cryptography to control read access to files, while write
access is still delegated to trusted monitors. We give an extension of the construction
that permits cryptographic control over write access. Our construction assumes
that key management uses out-of-band channels between the policy enforcer and
the users but eliminates completely the need for monitoring read/write access
to the data.
article_processing_charge: No
author:
- first_name: Anna
full_name: Ferrara, Anna
last_name: Ferrara
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Bin
full_name: Liu, Bin
last_name: Liu
- first_name: Bogdan
full_name: Warinschi, Bogdan
last_name: Warinschi
citation:
ama: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic
access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11'
apa: 'Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy
in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security
Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11'
chicago: Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy
Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11.
ieee: 'A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic
access control,” presented at the CSF: Computer Security Foundations, Verona,
Italy, 2015, pp. 46–60.'
ista: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic
access control. CSF: Computer Security Foundations, 46–60.'
mla: Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control.
IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.
short: A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.
conference:
end_date: 2015-07-17
location: Verona, Italy
name: 'CSF: Computer Security Foundations'
start_date: 2015-07-13
date_created: 2018-12-11T11:52:14Z
date_published: 2015-09-04T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '04'
department:
- _id: KrPi
doi: 10.1109/CSF.2015.11
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://epubs.surrey.ac.uk/808055/
month: '09'
oa: 1
oa_version: Submitted Version
page: 46-60
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: IEEE
publist_id: '5722'
quality_controlled: '1'
status: public
title: Policy privacy in cryptographic access control
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1483'
abstract:
- lang: eng
text: Topological data analysis offers a rich source of valuable information to
study vision problems. Yet, so far we lack a theoretically sound connection to
popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In
this work, we establish such a connection by designing a multi-scale kernel for
persistence diagrams, a stable summary representation of topological features
in data. We show that this kernel is positive definite and prove its stability
with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets
for 3D shape classification/retrieval and texture recognition show considerable
performance gains of the proposed method compared to an alternative approach that
is based on the recently introduced persistence landscapes.
author:
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
citation:
ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for
topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106'
apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale
kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR:
Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106'
chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable
Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.
ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel
for topological machine learning,” presented at the CVPR: Computer Vision and
Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.'
ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel
for topological machine learning. CVPR: Computer Vision and Pattern Recognition,
4741–4748.'
mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine
Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.
short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.
conference:
end_date: 2015-06-12
location: Boston, MA, USA
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2015-06-07
date_created: 2018-12-11T11:52:17Z
date_published: 2015-10-14T00:00:00Z
date_updated: 2021-01-12T06:51:03Z
day: '14'
department:
- _id: HeEd
doi: 10.1109/CVPR.2015.7299106
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1412.6821
month: '10'
oa: 1
oa_version: Preprint
page: 4741 - 4748
publication_identifier:
eisbn:
- '978-1-4673-6964-0 '
publication_status: published
publisher: IEEE
publist_id: '5709'
scopus_import: 1
status: public
title: A stable multi-scale kernel for topological machine learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1498'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. Nonetheless there is surprisingly little
language and verification support to build distributed systems based on fault-tolerant
algorithms. In this paper, we present some of the challenges that a designer has
to overcome to implement a fault-tolerant distributed system. Then we review different
models that have been proposed to reason about distributed algorithms and sketch
how such a model can form the basis for a domain-specific programming language.
Adopting a high-level programming model can simplify the programmer's life and
make the code amenable to automated verification, while still compiling to efficiently
executable code. We conclude by summarizing the current status of an ongoing language
design and implementation project that is based on this idea.
alternative_title:
- LIPIcs
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- 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: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant
distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language
support for fault-tolerant distributed systems. Presented at the SNAPL: Summit
oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90'
chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for
Language Support for Fault-Tolerant Distributed Systems.” Leibniz International
Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.
ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support
for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, pp. 90–102, 2015.
ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for
fault-tolerant distributed systems. 32, 90–102.
mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant
Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.
short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.
conference:
end_date: 2015-05-06
location: Asilomar, CA, United States
name: 'SNAPL: Summit oN Advances in Programming Languages'
start_date: 2015-05-03
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2020-08-11T10:09:14Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.SNAPL.2015.90
ec_funded: 1
file:
- access_level: open_access
checksum: cf5e94baa89a2dc4c5de01abc676eda8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:02Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5050'
file_name: IST-2016-499-v1+1_9.pdf
file_size: 489362
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 32'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 90 - 102
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- '978-3-939897-80-4 '
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5681'
pubrep_id: '499'
quality_controlled: '1'
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: The need for language support for fault-tolerant distributed systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '1497'
abstract:
- lang: eng
text: Detecting allelic biases from high-throughput sequencing data requires an
approach that maximises sensitivity while minimizing false positives. Here, we
present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which
uses high-throughput sequencing data from reciprocal crosses of two genetically
distinct mouse strains to detect allele-specific expression and chromatin modifications.
Allelome.PRO extends approaches used in previous studies that exclusively analyzed
imprinted expression to give a complete picture of the ‘allelome’ by automatically
categorising the allelic expression of all genes in a given cell type into imprinted,
strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity
to analyze lowly expressed transcripts, together with a robust false discovery
rate empirically calculated from variation in the sequencing data. We used RNA-seq
data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine
a biologically relevant allelic ratio cutoff, and define for the first time an
entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment
of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This
approach can be easily extended to analyze histone marks of active enhancers,
or transcription factor binding sites and therefore provides a powerful tool to
identify candidate cis regulatory elements genome wide.
acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09].
Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser
for advice during the early stages of this project. High-throughput sequencing was
conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna."
article_number: e146
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
- first_name: Tomasz
full_name: Kulinski, Tomasz
last_name: Kulinski
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Philipp
full_name: Bammer, Philipp
last_name: Bammer
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
- first_name: Florian
full_name: Pauler, Florian
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
citation:
ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define
allele-specific genomic features from high-throughput sequencing data. Nucleic
Acids Research. 2015;43(21). doi:10.1093/nar/gkv727
apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow,
D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research.
Oxford University Press. https://doi.org/10.1093/nar/gkv727
chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl,
Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO,
a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing
Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.
ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific
genomic features from high-throughput sequencing data,” Nucleic Acids Research,
vol. 43, no. 21. Oxford University Press, 2015.
ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler
F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic
features from high-throughput sequencing data. Nucleic Acids Research. 43(21),
e146.
mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific
Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research,
vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.
short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow,
F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).
date_created: 2018-12-11T11:52:22Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '21'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1093/nar/gkv727
file:
- access_level: open_access
checksum: 385b83854fd0eb2e4f386867da2823e2
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T14:18:57Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5768'
file_name: 2015_NucleicAcidsRes_Andergassen.pdf
file_size: 6863297
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 43'
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '5682'
quality_controlled: '1'
scopus_import: 1
status: public
title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput
sequencing data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1499'
abstract:
- lang: eng
text: "We consider weighted automata with both positive and negative integer weights
on edges and\r\nstudy the problem of synchronization using adaptive strategies
that may only observe whether\r\nthe current weight-level is negative or nonnegative.
We show that the synchronization problem is decidable in polynomial time for deterministic
weighted automata."
acknowledgement: "The research leading to these results has received funding from
the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center
IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM),
the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein
Award), the Czech Science Foundation under grant agreement P202/12/G061, and People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme
(FP7/2007-2013) REA Grant No 291734."
alternative_title:
- LIPIcs
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Kim
full_name: Larsen, Kim
last_name: Larsen
- first_name: Simon
full_name: Laursen, Simon
last_name: Laursen
- first_name: Jiří
full_name: Srba, Jiří
last_name: Srba
citation:
ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of
weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142'
apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial
time decidability of weighted synchronization under partial observability (Vol.
42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142'
chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time
Decidability of Weighted Synchronization under Partial Observability,” 42:142–54.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.
ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability
of weighted synchronization under partial observability,” presented at the CONCUR:
Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.'
ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability
of weighted synchronization under partial observability. CONCUR: Concurrency Theory,
LIPIcs, vol. 42, 142–154.'
mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization
under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.
short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2015, pp. 142–154.
conference:
end_date: 2015-09-04
location: Madrid, Spain
name: 'CONCUR: Concurrency Theory'
start_date: 2015-09-01
date_created: 2018-12-11T11:52:22Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:10Z
day: '01'
ddc:
- '000'
- '003'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2015.142
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:12Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4672'
file_name: IST-2016-498-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 42'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 142 - 154
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: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5680'
pubrep_id: '498'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polynomial time decidability of weighted synchronization under partial observability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '1495'
abstract:
- lang: eng
text: 'Motivated by biological questions, we study configurations of equal-sized
disks in the Euclidean plane that neither pack nor cover. Measuring the quality
by the probability that a random point lies in exactly one disk, we show that
the regular hexagonal grid gives the maximum among lattice configurations. '
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Vitaliy
full_name: Kurlin, Vitaliy
last_name: Kurlin
citation:
ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings
of the 27th Canadian Conference on Computational Geometry. Vol 2015-August.
