---
_id: '200'
abstract:
- lang: eng
text: This thesis is concerned with the inference of current population structure
based on geo-referenced genetic data. The underlying idea is that population structure
affects its spatial genetic structure. Therefore, genotype information can be
utilized to estimate important demographic parameters such as migration rates.
These indirect estimates of population structure have become very attractive,
as genotype data is now widely available. However, there also has been much concern
about these approaches. Importantly, genetic structure can be influenced by many
complex patterns, which often cannot be disentangled. Moreover, many methods merely
fit heuristic patterns of genetic structure, and do not build upon population
genetics theory. Here, I describe two novel inference methods that address these
shortcomings. In Chapter 2, I introduce an inference scheme based on a new type
of signal, identity by descent (IBD) blocks. Recently, it has become feasible
to detect such long blocks of genome shared between pairs of samples. These blocks
are direct traces of recent coalescence events. As such, they contain ample signal
for inferring recent demography. I examine sharing of IBD blocks in two-dimensional
populations with local migration. Using a diffusion approximation, I derive formulas
for an isolation by distance pattern of long IBD blocks and show that sharing
of long IBD blocks approaches rapid exponential decay for growing sample distance.
I describe an inference scheme based on these results. It can robustly estimate
the dispersal rate and population density, which is demonstrated on simulated
data. I also show an application to estimate mean migration and the rate of recent
population growth within Eastern Europe. Chapter 3 is about a novel method to
estimate barriers to gene flow in a two dimensional population. This inference
scheme utilizes geographically localized allele frequency fluctuations - a classical
isolation by distance signal. The strength of these local fluctuations increases
on average next to a barrier, and there is less correlation across it. I again
use a framework of diffusion of ancestral lineages to model this effect, and provide
an efficient numerical implementation to fit the results to geo-referenced biallelic
SNP data. This inference scheme is able to robustly estimate strong barriers to
gene flow, as tests on simulated data confirm.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
citation:
ama: Ringbauer H. Inferring recent demography from spatial genetic structure. 2018.
doi:10.15479/AT:ISTA:th_963
apa: Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963
chicago: Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.
ieee: H. Ringbauer, “Inferring recent demography from spatial genetic structure,”
Institute of Science and Technology Austria, 2018.
ista: Ringbauer H. 2018. Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria.
mla: Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.
short: H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:10Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '21'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:th_963
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file_size: 113365
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language:
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license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '146'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7713'
pubrep_id: '963'
related_material:
record:
- id: '563'
relation: part_of_dissertation
status: public
- id: '1074'
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: Inferring recent demography from spatial genetic structure
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legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
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short: CC BY-NC (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '1064'
abstract:
- lang: eng
text: 'In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by
P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it
is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot
be separated into two subfamilies by a straight line disjoint from the disks.
In this note we show that essentially the same idea may work for different analogues
and generalizations of their result. In particular, we prove the following: Given
a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety
coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate
of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane
disjoint from the homothets.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Mikhail
full_name: Grigorev, Mikhail
last_name: Grigorev
citation:
ama: Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W.
Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009.
doi:10.1007/s00454-017-9883-x
apa: Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering
theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-017-9883-x
chicago: Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle
Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational
Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.
ieee: A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem
by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry,
vol. 59, no. 4. Springer, pp. 1001–1009, 2018.
ista: Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by
A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.
mla: Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and
R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer,
2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.
short: A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry
59 (2018) 1001–1009.
date_created: 2018-12-11T11:49:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:51Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-017-9883-x
ec_funded: 1
external_id:
isi:
- '000432205500011'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:27:36Z
date_updated: 2019-01-18T09:27:36Z
file_id: '5844'
file_name: 2018_DiscreteComp_Akopyan.pdf
file_size: 482518
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:27:36Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 1001-1009
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the circle covering theorem by A.W. Goodman and R.E. Goodman
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 59
year: '2018'
...