Queen’s University; 2015:128-135.'
apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk
packing. In Proceedings of the 27th Canadian Conference on Computational Geometry
(Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.'
chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed
Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational
Geometry, 2015–August:128–35. Queen’s University, 2015.
ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in
Proceedings of the 27th Canadian Conference on Computational Geometry,
Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.
ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings
of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference
on Computational Geometry vol. 2015–August, 128–135.'
mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the
27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s
University, 2015, pp. 128–35.
short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th
Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.
conference:
end_date: 2015-08-12
location: Ontario, Canada
name: 'CCCG: Canadian Conference on Computational Geometry'
start_date: 2015-08-10
date_created: 2018-12-11T11:52:21Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '01'
department:
- _id: HeEd
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03402
month: '08'
oa: 1
oa_version: Submitted Version
page: 128-135
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Proceedings of the 27th Canadian Conference on Computational Geometry
publication_status: published
publisher: Queen's University
publist_id: '5684'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relaxed disk packing
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015-August
year: '2015'
...
---
_id: '1510'
abstract:
- lang: eng
text: 'The concept of well group in a special but important case captures homological
properties of the zero set of a continuous map f from K to R^n on a compact space
K that are invariant with respect to perturbations of f. The perturbations are
arbitrary continuous maps within L_infty distance r from f for a given r >
0. The main drawback of the approach is that the computability of well groups
was shown only when dim K = n or n = 1. Our contribution to the theory of well
groups is twofold: on the one hand we improve on the computability issue, but
on the other hand we present a range of examples where the well groups are incomplete
invariants, that is, fail to capture certain important robust properties of the
zero set. For the first part, we identify a computable subgroup of the well group
that is obtained by cap product with the pullback of the orientation of R^n by
f. In other words, well groups can be algorithmically approximated from below.
When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well
group is exact. For the second part, we find examples of maps f, f'' from K to
R^n with all well groups isomorphic but whose perturbations have different zero
sets. We discuss on a possible replacement of the well groups of vector valued
maps by an invariant of a better descriptive power and computability status. '
alternative_title:
- LIPIcs
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: 'Franek P, Krcál M. On computability and triviality of well groups. In: Vol
34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842'
apa: 'Franek, P., & Krcál, M. (2015). On computability and triviality of well
groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational
Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SOCG.2015.842'
chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well
Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.
ieee: 'P. Franek and M. Krcál, “On computability and triviality of well groups,”
presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands,
2015, vol. 34, pp. 842–856.'
ista: 'Franek P, Krcál M. 2015. On computability and triviality of well groups.
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.'
mla: Franek, Peter, and Marek Krcál. On Computability and Triviality of Well
Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015,
pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842.
short: P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015, pp. 842–856.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:26Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2023-02-21T17:02:57Z
day: '11'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4230/LIPIcs.SOCG.2015.842
ec_funded: 1
file:
- access_level: open_access
checksum: 49eb5021caafaabe5356c65b9c5f8c9c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:19Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5001'
file_name: IST-2016-503-v1+1_32.pdf
file_size: 623563
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
intvolume: ' 34'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 842 - 856
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5667'
pubrep_id: '503'
quality_controlled: '1'
related_material:
record:
- id: '1408'
relation: later_version
status: public
scopus_import: 1
status: public
title: On computability and triviality of well groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1505'
abstract:
- lang: eng
text: This paper is aimed at deriving the universality of the largest eigenvalue
of a class of high-dimensional real or complex sample covariance matrices of the
form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent
entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality,
we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic
positive-definite M × M matrices Σ , under some additional assumptions on the
distribution of xij 's, we show that the limiting behavior of the largest eigenvalue
of W N is universal, via pursuing a Green function comparison strategy raised
in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515]
by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann.
Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case
(&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing
this universality property and the results known for Gaussian matrices obtained
by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski
in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after
an appropriate normalization the largest eigenvalue of W N converges weakly to
the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show
that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom
limit TW1 holds for the normalized largest eigenvalue of W N , which extends a
result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario
of nondiagonal Σ and more generally distributed X . In summary, we establish the
Tracy-Widom type universality for the largest eigenvalue of generally distributed
sample covariance matrices under quite light assumptions on &Sigma . Applications
of these limiting results to statistical signal detection and structure recognition
of separable covariance matrices are also discussed.
acknowledgement: "B.Z. was supported in part by NSFC Grant 11071213, ZJNSF
\ Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part
by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported
\ in part by the Ministry of Education, Singapore, under Grant ARC 14/11,
\ and by a Grant R-155-000-131-112 at the National University of Singapore\r\n"
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance
matrices with general population. Annals of Statistics. 2015;43(1):382-421.
doi:10.1214/14-AOS1281
apa: Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue
of sample covariance matrices with general population. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest
Eigenvalue of Sample Covariance Matrices with General Population.” Annals of
Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.
ieee: Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample
covariance matrices with general population,” Annals of Statistics, vol.
43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample
covariance matrices with general population. Annals of Statistics. 43(1), 382–421.
mla: Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance
Matrices with General Population.” Annals of Statistics, vol. 43, no. 1,
Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.
short: Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/14-AOS1281
intvolume: ' 43'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.5690
month: '02'
oa: 1
oa_version: Preprint
page: 382 - 421
publication: Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5672'
quality_controlled: '1'
status: public
title: Universality for the largest eigenvalue of sample covariance matrices with
general population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '1508'
abstract:
- lang: eng
text: We consider generalized Wigner ensembles and general β-ensembles with analytic
potentials for any β ≥ 1. The recent universality results in particular assert
that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum
are universal in the sense that they coincide with those of the corresponding
Gaussian β-ensembles. In this article, we show that local averaging is not necessary
for this result, i.e. we prove that the single gap distributions in the bulk are
universal. In fact, with an additional step, our result can be extended to any
C4(ℝ) potential.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal
of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548
apa: Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and
β ensembles. Journal of the European Mathematical Society. European Mathematical
Society. https://doi.org/10.4171/JEMS/548
chicago: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and
β Ensembles.” Journal of the European Mathematical Society. European Mathematical
Society, 2015. https://doi.org/10.4171/JEMS/548.
ieee: L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,”
Journal of the European Mathematical Society, vol. 17, no. 8. European
Mathematical Society, pp. 1927–2036, 2015.
ista: Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles.
Journal of the European Mathematical Society. 17(8), 1927–2036.
mla: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β
Ensembles.” Journal of the European Mathematical Society, vol. 17, no.
8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.
short: L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015)
1927–2036.
date_created: 2018-12-11T11:52:26Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:15Z
day: '01'
department:
- _id: LaEr
doi: 10.4171/JEMS/548
intvolume: ' 17'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1211.3786
month: '08'
oa: 1
oa_version: Preprint
page: 1927 - 2036
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '5669'
quality_controlled: '1'
scopus_import: 1
status: public
title: Gap universality of generalized Wigner and β ensembles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '1506'
abstract:
- lang: eng
text: Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i,
j = 1, . . . , n} is a collection of independent real random variables with means
zero and variances one. Under the additional moment condition supn max1≤i,j ≤n
Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞
log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: Guangming
full_name: Pan, Guangming
last_name: Pan
- first_name: Wang
full_name: Zhou, Wang
last_name: Zhou
citation:
ama: Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli.
2015;21(3):1600-1628. doi:10.3150/14-BEJ615
apa: Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant.
Bernoulli. Bernoulli Society for Mathematical Statistics and Probability.
https://doi.org/10.3150/14-BEJ615
chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random
Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics
and Probability, 2015. https://doi.org/10.3150/14-BEJ615.
ieee: Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,”
Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics
and Probability, pp. 1600–1628, 2015.
ista: Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli.
21(3), 1600–1628.
mla: Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli,
vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability,
2015, pp. 1600–28, doi:10.3150/14-BEJ615.
short: Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.
date_created: 2018-12-11T11:52:25Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:14Z
day: '01'
department:
- _id: LaEr
doi: 10.3150/14-BEJ615
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.5823
month: '08'
oa: 1
oa_version: Preprint
page: 1600 - 1628
publication: Bernoulli
publication_status: published
publisher: Bernoulli Society for Mathematical Statistics and Probability
publist_id: '5671'
quality_controlled: '1'
status: public
title: The logarithmic law of random determinant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2015'
...
---
_id: '1513'
abstract:
- lang: eng
text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms
of sex determination, including genetic sex determination, paternal genome elimination,
and haplodiploidy. Genetic sex determination, the prevalent mode, is generally
controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different
configurations that include additional sex chromosomes are also present. Although
this diversity of sex determining systems has been extensively studied at the
cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon
pisum has been analyzed at the genomic level, and little is known about X chromosome
biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published
DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative
analysis of the gene content and expression of the X chromosome throughout this
clade. We find that, despite showing evidence of dosage compensation, the X chromosomes
of these species show female-biased expression, and a deficit of male-biased genes,
in direct contrast to the pea aphid X. We further detect an excess of shared gene
content between these very distant species, suggesting that despite the diversity
of sex determining systems, the same chromosomal element is used as the X throughout
a large portion of the order. "
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage
compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268.
doi:10.1093/gbe/evv215'
apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects:
Conservation, dosage compensation and sex-biased expression. Genome Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215'
chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects:
Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology
and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.'
ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression,” Genome Biology and Evolution,
vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.'
ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation,
dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12),
3259–3268.'
mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation,
Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution,
vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.'
short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.
date_created: 2018-12-11T11:52:27Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:18Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evv215
ec_funded: 1
file:
- access_level: open_access
checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:29Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5284'
file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf
file_size: 858027
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3259 - 3268
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5664'
pubrep_id: '496'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation
and sex-biased expression'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '1517'
abstract:
- lang: eng
text: "We study the large deviation rate functional for the empirical distribution
of independent Brownian particles with drift. In one dimension, it has been shown
by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent
(in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising
in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher
dimensions, part of this statement (the lower bound) has been recently proved
by Duong, Laschos and Renger, but the upper bound remained open, since the proof
of Duong et al relies on regularity properties of optimal transport maps that
are restricted to one dimension. In this note we present a new proof of the upper
bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"
article_number: '89'
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Michiel
full_name: Renger, Michiel
last_name: Renger
citation:
ama: Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows
in multiple dimensions. Electronic Communications in Probability. 2015;20.
doi:10.1214/ECP.v20-4315
apa: Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein
gradient flows in multiple dimensions. Electronic Communications in Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315
chicago: Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to
Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications
in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.
ieee: M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient
flows in multiple dimensions,” Electronic Communications in Probability,
vol. 20. Institute of Mathematical Statistics, 2015.
ista: Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient
flows in multiple dimensions. Electronic Communications in Probability. 20, 89.
mla: Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows
in Multiple Dimensions.” Electronic Communications in Probability, vol.
20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.
short: M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20
(2015).
date_created: 2018-12-11T11:52:29Z
date_published: 2015-11-29T00:00:00Z
date_updated: 2021-01-12T06:51:19Z
day: '29'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1214/ECP.v20-4315
file:
- access_level: open_access
checksum: 135741c17d3e1547ca696b6fbdcd559c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:39Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4828'
file_name: IST-2016-494-v1+1_4315-23820-1-PB.pdf
file_size: 230525
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 20'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5660'
pubrep_id: '494'
quality_controlled: '1'
scopus_import: 1
status: public
title: From large deviations to Wasserstein gradient flows in multiple dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2015'
...
---
_id: '1519'
abstract:
- lang: eng
text: Evolutionary biologists have an array of powerful theoretical techniques that
can accurately predict changes in the genetic composition of populations. Changes
in gene frequencies and genetic associations between loci can be tracked as they
respond to a wide variety of evolutionary forces. However, it is often less clear
how to decompose these various forces into components that accurately reflect
the underlying biology. Here, we present several issues that arise in the definition
and interpretation of selection and selection coefficients, focusing on insights
gained through the examination of selection coefficients in multilocus notation.
Using this notation, we discuss how its flexibility-which allows different biological
units to be identified as targets of selection-is reflected in the interpretation
of the coefficients that the notation generates. In many situations, it can be
difficult to agree on whether loci can be considered to be under "direct"
versus "indirect" selection, or to quantify this selection. We present
arguments for what the terms direct and indirect selection might best encompass,
considering a range of issues, from viability and sexual selection to kin selection.
We show how multilocus notation can discriminate between direct and indirect selection,
and describe when it can do so.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Maria
full_name: Servedio, Maria
last_name: Servedio
citation:
ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution.
2015;69(5):1101-1112. doi:10.1111/evo.12641
apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients.
Evolution. Wiley. https://doi.org/10.1111/evo.12641
chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection
Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.
ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,”
Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.
ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients.
Evolution. 69(5), 1101–1112.
mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.”
Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.
short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.
date_created: 2018-12-11T11:52:29Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:20Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.12641
ec_funded: 1
file:
- access_level: open_access
checksum: fd8d23f476bc194419929b72ca265c02
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:34Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4822'
file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf
file_size: 188872
relation: main_file
- access_level: open_access
checksum: b774911e70044641d556e258efcb52ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf
file_size: 577415
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 69'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1101 - 1112
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley
publist_id: '5656'
pubrep_id: '560'
quality_controlled: '1'
scopus_import: 1
status: public
title: The interpretation of selection coefficients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2015'
...
---
_id: '1525'
abstract:
- lang: eng
text: 'Based on 16 recommendations, efforts should be made to achieve the following
goal: By 2025, all scholarly publication activity in Austria should be Open Access.
In other words, the final versions of all scholarly publications resulting from
the support of public resources must be freely accessible on the Internet without
delay (Gold Open Access). The resources required to meet this obligation shall
be provided to the authors, or the cost of the publication venues shall be borne
directly by the research organisations.'
article_processing_charge: No
article_type: original
author:
- first_name: Bruno
full_name: Bauer, Bruno
last_name: Bauer
- first_name: Guido
full_name: Blechl, Guido
last_name: Blechl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Anton
full_name: Graschopf, Anton
last_name: Graschopf
- first_name: Thomas
full_name: König, Thomas
last_name: König
- first_name: Katja
full_name: Mayer, Katja
last_name: Mayer
- first_name: Falk
full_name: Reckling, Falk
last_name: Reckling
- first_name: Katharina
full_name: Rieck, Katharina
last_name: Rieck
- first_name: Peter
full_name: Seitz, Peter
last_name: Seitz
- first_name: Herwig
full_name: Stöger, Herwig
last_name: Stöger
- first_name: Elvira
full_name: Welzig, Elvira
last_name: Welzig
citation:
ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open
Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178
apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., …
Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network
Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare.
https://doi.org/10.5281/zenodo.33178
chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus,
Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des
Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer
Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178.
ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access
Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer
Bibliothekare, pp. 580–607, 2015.
ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer
K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale
Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.
mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network
Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer
Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.
short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König,
K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen
68 (2015) 580–607.
date_created: 2018-12-11T11:52:31Z
date_published: 2015-11-12T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '12'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.33178
file:
- access_level: open_access
checksum: a495fe253bbc7615b1d60e9e85c94408
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:59Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5317'
file_name: IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf
file_size: 931707
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 68'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 580 - 607
publication: VÖB Mitteilungen
publication_status: published
publisher: Verein Österreichischer Bibliothekare
publist_id: '5648'
pubrep_id: '720'
quality_controlled: '1'
scopus_import: 1
status: public
title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2015'
...
---
_id: '1520'
abstract:
- lang: eng
text: Creating mechanical automata that can walk in stable and pleasing manners
is a challenging task that requires both skill and expertise. We propose to use
computational design to offset the technical difficulties of this process. A simple
drag-and-drop interface allows casual users to create personalized walking toys
from a library of pre-defined template mechanisms. Provided with this input, our
method leverages physical simulation and evolutionary optimization to refine the
mechanical designs such that the resulting toys are able to walk. The optimization
process is guided by an intuitive set of objectives that measure the quality of
the walking motions. We demonstrate our approach on a set of simulated mechanical
toys with different numbers of legs and various distinct gaits. Two fabricated
prototypes showcase the feasibility of our designs.
author:
- first_name: Gaurav
full_name: Bharaj, Gaurav
last_name: Bharaj
- first_name: Stelian
full_name: Coros, Stelian
last_name: Coros
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: James
full_name: Tompkin, James
last_name: Tompkin
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
citation:
ama: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational
design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803'
apa: 'Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & Pfister,
H. (2015). Computational design of walking automata (pp. 93–100). Presented at
the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles,
CA, United States: ACM. https://doi.org/10.1145/2786784.2786803'
chicago: Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd
Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100.
ACM, 2015. https://doi.org/10.1145/2786784.2786803.
ieee: 'G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister,
“Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics
Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.'
ista: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015.
Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium
on Computer animation, 93–100.'
mla: Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM,
2015, pp. 93–100, doi:10.1145/2786784.2786803.
short: G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister,
in:, ACM, 2015, pp. 93–100.
conference:
end_date: 2015-08-09
location: Los Angeles, CA, United States
name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation'
start_date: 2015-08-07
date_created: 2018-12-11T11:52:30Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:21Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/2786784.2786803
language:
- iso: eng
month: '08'
oa_version: None
page: 93 - 100
publication_identifier:
isbn:
- 978-1-4503-3496-9
publication_status: published
publisher: ACM
publist_id: '5655'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational design of walking automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1532'
abstract:
- lang: eng
text: Ammonium is the major nitrogen source in some plant ecosystems but is toxic
at high concentrations, especially when available as the exclusive nitrogen source.
Ammonium stress rapidly leads to various metabolic and hormonal imbalances that
ultimately inhibit root and shoot growth in many plant species, including Arabidopsis
thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling
survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with
microarrays was used. Substantial transcriptional differences were most pronounced
in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent
with previous physiological analyses, major differences in the expression modules
of photosynthesis-related genes, an altered mitochondrial metabolism, differential
expression of the primary NH4+ assimilation, alteration of transporter gene expression
and crucial changes in cell wall biosynthesis were found. A major difference in
plant hormone responses, particularly of auxin but not cytokinin, was striking.