---
_id: '418'
abstract:
- lang: eng
text: "The aim of this thesis was the development of new strategies for optical
and optogenetic control of proliferative and pro-survival signaling, and characterizing
them from the molecular mechanism up to cellular effects. These new light-based
methods have unique features, such as red light as an activator, or the avoidance
of gene delivery, which enable to overcome current limitations, such as light
delivery to target tissues and feasibility as therapeutic approach. A special
focus was placed on implementing these new light-based approaches in pancreatic
β-cells, as β-cells are the key players in diabetes and especially their loss
in number negatively affects disease progression. Currently no treatment options
are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn
a first approach, red-light-activated growth factor receptors, in particular receptor
tyrosine kinases were engineered and characterized. Receptor activation with light
allows spatio-temporal control compared to ligand-based activation, and especially
red light exhibits deeper tissue penetration than other wavelengths of the visible
spectrum. Red-light-activated receptor tyrosine kinases robustly activated major
growth factor related signaling pathways with a high temporal resolution. Moreover,
the remote activation of the proliferative MAPK/Erk pathway by red-light-activated
receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through
one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine
kinases are particularly attractive for applications in animal models due to the
deep tissue penetration of red light, a drawback, especially with regard to translation
into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous
light-sensitive mechanism was identified and its potential to promote proliferative
and pro-survival signals was explored, towards light-based tissue regeneration
without the need for gene transfer. Blue-green light illumination was found to
be sufficient for the activation of proliferation and survival promoting signaling
pathways in primary pancreatic murine and human islets. Blue-green light also
led to an increase in proliferation of primary islet cells, an effect which was
shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated
that this approach of pancreatic β-cell expansion did not have any negative effect
on the β-cell function, in particular on their insulin secretion capacity. In
contrast, a trend for enhanced insulin secretion under high glucose conditions
after illumination was detected. In order to unravel the detailed characteristics
of this endogenous light-sensitive mechanism, the precise light requirements were
determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin,
was detected. The observed effects were found to be independent of handling effects
such as temperature differences and cytochrome c oxidase dependent ATP increase,
but they were found to be enhanced through the knockout of OPN3. The exact mechanism
of how islets cells sense light and the identity of the photoreceptor remains
unknown.\r\nSummarized two new light-based systems with unique features were established
that enable the activation of proliferative and pro-survival signaling pathways.
While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics
research, by allowing non-invasive control of signaling in vivo, the identified
endogenous light-sensitive mechanism has the potential to be the basis of a gene
therapy-free therapeutical approach for light-based β-cell expansion."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
citation:
ama: Gschaider-Reichhart E. Optical and optogenetic control of proliferation and
survival . 2018. doi:10.15479/AT:ISTA:th_913
apa: Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation
and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913
chicago: Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation
and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.
ieee: E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation
and survival ,” Institute of Science and Technology Austria, 2018.
ista: Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation
and survival . Institute of Science and Technology Austria.
mla: Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation
and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.
short: E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation
and Survival , Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-01-08T00:00:00Z
date_updated: 2023-09-22T09:20:10Z
day: '08'
ddc:
- '571'
- '570'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/AT:ISTA:th_913
file:
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creator: dernst
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date_updated: 2020-07-14T12:46:24Z
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file_name: 2018_THESIS_Gschaider-Reichhart_source.docx
file_size: 7012495
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7405'
pubrep_id: '913'
related_material:
record:
- id: '1441'
relation: part_of_dissertation
status: public
- id: '1678'
relation: part_of_dissertation
status: public
- id: '2084'
relation: part_of_dissertation
status: public
- id: '1028'
relation: part_of_dissertation
status: public
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 and optogenetic control of proliferation and survival '
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: '2018'
...