The activity of the DR5::GUS reporter revealed a dramatically decreased auxin
response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4
was partially rescued by exogenous auxin or in specific mutants in the auxin pathway.
The data suggest that NH4+-induced nutritional and metabolic imbalances can be
partially overcome by elevated auxin levels.
article_processing_charge: No
article_type: original
author:
- first_name: Huaiyu
full_name: Yang, Huaiyu
last_name: Yang
- first_name: Jenny
full_name: Von Der Fecht Bartenbach, Jenny
last_name: Von Der Fecht Bartenbach
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Lohmann, Jan
last_name: Lohmann
- first_name: Benjamin
full_name: Neuhäuser, Benjamin
last_name: Neuhäuser
- first_name: Uwe
full_name: Ludewig, Uwe
last_name: Ludewig
citation:
ama: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig
U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with
ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251.
doi:10.1071/FP14171
apa: Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser,
B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis
thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant
Biology. CSIRO. https://doi.org/10.1071/FP14171
chicago: Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann,
Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in
Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional
Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.
ieee: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser,
and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana
seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology,
vol. 42, no. 3. CSIRO, pp. 239–251, 2015.
ista: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig
U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings
with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.
mla: Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis
Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant
Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.
short: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser,
U. Ludewig, Functional Plant Biology 42 (2015) 239–251.
date_created: 2018-12-11T11:52:34Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2022-05-24T09:02:24Z
day: '01'
department:
- _id: JiFr
doi: 10.1071/FP14171
external_id:
pmid:
- '32480670'
intvolume: ' 42'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 239 - 251
pmid: 1
publication: Functional Plant Biology
publication_identifier:
issn:
- 1445-4408
publication_status: published
publisher: CSIRO
publist_id: '5639'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with
ammonium as the sole nitrogen source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2015'
...
---
_id: '1531'
abstract:
- lang: eng
text: The Heat Kernel Signature (HKS) is a scalar quantity which is derived from
the heat kernel of a given shape. Due to its robustness, isometry invariance,
and multiscale nature, it has been successfully applied in many geometric applications.
From a more general point of view, the HKS can be considered as a descriptor of
the metric of a Riemannian manifold. Given a symmetric positive definite tensor
field we may interpret it as the metric of some Riemannian manifold and thereby
apply the HKS to visualize and analyze the given tensor data. In this paper, we
propose a generalization of this approach that enables the treatment of indefinite
tensor fields, like the stress tensor, by interpreting them as a generator of
a positive definite tensor field. To investigate the usefulness of this approach
we consider the stress tensor from the two-point-load model example and from a
mechanical work piece.
alternative_title:
- Mathematics and Visualization
article_processing_charge: No
author:
- first_name: Valentin
full_name: Zobel, Valentin
last_name: Zobel
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
citation:
ama: 'Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor
fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40.
1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13'
apa: Zobel, V., Reininghaus, J., & Hotz, I. (2015). Visualizing symmetric indefinite
2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz
(Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued
Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13
chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric
Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data, edited by
Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13.
ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D
tensor fields using The Heat Kernel Signature,” in Visualization and Processing
of Higher Order Descriptors for Multi-Valued Data, 1st ed., vol. 40, I. Hotz
and T. Schultz, Eds. Springer, 2015, pp. 257–267.
ista: 'Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D
tensor fields using The Heat Kernel Signature. In: Visualization and Processing
of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization,
vol. 40, 257–267.'
mla: Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields
Using The Heat Kernel Signature.” Visualization and Processing of Higher Order
Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz,
1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13.
short: V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization
and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer,
2015, pp. 257–267.
date_created: 2018-12-11T11:52:33Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-06-10T09:50:14Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-319-15090-1_13
edition: '1'
editor:
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Thomas
full_name: Schultz, Thomas
last_name: Schultz
intvolume: ' 40'
language:
- iso: eng
month: '01'
oa_version: None
page: 257 - 267
publication: Visualization and Processing of Higher Order Descriptors for Multi-Valued
Data
publication_identifier:
isbn:
- 978-3-319-15089-5
publication_status: published
publisher: Springer
publist_id: '5640'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2015'
...
---
_id: '1530'
abstract:
- lang: eng
text: In growing cells, protein synthesis and cell growth are typically not synchronous,
and, thus, protein concentrations vary over the cell division cycle. We have developed
a theoretical description of genetic regulatory systems in bacteria that explicitly
considers the cell division cycle to investigate its impact on gene expression.
We calculate the cell-to-cell variations arising from cells being at different
stages in the division cycle for unregulated genes and for basic regulatory mechanisms.
These variations contribute to the extrinsic noise observed in single-cell experiments,
and are most significant for proteins with short lifetimes. Negative autoregulation
buffers against variation of protein concentration over the division cycle, but
the effect is found to be relatively weak. Stronger buffering is achieved by an
increased protein lifetime. Positive autoregulation can strongly amplify such
variation if the parameters are set to values that lead to resonance-like behaviour.
For cooperative positive autoregulation, the concentration variation over the
division cycle diminishes the parameter region of bistability and modulates the
switching times between the two stable states. The same effects are seen for a
two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit,
the repressilator, is only weakly affected by the division cycle.
article_number: '066003'
author:
- first_name: Veronika
full_name: Bierbaum, Veronika
id: 3FD04378-F248-11E8-B48F-1D18A9856A87
last_name: Bierbaum
- first_name: Stefan
full_name: Klumpp, Stefan
last_name: Klumpp
citation:
ama: Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical
Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003
apa: Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on
gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003
chicago: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle
on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003.
ieee: V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,”
Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015.
ista: Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits.
Physical Biology. 12(6), 066003.
mla: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on
Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing
Ltd., 2015, doi:10.1088/1478-3975/12/6/066003.
short: V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).
date_created: 2018-12-11T11:52:33Z
date_published: 2015-09-25T00:00:00Z
date_updated: 2021-01-12T06:51:25Z
day: '25'
department:
- _id: MiSi
doi: 10.1088/1478-3975/12/6/066003
intvolume: ' 12'
issue: '6'
language:
- iso: eng
month: '09'
oa_version: None
publication: Physical Biology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5641'
quality_controlled: '1'
scopus_import: 1
status: public
title: Impact of the cell division cycle on gene circuits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2015'
...
---
_id: '1539'
abstract:
- lang: eng
text: 'Many stochastic models of biochemical reaction networks contain some chemical
species for which the number of molecules that are present in the system can only
be finite (for instance due to conservation laws), but also other species that
can be present in arbitrarily large amounts. The prime example of such networks
are models of gene expression, which typically contain a small and finite number
of possible states for the promoter but an infinite number of possible states
for the amount of mRNA and protein. One of the main approaches to analyze such
models is through the use of equations for the time evolution of moments of the
chemical species. Recently, a new approach based on conditional moments of the
species with infinite state space given all the different possible states of the
finite species has been proposed. It was argued that this approach allows one
to capture more details about the full underlying probability distribution with
a smaller number of equations. Here, I show that the result that less moments
provide more information can only stem from an unnecessarily complicated description
of the system in the classical formulation. The foundation of this argument will
be the derivation of moment equations that describe the complete probability distribution
over the finite state space but only low-order moments over the infinite state
space. I will show that the number of equations that is needed is always less
than what was previously claimed and always less than the number of conditional
moment equations up to the same order. To support these arguments, a symbolic
algorithm is provided that can be used to derive minimal systems of unconditional
moment equations for models with partially finite state space. '
article_number: '244103'
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space. Journal of Chemical Physics.
2015;143(24). doi:10.1063/1.4937937
apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
American Institute of Physics. https://doi.org/10.1063/1.4937937
chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics.
American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.
ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction
networks with partially finite state space,” Journal of Chemical Physics,
vol. 143, no. 24. American Institute of Physics, 2015.
ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical
reaction networks with partially finite state space. Journal of Chemical Physics.
143(24), 244103.
mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical
Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics,
vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.
short: J. Ruess, Journal of Chemical Physics 143 (2015).
date_created: 2018-12-11T11:52:36Z
date_published: 2015-12-22T00:00:00Z
date_updated: 2021-01-12T06:51:28Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1063/1.4937937
ec_funded: 1
file:
- access_level: open_access
checksum: 838657118ae286463a2b7737319f35ce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:43Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4641'
file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf
file_size: 605355
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 143'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Chemical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5632'
pubrep_id: '593'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimal moment equations for stochastic models of biochemical reaction networks
with partially finite state space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2015'
...
---
_id: '1534'
abstract:
- lang: eng
text: PIN proteins are auxin export carriers that direct intercellular auxin flow
and in turn regulate many aspects of plant growth and development including responses
to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS
(FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development,
as well as female reproductive development and stress responses. Here we show
that FLP and MYB88 act redundantly but differentially in regulating the transcription
of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the
one hand, FLP is involved in responses to gravity stimulation in primary roots,
whereas on the other, FLP and MYB88 function complementarily in establishing the
gravitropic set-point angles of lateral roots. Our results support a model in
which FLP and MYB88 expression specifically determines the temporal-spatial patterns
of PIN3 and PIN7 transcription that are closely associated with their preferential
functions during root responses to gravity.
article_number: '8822'
author:
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Kezhen
full_name: Yang, Kezhen
last_name: Yang
- first_name: Junjie
full_name: Zou, Junjie
last_name: Zou
- first_name: Lingling
full_name: Zhu, Lingling
last_name: Zhu
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Miyoterao
full_name: Morita, Miyoterao
last_name: Morita
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Jie
full_name: Le, Jie
last_name: Le
citation:
ama: Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR
LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
2015;6. doi:10.1038/ncomms9822
apa: Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015).
Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822
chicago: Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao
Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR
LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.
ieee: H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS
and MYB88 during Arabidopsis root gravitropism,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold
E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN
genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications.
6, 8822.
mla: Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS
and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications,
vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.
short: H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml,
E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:34Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '18'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1038/ncomms9822
ec_funded: 1
file:
- access_level: open_access
checksum: 3c06735fc7cd7e482ca830cbd26001bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:07Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5259'
file_name: IST-2016-485-v1+1_ncomms9822.pdf
file_size: 1852268
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5637'
pubrep_id: '485'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis
root gravitropism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1538'
abstract:
- lang: eng
text: Systems biology rests on the idea that biological complexity can be better
unraveled through the interplay of modeling and experimentation. However, the
success of this approach depends critically on the informativeness of the chosen
experiments, which is usually unknown a priori. Here, we propose a systematic
scheme based on iterations of optimal experiment design, flow cytometry experiments,
and Bayesian parameter inference to guide the discovery process in the case of
stochastic biochemical reaction networks. To illustrate the benefit of our methodology,
we apply it to the characterization of an engineered light-inducible gene expression
circuit in yeast and compare the performance of the resulting model with models
identified from nonoptimal experiments. In particular, we compare the parameter
posterior distributions and the precision to which the outcome of future experiments
can be predicted. Moreover, we illustrate how the identified stochastic model
can be used to determine light induction patterns that make either the average
amount of protein or the variability in a population of cells follow a desired
profile. Our results show that optimal experiment design allows one to derive
models that are accurate enough to precisely predict and regulate the protein
expression in heterogeneous cell populations over extended periods of time.
acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission
under the Network of Excellence HYCON2 (highly-complex and networked control systems)
and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme
FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges
support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). '
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: Andreas
full_name: Milias Argeitis, Andreas
last_name: Milias Argeitis
- first_name: Mustafa
full_name: Khammash, Mustafa
last_name: Khammash
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
citation:
ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment
design guides the characterization of a light-inducible gene expression circuit.
PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112
apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J.
(2015). Iterative experiment design guides the characterization of a light-inducible
gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112
chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash,
and John Lygeros. “Iterative Experiment Design Guides the Characterization of
a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1423947112.
ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153,
2015.
ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative
experiment design guides the characterization of a light-inducible gene expression
circuit. PNAS. 112(26), 8148–8153.
mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization
of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26,
National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.
short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112
(2015) 8148–8153.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T06:51:27Z
day: '30'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1073/pnas.1423947112
ec_funded: 1
external_id:
pmid:
- '26085136'
intvolume: ' 112'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/
month: '06'
oa: 1
oa_version: Submitted Version
page: 8148 - 8153
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5633'
quality_controlled: '1'
scopus_import: 1
status: public
title: Iterative experiment design guides the characterization of a light-inducible
gene expression circuit
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1535'
abstract:
- lang: eng
text: Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open
readily at relatively low membrane potentials and allow Ca2+ to enter the cells
near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential
waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation,
hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the
adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the
pacemaking current that sustains action potential (AP) firings and part of the
catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating
BK channels and drives the resting SK currents. These latter set the inter-spike
interval duration between consecutive spikes during spontaneous firing and the
rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a
primary role in the switch from “tonic” to “burst” firing that occurs in mouse
CCs when either the availability of voltage-gated Na channels (Nav) is reduced
or the β2 subunit featuring the fast inactivating BK channels is deleted. Here,
we discuss the functional role of these “neuronlike” firing modes in CCs and how
Cav1.3 contributes to them. The open issue is to understand how these novel firing
patterns are adapted to regulate the quantity of circulating catecholamines during
resting condition or in response to acute and chronic stress.
acknowledgement: This work was supported by the Italian MIUR (PRIN 2010/2011 project
2010JFYFY2) and the University of Torino.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Andrea
full_name: Marcantoni, Andrea
last_name: Marcantoni
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
citation:
ama: Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like
firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology.
2015;8(2):149-161. doi:10.2174/1874467208666150507105443
apa: Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as
key regulators of neuron-like firings and catecholamine release in chromaffin
cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443
chicago: Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels
as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin
Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015.
https://doi.org/10.2174/1874467208666150507105443.
ieee: D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells,” Current
Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161,
2015.
ista: Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators
of neuron-like firings and catecholamine release in chromaffin cells. Current
Molecular Pharmacology. 8(2), 149–161.
mla: Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like
Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology,
vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.
short: D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8
(2015) 149–161.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '01'
department:
- _id: PeJo
doi: 10.2174/1874467208666150507105443
external_id:
pmid:
- '25966692'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/
month: '10'
oa: 1
oa_version: Submitted Version
page: 149 - 161
pmid: 1
publication: Current Molecular Pharmacology
publication_status: published
publisher: Bentham Science Publishers
publist_id: '5636'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cav1.3 channels as key regulators of neuron-like firings and catecholamine
release in chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...
---
_id: '1536'
abstract:
- lang: eng
text: Strigolactones, first discovered as germination stimulants for parasitic weeds
[1], are carotenoid-derived phytohormones that play major roles in inhibiting
lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore,
strigolactones are involved in the regulation of lateral and adventitious root
development, root cell division [5, 6], secondary growth [7], and leaf senescence
[8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC
DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization
and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported
through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific
asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed
with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the
apical membrane of root hypodermal cells, presumably mediating the shootward transport
of strigolactone. Above the root tip, in the hypodermal passage cells that form
gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral
membrane, compatible with its postulated function as strigolactone exporter from
root to soil. Transport studies are in line with our localization studies since
(1) a papdr1 mutant displays impaired transport of strigolactones out of the root
tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2
levels change in plants deregulated for PDR1 expression, suggestive of variations
in endogenous strigolactone contents. In conclusion, our results indicate that
the polar localizations of PaPDR1 mediate directional shootward strigolactone
transport as well as localized exudation into the soil.
acknowledgement: "This work was funded by a grant of the Swiss National Foundation
to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us
with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands)
for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel
(University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel
(University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for
hints on protein quantification."
author:
- first_name: Joëlle
full_name: Sasse, Joëlle
last_name: Sasse
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Christian
full_name: Gübeli, Christian
last_name: Gübeli
- first_name: Guowei
full_name: Liu, Guowei
last_name: Liu
- first_name: Xi
full_name: Cheng, Xi
last_name: Cheng
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Harro
full_name: Bouwmeester, Harro
last_name: Bouwmeester
- first_name: Enrico
full_name: Martinoia, Enrico
last_name: Martinoia
- first_name: Lorenzo
full_name: Borghi, Lorenzo
last_name: Borghi
citation:
ama: Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter
PaPDR1 trace paths of directional strigolactone transport. Current Biology.
2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015
apa: Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi,
L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths
of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015
chicago: Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří
Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations
of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.”
Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.
ieee: J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1
trace paths of directional strigolactone transport,” Current Biology, vol.
25, no. 5. Cell Press, pp. 647–655, 2015.
ista: Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia
E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace
paths of directional strigolactone transport. Current Biology. 25(5), 647–655.
mla: Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1
Trace Paths of Directional Strigolactone Transport.” Current Biology, vol.
25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.
short: J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester,
E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-02-12T00:00:00Z
date_updated: 2021-01-12T06:51:27Z
day: '12'
department:
- _id: JiFr
doi: 10.1016/j.cub.2015.01.015
intvolume: ' 25'
issue: '5'
language:
- iso: eng
month: '02'
oa_version: None
page: 647 - 655
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5635'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional
strigolactone transport
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1533'
abstract:
- lang: eng
text: This paper addresses the problem of semantic segmentation, where the possible
class labels are from a predefined set. We exploit top-down guidance, i.e., the
coarse localization of the objects and their class labels provided by object detectors.