---
_id: '1012'
abstract:
- lang: eng
text: We prove a new central limit theorem (CLT) for the difference of linear eigenvalue
statistics of a Wigner random matrix H and its minor H and find that the fluctuation
is much smaller than the fluctuations of the individual linear statistics, as
a consequence of the strong correlation between the eigenvalues of H and H. In
particular, our theorem identifies the fluctuation of Kerov's rectangular Young
diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic
shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel
measure follow the same limiting shape. For this, algebraically motivated, ensemble
a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar
to our result but the variance is different, indicating that the analogy between
the two models has its limitations. Moreover, our theorem shows that Borodin's
result [7] on the convergence of the spectral distribution of Wigner matrices
to a Gaussian free field also holds in derivative sense.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing
wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298.
doi:10.1093/imrn/rnw330
apa: Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young
diagrams of interlacing wigner eigenvalues. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330
chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330.
ieee: L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues,” International Mathematics Research Notices,
vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.
ista: Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10),
3255–3298.
mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.
short: L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018
(2018) 3255–3298.
date_created: 2018-12-11T11:49:41Z
date_published: 2018-05-18T00:00:00Z
date_updated: 2023-09-22T09:44:21Z
day: '18'
department:
- _id: LaEr
doi: 10.1093/imrn/rnw330
ec_funded: 1
external_id:
arxiv:
- '1608.05163'
isi:
- '000441668300009'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05163
month: '05'
oa: 1
oa_version: Preprint
page: 3255-3298
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: International Mathematics Research Notices
publication_identifier:
issn:
- '10737928'
publication_status: published
publisher: Oxford University Press
publist_id: '6383'
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '6006'
abstract:
- lang: eng
text: 'Network games (NGs) are played on directed graphs and are extensively used
in network design and analysis. Search problems for NGs include finding special
strategy profiles such as a Nash equilibrium and a globally-optimal solution.
The networks modeled by NGs may be huge. In formal verification, abstraction has
proven to be an extremely effective technique for reasoning about systems with
big and even infinite state spaces. We describe an abstraction-refinement methodology
for reasoning about NGs. Our methodology is based on an abstraction function that
maps the state space of an NG to a much smaller state space. We search for a global
optimum and a Nash equilibrium by reasoning on an under- and an over-approximation
defined on top of this smaller state space. When the approximations are too coarse
to find such profiles, we refine the abstraction function. We extend the abstraction-refinement
methodology to labeled networks, where the objectives of the players are regular
languages. Our experimental results demonstrate the effectiveness of the methodology. '
article_number: '39'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning
about network games. Games. 2018;9(3). doi:10.3390/g9030039
apa: Avni, G., Guha, S., & Kupferman, O. (2018). An abstraction-refinement methodology
for reasoning about network games. Games. MDPI AG. https://doi.org/10.3390/g9030039
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement
Methodology for Reasoning about Network Games.” Games. MDPI AG, 2018. https://doi.org/10.3390/g9030039.
ieee: G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology
for reasoning about network games,” Games, vol. 9, no. 3. MDPI AG, 2018.
ista: Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for
reasoning about network games. Games. 9(3), 39.
mla: Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about
Network Games.” Games, vol. 9, no. 3, 39, MDPI AG, 2018, doi:10.3390/g9030039.
short: G. Avni, S. Guha, O. Kupferman, Games 9 (2018).
date_created: 2019-02-14T14:17:54Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-22T09:48:59Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.3390/g9030039
file:
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checksum: 749d65ca4ce74256a029d9644a1b1cb0
content_type: application/pdf
creator: kschuh
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has_accepted_license: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _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: Games
publication_identifier:
issn:
- 2073-4336
publication_status: published
publisher: MDPI AG
quality_controlled: '1'
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scopus_import: 1
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title: An abstraction-refinement methodology for reasoning about network games
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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: 9
year: '2018'
...
---
_id: '35'
abstract:
- lang: eng
text: 'We consider planning problems for graphs, Markov decision processes (MDPs),
and games on graphs. While graphs represent the most basic planning model, MDPs
represent interaction with nature and games on graphs represent interaction with
an adversarial environment. We consider two planning problems where there are
k different target sets, and the problems are as follows: (a) the coverage problem
asks whether there is a plan for each individual target set; and (b) the sequential
target reachability problem asks whether the targets can be reached in sequence.