For each detected bounding box, figure-ground segmentation is performed and the
final result is achieved by merging the figure-ground segmentations. The main
idea of the proposed approach, which is presented in our preliminary work, is
to reformulate the figure-ground segmentation problem as sparse reconstruction
pursuing the object mask in a nonparametric manner. The latent segmentation mask
should be coherent subject to sparse error caused by intra-category diversity;
thus, the object mask is inferred by making use of sparse representations over
the training set. To handle local spatial deformations, local patch-level masks
are also considered and inferred by sparse representations over the spatially
nearby patches. The sparse reconstruction coefficients and the latent mask are
alternately optimized by applying the Lasso algorithm and the accelerated proximal
gradient method. The proposed formulation results in a convex optimization problem;
thus, the global optimal solution is achieved. In this paper, we provide theoretical
analysis of the convergence and optimality. We also give an extended numerical
analysis of the proposed algorithm and a comprehensive comparison with the related
semantic segmentation methods on the challenging PASCAL visual object class object
segmentation datasets and the Weizmann horse dataset. The experimental results
demonstrate that the proposed algorithm achieves a competitive performance when
compared with the state of the arts.
author:
- first_name: Wei
full_name: Xia, Wei
last_name: Xia
- first_name: Csaba
full_name: Domokos, Csaba
id: 492DACF8-F248-11E8-B48F-1D18A9856A87
last_name: Domokos
- first_name: Junjun
full_name: Xiong, Junjun
last_name: Xiong
- first_name: Loongfah
full_name: Cheong, Loongfah
last_name: Cheong
- first_name: Shuicheng
full_name: Yan, Shuicheng
last_name: Yan
citation:
ama: Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via
optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for
Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972
apa: Xia, W., Domokos, C., Xiong, J., Cheong, L., & Yan, S. (2015). Segmentation
over detection via optimal sparse reconstructions. IEEE Transactions on Circuits
and Systems for Video Technology. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972
chicago: Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan.
“Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions
on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972.
ieee: W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection
via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems
for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.
ista: Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection
via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems
for Video Technology. 25(8), 1295–1308.
mla: Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.”
IEEE Transactions on Circuits and Systems for Video Technology, vol. 25,
no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972.
short: W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits
and Systems for Video Technology 25 (2015) 1295–1308.
date_created: 2018-12-11T11:52:34Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:26Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/TCSVT.2014.2379972
intvolume: ' 25'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1295 - 1308
publication: IEEE Transactions on Circuits and Systems for Video Technology
publication_status: published
publisher: IEEE
publist_id: '5638'
quality_controlled: '1'
scopus_import: 1
status: public
title: Segmentation over detection via optimal sparse reconstructions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: 1
status: public
title: Toward a unifying framework for evolutionary processes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2015'
...
---
_id: '1546'
abstract:
- lang: eng
text: Synaptic efficacy and precision are influenced by the coupling of voltage-gated
Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their
proximity to vesicles is unknown, a quantitative understanding of the determinants
of vesicular release at nanometer scale is lacking. To investigate this, we combined
freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging,
and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day
7 and 21, VGCCs formed variable sized clusters and vesicular release became less
sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally
constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular
release are located at the perimeter of VGCC clusters (<30nm) and predict that
VGCC number per cluster determines vesicular release probability without altering
release time course. This "perimeter release model" provides a unifying
framework accounting for developmental changes in both synaptic efficacy and time
course.
acknowledgement: This work was supported by the Core Research for Evolutional Science
and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.;
by the funding provided by Okinawa Institute of Science and Technology (OIST) to
T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the
Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture,
Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la
Recherche Scientifique through the Actions Thematiques et Initatives sur Programme,
Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche
sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01)
to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063)
to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413)
and Principal (095667) Research Fellowship and an ERC advance grant (294667) to
RAS.
author:
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
- first_name: Jason
full_name: Rothman, Jason
last_name: Rothman
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: R Angus
full_name: Silver, R Angus
last_name: Silver
- first_name: David
full_name: Digregorio, David
last_name: Digregorio
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic
Ca2+ channels and its impact on vesicular release during development. Neuron.
2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019
apa: Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto,
R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.11.019
chicago: Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman,
Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale
Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release
during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.
ieee: Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels
and its impact on vesicular release during development,” Neuron, vol. 85,
no. 1. Elsevier, pp. 145–158, 2015.
ista: Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver
RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+
channels and its impact on vesicular release during development. Neuron. 85(1),
145–158.
mla: Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels
and Its Impact on Vesicular Release during Development.” Neuron, vol. 85,
no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.
short: Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto,
R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-01-07T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '07'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.neuron.2014.11.019
file:
- access_level: open_access
checksum: 725f4d5be2dbb44b283ce722645ef37d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:47Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5170'
file_name: IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf
file_size: 3080111
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 85'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 145 - 158
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5625'
pubrep_id: '482'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular
release during development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2015'
...
---
_id: '1541'
abstract:
- lang: eng
text: We present XSpeed a parallel state-space exploration algorithm for continuous
systems with linear dynamics and nondeterministic inputs. The motivation of having
parallel algorithms is to exploit the computational power of multi-core processors
to speed-up performance. The parallelization is achieved on two fronts. First,
we propose a parallel implementation of the support function algorithm by sampling
functions in parallel. Second, we propose a parallel state-space exploration by
slicing the time horizon and computing the reachable states in the time slices
in parallel. The second method can be however applied only to a class of linear
systems with invertible dynamics and fixed input. A GP-GPU implementation is also
presented following a lazy evaluation strategy on support functions. The parallel
algorithms are implemented in the tool XSpeed. We evaluated the performance on
two benchmarks including an 28 dimension Helicopter model. Comparison with the
sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread
Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up
of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario),
the state of the art tool for reachability analysis of linear hybrid systems.
Experiments illustrate that our parallel algorithm with time slicing not only
speeds-up performance but also improves precision.
acknowledgement: This work was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants
S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Amit
full_name: Gurung, Amit
last_name: Gurung
- first_name: Binayak
full_name: Das, Binayak
last_name: Das
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating
reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1'
apa: 'Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R.
(2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented
at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1'
chicago: 'Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov,
and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.”
Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.'
ieee: 'R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed:
Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer,
pp. 3–18, 2015.'
ista: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating
reachability analysis on multi-core processors. 9434, 3–18.'
mla: 'Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core
Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.'
short: R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015)
3–18.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:37Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2020-08-11T10:09:17Z
day: '28'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_1
ec_funded: 1
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa_version: None
page: 3 - 18
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _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_status: published
publisher: Springer
publist_id: '5630'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'XSpeed: Accelerating reachability analysis on multi-core processors'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1543'
abstract:
- lang: eng
text: A plethora of diverse programmed cell death (PCD) processes has been described
in living organisms. In animals and plants, different forms of PCD play crucial
roles in development, immunity, and responses to the environment. While the molecular
control of some animal PCD forms such as apoptosis is known in great detail, we
still know comparatively little about the regulation of the diverse types of plant
PCD. In part, this deficiency in molecular understanding is caused by the lack
of reliable reporters to detect PCD processes. Here, we addressed this issue by
using a combination of bioinformatics approaches to identify commonly regulated
genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana).
Our results indicate that the transcriptional signatures of developmentally controlled
cell death are largely distinct from the ones associated with environmentally
induced cell death. Moreover, different cases of developmental PCD share a set
of cell death-associated genes. Most of these genes are evolutionary conserved
within the green plant lineage, arguing for an evolutionary conserved core machinery
of developmental PCD. Based on this information, we established an array of specific
promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators
represent a powerful resource that can be used in addition to established morphological
and biochemical methods to detect and analyze PCD processes in vivo and in planta.
author:
- first_name: Yadira
full_name: Olvera Carrillo, Yadira
last_name: Olvera Carrillo
- first_name: Michiel
full_name: Van Bel, Michiel
last_name: Van Bel
- first_name: Tom
full_name: Van Hautegem, Tom
last_name: Van Hautegem
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Pierre
full_name: Buscaill, Pierre
last_name: Buscaill
- first_name: Susana
full_name: Rivas, Susana
last_name: Rivas
- first_name: Núria
full_name: Coll, Núria
last_name: Coll
- first_name: Frederik
full_name: Coppens, Frederik
last_name: Coppens
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed
cell death indicator genes discriminates developmentally and environmentally induced
programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699.
doi:10.1104/pp.15.00769
apa: Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans,
M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1104/pp.15.00769
chicago: Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych,
Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core
of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally
Induced Programmed Cell Death in Plants.” Plant Physiology. American Society
of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.
ieee: Y. Olvera Carrillo et al., “A conserved core of programmed cell death
indicator genes discriminates developmentally and environmentally induced programmed
cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society
of Plant Biologists, pp. 2684–2699, 2015.
ista: Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková
M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015.
A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants. Plant Physiology.
169(4), 2684–2699.
mla: Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death
Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed
Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society
of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.
short: Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans,
M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere,
M. Nowack, Plant Physiology 169 (2015) 2684–2699.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.15.00769
intvolume: ' 169'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 2684 - 2699
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5628'
scopus_import: 1
status: public
title: A conserved core of programmed cell death indicator genes discriminates developmentally
and environmentally induced programmed cell death in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2015'
...
---
_id: '1544'
abstract:
- lang: eng
text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the
well-controlled binding of proteins to the cytoplasmic side of the cell membrane.
However, a precise characterization of the spatiotemporal dynamics of membrane-bound
proteins is often difficult to achieve in vivo. Here, we present protocols for
the use of supported lipid bilayers to rebuild the cytokinetic machineries of
cells with greatly different dimensions: the bacterium Escherichia coli and eggs
of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence
microscopy, these experimental setups allow for precise quantitative analyses
of membrane-bound proteins. The protocols described to obtain glass-supported
membranes from bacterial and vertebrate lipids can be used as starting points
for other reconstitution experiments. We believe that similar biochemical assays
will be instrumental to study the biochemistry and biophysics underlying a variety
of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.'
author:
- first_name: Phuong
full_name: Nguyen, Phuong
last_name: Nguyen
- first_name: Christine
full_name: Field, Christine
last_name: Field
- first_name: Aaron
full_name: Groen, Aaron
last_name: Groen
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007'
apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using
supported bilayers to study the spatiotemporal organization of membrane-bound
proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241).
Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007
chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin
Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound
Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic
Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.
ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported
bilayers to study the spatiotemporal organization of membrane-bound proteins,”
in Building a Cell from its Components Parts, vol. 128, Academic Press,
2015, pp. 223–241.
ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers
to study the spatiotemporal organization of membrane-bound proteins. In: Building
a Cell from its Components Parts. vol. 128, 223–241.'
mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal
Organization of Membrane-Bound Proteins.” Building a Cell from Its Components
Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.
short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell
from Its Components Parts, Academic Press, 2015, pp. 223–241.
date_created: 2018-12-11T11:52:38Z
date_published: 2015-04-08T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '08'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2015.01.007
external_id:
pmid:
- '25997350'
intvolume: ' 128'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/
month: '04'
oa: 1
oa_version: Submitted Version
page: 223 - 241
pmid: 1
publication: Building a Cell from its Components Parts
publication_status: published
publisher: Academic Press
publist_id: '5627'
quality_controlled: '1'
scopus_import: 1
status: public
title: Using supported bilayers to study the spatiotemporal organization of membrane-bound
proteins
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1540'
abstract:
- lang: eng
text: 'Plant sexual reproduction involves highly structured and specialized organs:
stamens (male) and gynoecia (female, containing ovules). These organs synchronously
develop within protective flower buds, until anthesis, via tightly coordinated
mechanisms that are essential for effective fertilization and production of viable
seeds. The phytohormone auxin is one of the key endogenous signalling molecules
controlling initiation and development of these, and other, plant organs. In particular,
its uneven distribution, resulting from tightly controlled production, metabolism
and directional transport, is an important morphogenic factor. In this review
we discuss how developmentally controlled and localized auxin biosynthesis and
transport contribute to the coordinated development of plants'' reproductive organs,
and their fertilized derivatives (embryos) via the regulation of auxin levels
and distribution within and around them. Current understanding of the links between
de novo local auxin biosynthesis, auxin transport and/or signalling is presented
to highlight the importance of the non-cell autonomous action of auxin production
on development and morphogenesis of reproductive organs and embryos. An overview
of transcription factor families, which spatiotemporally define local auxin production
by controlling key auxin biosynthetic enzymes, is also presented.'
acknowledgement: 'The work was supported by grants from: the Employment of Best Young
Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037)
to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and
the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and
the EU (FP7/2007–2013 People Programme), to HSR.'
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Lucie
full_name: Crhák Khaitová, Lucie
last_name: Crhák Khaitová
- first_name: Souad
full_name: Mroue, Souad
last_name: Mroue
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256
apa: Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance
of localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis. Journal of Experimental Botany. Oxford University Press.
https://doi.org/10.1093/jxb/erv256
chicago: Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The
Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs
and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University
Press, 2015. https://doi.org/10.1093/jxb/erv256.
ieee: H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of
localized auxin production for morphogenesis of reproductive organs and embryos
in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford
University Press, pp. 5029–5042, 2015.
ista: Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized
auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis.
Journal of Experimental Botany. 66(16), 5029–5042.
mla: Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis
of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental
Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.
short: H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental
Botany 66 (2015) 5029–5042.
date_created: 2018-12-11T11:52:36Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2021-01-12T06:51:29Z
day: '05'
department:
- _id: EvBe
doi: 10.1093/jxb/erv256
intvolume: ' 66'
issue: '16'
language:
- iso: eng
month: '05'
oa_version: None
page: 5029 - 5042
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5631'
quality_controlled: '1'
scopus_import: 1
status: public
title: The importance of localized auxin production for morphogenesis of reproductive
organs and embryos in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2015'
...
---
_id: '1551'
abstract:
- lang: eng
text: 'Reciprocal coevolution between host and pathogen is widely seen as a major
driver of evolution and biological innovation. Yet, to date, the underlying genetic
mechanisms and associated trait functions that are unique to rapid coevolutionary
change are generally unknown. We here combined experimental evolution of the bacterial
biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans
with large-scale phenotyping, whole genome analysis, and functional genetics to
demonstrate the selective benefit of pathogen virulence and the underlying toxin
genes during the adaptation process. We show that: (i) high virulence was specifically
favoured during pathogen–host coevolution rather than pathogen one-sided adaptation
to a nonchanging host or to an environment without host; (ii) the pathogen genotype
BT-679 with known nematocidal toxin genes and high virulence specifically swept
to fixation in all of the independent replicate populations under coevolution
but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated
populations correlated with elevated copy numbers of the plasmid containing the
nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679
isolate was reconstituted by genetic reintroduction or external addition of the
toxins.We conclude that sustained coevolution is distinct from unidirectional
selection in shaping the pathogen''s genome and life history characteristics.
To our knowledge, this study is the first to characterize the pathogen genes involved
in coevolutionary adaptation in an animal host–pathogen interaction system.'
acknowledgement: We are very grateful for funding from the German Science Foundation
(DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI
1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence
Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program
(Co-fund Marie Curie Actions of the European Commission) to LM.
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Antoine
full_name: Branca, Antoine
last_name: Branca
- first_name: Anna
full_name: Sheppard, Anna
last_name: Sheppard
- first_name: Andrei
full_name: Papkou, Andrei
last_name: Papkou
- first_name: David
full_name: Laehnemann, David
last_name: Laehnemann
- first_name: Patrick
full_name: Guenther, Patrick
last_name: Guenther
- first_name: Swantje
full_name: Prahl, Swantje
last_name: Prahl
- first_name: Manja
full_name: Saebelfeld, Manja
last_name: Saebelfeld
- first_name: Jacqueline
full_name: Hollensteiner, Jacqueline
last_name: Hollensteiner
- first_name: Heiko
full_name: Liesegang, Heiko
last_name: Liesegang
- first_name: Elzbieta
full_name: Brzuszkiewicz, Elzbieta
last_name: Brzuszkiewicz
- first_name: Rolf
full_name: Daniel, Rolf
last_name: Daniel
- first_name: Nico
full_name: Michiels, Nico
last_name: Michiels
- first_name: Rebecca
full_name: Schulte, Rebecca
last_name: Schulte
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Arndt
full_name: Telschow, Arndt
last_name: Telschow
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: 'El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective
advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS
Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169'
apa: 'El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther,
P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169'
chicago: 'El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann,
Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective
Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS
Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.'
ieee: 'L. El Masri et al., “Host–pathogen coevolution: The selective advantage
of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology,
vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.'
ista: 'El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl
S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels
N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg
H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.'
mla: 'El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage
of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology,
vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.'
short: L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther,
S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R.
Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg
Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '04'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1371/journal.pbio.1002169
ec_funded: 1
file:
- access_level: open_access
checksum: 30dee7a2c11ed09f2f5634655c0146f8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:13Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5063'
file_name: IST-2016-481-v1+1_journal.pbio.1002169.pdf
file_size: 3468956
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1 - 30
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5620'
pubrep_id: '481'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis
virulence and its cry toxin genes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '1549'
abstract:
- lang: eng
text: Nature has incorporated small photochromic molecules, colloquially termed
'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis
and vision. While Nature's ability to employ light-responsive functionalities
has long been recognized, it was not until recently that scientists designed,
synthesized and applied synthetic photochromes to manipulate many of which open
rapidly and locally in their native cell types, biological processes with the
temporal and spatial resolution of light. Ion channels in particular have come
to the forefront of proteins that can be put under the designer control of synthetic
photochromes. Photochromic ion channel controllers are comprised of three classes,
photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and
photochromic crosslinkers (PXs), and in each class ion channel functionality is
controlled through reversible changes in photochrome structure. By acting as light-dependent
ion channel agonists, antagonist or modulators, photochromic controllers effectively
converted a wide range of ion channels, including voltage-gated ion channels,
'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive
ion channels, into man-made photoreceptors. Control by photochromes can be reversible,
unlike in the case of 'caged' compounds, and non-invasive with high spatial precision,
unlike pharmacology and electrical manipulation. Here, we introduce design principles
of emerging photochromic molecules that act on ion channels and discuss the impact
that these molecules are beginning to have on ion channel biophysics and neuronal
physiology.
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels
under light control. In: Novel Chemical Tools to Study Ion Channel Biology.
Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117.
doi:10.1007/978-1-4939-2845-3_6'
apa: 'Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the
photoswitch: Ion channels under light control. In Novel chemical tools to study
ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6'
chicago: 'Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak.
“Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical
Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine
and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.'
ieee: 'C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch:
Ion channels under light control,” in Novel chemical tools to study ion channel
biology, vol. 869, Springer, 2015, pp. 101–117.'
ista: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch:
Ion channels under light control. In: Novel chemical tools to study ion channel
biology. vol. 869, 101–117.'
mla: 'Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under
Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol.
869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.'
short: C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools
to Study Ion Channel Biology, Springer, 2015, pp. 101–117.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-09-18T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '18'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-2845-3_6
file:
- access_level: open_access
checksum: bd1bfdf2423a0c3b6e7cabfa8b44bc0f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:45:01Z
file_id: '4854'
file_name: IST-2017-839-v1+1_mckenzie.pdf
file_size: 1919655
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 869'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 101 - 117
publication: Novel chemical tools to study ion channel biology
publication_identifier:
isbn:
- 978-1-4939-2844-6
publication_status: published
publisher: Springer
publist_id: '5622'
pubrep_id: '839'
quality_controlled: '1'
scopus_import: 1
series_title: Advances in Experimental Medicine and Biology
status: public
title: 'Flipping the photoswitch: Ion channels under light control'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 869
year: '2015'
...
---
_id: '1548'
abstract:
- lang: eng
text: Reproduction within a host and transmission to the next host are crucial for
the virulence and fitness of pathogens. Nevertheless, basic knowledge about such
parameters is often missing from the literature, even for well-studied bacteria,
such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects
its hosts via the oral route. To characterize bacterial replication success, we
made use of an experimental oral infection system for the red flour beetle Tribolium
castaneum and developed a flow cytometric assay for the quantification of both
spore ingestion by the individual beetle larvae and the resulting spore load after
bacterial replication and resporulation within cadavers. On average, spore numbers
increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully
in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial
stock cultures into nutrient medium, we next investigated outgrowth characteristics
of vegetative cells and found that cadaver- derived bacteria showed reduced growth
compared to bacteria from the stock cultures. Interestingly, this reduced growth
was a consequence of inhibited spore germination, probably originating from the
host and resulting in reduced host mortality in subsequent infections by cadaver-derived
spores. Nevertheless, we further showed that Bacillus thuringiensis transmission
was possible via larval cannibalism when no other food was offered. These results
contribute to our understanding of the ecology of Bacillus thuringiensis as an
insect pathogen.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Christina
full_name: Höfling, Christina
last_name: Höfling
- first_name: Momir
full_name: Futo, Momir
last_name: Futo
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium
castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15'
apa: 'Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015).
Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of
bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination. Applied and Environmental Microbiology. American
Society for Microbiology. https://doi.org/10.1128/AEM.02051-15'
chicago: 'Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and
Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis:
Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism,
and Inhibition of Spore Germination.” Applied and Environmental Microbiology.
American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.'
ieee: 'B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection
of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial
replication within cadavers, transmission via cannibalism, and inhibition of spore
germination,” Applied and Environmental Microbiology, vol. 81, no. 23.
American Society for Microbiology, pp. 8135–8144, 2015.'
ista: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of
Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication
within cadavers, transmission via cannibalism, and inhibition of spore germination.
Applied and Environmental Microbiology. 81(23), 8135–8144.'
mla: 'Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus
Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission
via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental
Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp.
8135–44, doi:10.1128/AEM.02051-15.'
short: B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and
Environmental Microbiology 81 (2015) 8135–8144.
date_created: 2018-12-11T11:52:39Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1128/AEM.02051-15
external_id:
pmid:
- '26386058'
intvolume: ' 81'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/
month: '12'
oa: 1
oa_version: Submitted Version
page: 8135 - 8144
pmid: 1
publication: Applied and Environmental Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '5623'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification
of bacterial replication within cadavers, transmission via cannibalism, and inhibition
of spore germination'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2015'
...
---
_id: '1553'
abstract:
- lang: eng
text: Cell movement has essential functions in development, immunity, and cancer.
Various cell migration patterns have been reported, but no general rule has emerged
so far. Here, we show on the basis of experimental data in vitro and in vivo that
cell persistence, which quantifies the straightness of trajectories, is robustly
coupled to cell migration speed. We suggest that this universal coupling constitutes
a generic law of cell migration, which originates in the advection of polarity
cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis
relies on a theoretical model that we validate by measuring the persistence of
cells upon modulation of actin flow speeds and upon optogenetic manipulation of
the binding of an actin regulator to actin filaments. Beyond the quantitative
prediction of the coupling, the model yields a generic phase diagram of cellular
trajectories, which recapitulates the full range of observed migration patterns.
author:
- first_name: Paolo
full_name: Maiuri, Paolo
last_name: Maiuri
- first_name: Jean
full_name: Rupprecht, Jean
last_name: Rupprecht
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Olivier
full_name: Bénichou, Olivier
last_name: Bénichou
- first_name: Nicolas
full_name: Carpi, Nicolas
last_name: Carpi
- first_name: Mathieu
full_name: Coppey, Mathieu
last_name: Coppey
- first_name: Simon
full_name: De Beco, Simon
last_name: De Beco
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Carolina
full_name: Lage Crespo, Carolina
last_name: Lage Crespo
- first_name: Franziska
full_name: Lautenschlaeger, Franziska
last_name: Lautenschlaeger
- first_name: Maël
full_name: Le Berre, Maël
last_name: Le Berre
- first_name: Ana
full_name: Lennon Duménil, Ana
last_name: Lennon Duménil
- first_name: Matthew
full_name: Raab, Matthew
last_name: Raab
- first_name: Hawa
full_name: Thiam, Hawa
last_name: Thiam
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- 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: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling
between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056
apa: Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N.,
… Voituriez, R. (2015). Actin flows mediate a universal coupling between cell
speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056
chicago: Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier
Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal
Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015.
https://doi.org/10.1016/j.cell.2015.01.056.
ieee: P. Maiuri et al., “Actin flows mediate a universal coupling between
cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp.
374–386, 2015.
ista: Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M,
De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre
M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin
flows mediate a universal coupling between cell speed and cell persistence. Cell.
161(2), 374–386.
mla: Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell
Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp.
374–86, doi:10.1016/j.cell.2015.01.056.
short: P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M.
Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger,
M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez,
Cell 161 (2015) 374–386.
date_created: 2018-12-11T11:52:41Z
date_published: 2015-04-09T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '09'
department:
- _id: MiSi
- _id: CaHe
doi: 10.1016/j.cell.2015.01.056
ec_funded: 1
intvolume: ' 161'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 374 - 386
project:
- _id: 2529486C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T 560-B17
name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25ABD200-B435-11E9-9278-68D0E5697425
grant_number: RGP0058/2011
name: 'Cell migration in complex environments: from in vivo experiments to theoretical
models'
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '5618'
quality_controlled: '1'
scopus_import: 1
status: public
title: Actin flows mediate a universal coupling between cell speed and cell persistence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 161
year: '2015'
...
---
_id: '1550'
abstract:
- lang: eng
text: The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain
interneurons. Here, we examine the lineage relationship among MGE-derived interneurons
using a replication-defective retroviral library containing a highly diverse set
of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor
cells enabled us to unambiguously determine their respective lineal relationship.
We found that clonal dispersion occurs across large areas of the brain and is
not restricted by anatomical divisions. As such, sibling interneurons can populate
the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons
appeared to be generated from asymmetric divisions of MGE progenitor cells, followed
by symmetric divisions within the subventricular zone. Altogether, our findings
uncover that lineage relationships do not appear to determine interneuron allocation
to particular regions. As such, it is likely that clonally related interneurons
have considerable flexibility as to the particular forebrain circuits to which
they can contribute.
acknowledgement: "Research in the G.F. laboratory is supported by NIH (NS 081297,
MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory
is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF
(1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n"
author:
- first_name: Christian
full_name: Mayer, Christian
last_name: Mayer
- first_name: Xavier
full_name: Jaglin, Xavier
last_name: Jaglin
- first_name: Lucy
full_name: Cobbs, Lucy
last_name: Cobbs
- first_name: Rachel
full_name: Bandler, Rachel
last_name: Bandler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Constance
full_name: Cepko, Constance
last_name: Cepko
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gord
full_name: Fishell, Gord
last_name: Fishell
citation:
ama: Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons
disperse broadly across both functional areas and structural boundaries. Neuron.
2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011
apa: Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., …
Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011
chicago: Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher,
Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain
Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.”
Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011.
ieee: C. Mayer et al., “Clonally related forebrain interneurons disperse
broadly across both functional areas and structural boundaries,” Neuron,
vol. 87, no. 5. Elsevier, pp. 989–998, 2015.
ista: Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S,
Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across
both functional areas and structural boundaries. Neuron. 87(5), 989–998.
mla: Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse
Broadly across Both Functional Areas and Structural Boundaries.” Neuron,
vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.
short: C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer,
G. Fishell, Neuron 87 (2015) 989–998.
date_created: 2018-12-11T11:52:40Z
date_published: 2015-09-02T00:00:00Z
date_updated: 2021-01-12T06:51:32Z
day: '02'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2015.07.011
external_id:
pmid:
- '26299473'
intvolume: ' 87'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/
month: '09'
oa: 1
oa_version: Submitted Version
page: 989 - 998
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5621'
quality_controlled: '1'
scopus_import: 1
status: public
title: Clonally related forebrain interneurons disperse broadly across both functional
areas and structural boundaries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2015'
...