For the coverage problem, we present a linear-time algorithm for graphs, and quadratic
conditional lower bound for MDPs and games on graphs. For the sequential target
problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm
for MDPs, and a quadratic conditional lower bound for games on graphs. Our results
with conditional lower bounds establish (i) model-separation results showing that
for the coverage problem MDPs and games on graphs are harder than graphs and for
the sequential reachability problem games on graphs are harder than MDPs and graphs;
and (ii) objective-separation results showing that for MDPs the coverage problem
is harder than the sequential target problem.'
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: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional
lower bounds for planning problems. In: 28th International Conference on Automated
Planning and Scheduling . AAAI Press; 2018.'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms
and conditional lower bounds for planning problems. In 28th International Conference
on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander
Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th
International Conference on Automated Planning and Scheduling . AAAI Press,
2018.
ieee: K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and
conditional lower bounds for planning problems,” in 28th International Conference
on Automated Planning and Scheduling , Delft, Netherlands, 2018.
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional
lower bounds for planning problems. 28th International Conference on Automated
Planning and Scheduling . ICAPS: International Conference on Automated Planning
and Scheduling.'
mla: Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for
Planning Problems.” 28th International Conference on Automated Planning and
Scheduling , AAAI Press, 2018.
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International
Conference on Automated Planning and Scheduling , AAAI Press, 2018.
conference:
end_date: 2018-06-29
location: Delft, Netherlands
name: 'ICAPS: International Conference on Automated Planning and Scheduling'
start_date: 2018-06-24
date_created: 2018-12-11T11:44:17Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-26T10:41:41Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1804.07031'
isi:
- '000492986200007'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07031
month: '06'
oa: 1
oa_version: None
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: '28th International Conference on Automated Planning and Scheduling '
publication_status: published
publisher: AAAI Press
publist_id: '8020'
quality_controlled: '1'
related_material:
record:
- id: '9293'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Algorithms and conditional lower bounds for planning problems
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '738'
abstract:
- lang: eng
text: 'This paper is devoted to automatic competitive analysis of real-time scheduling
algorithms for firm-deadline tasksets, where only completed tasks con- tribute
some utility to the system. Given such a taskset T , the competitive ratio of
an on-line scheduling algorithm A for T is the worst-case utility ratio of A over
the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative
graph games to address the competitive analysis and competitive synthesis problems.
For the competitive analysis case, given any taskset T and any finite-memory on-
line scheduling algorithm A , we show that the competitive ratio of A in T can
be computed in polynomial time in the size of the state space of A . Our approach
is flexible as it also provides ways to model meaningful constraints on the released
task sequences that determine the competitive ratio. We provide an experimental
study of many well-known on-line scheduling algorithms, which demonstrates the
feasibility of our competitive analysis approach that effectively replaces human
ingenuity (required Preliminary versions of this paper have appeared in Chatterjee
et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu
Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid
s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria),
Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group,
Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 Real-Time
Syst for finding worst-case scenarios) by computing power. For the competitive
synthesis case, we are just given a taskset T , and the goal is to automatically
synthesize an opti- mal on-line scheduling algorithm A , i.e., one that guarantees
the largest competitive ratio possible for T . We show how the competitive synthesis
problem can be reduced to a two-player graph game with partial information, and
establish that the compu- tational complexity of solving this game is Np -complete.
The competitive synthesis problem is hence in Np in the size of the state space
of the non-deterministic labeled transition system encoding the taskset. Overall,
the proposed framework assists in the selection of suitable scheduling algorithms
for a given taskset, which is in fact the most common situation in real-time systems
design. '
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: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Alexander
full_name: Kößler, Alexander
last_name: Kößler
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. Automated competitive analysis
of real time scheduling with graph games. Real-Time Systems. 2018;54(1):166-207.
doi:10.1007/s11241-017-9293-4
apa: Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2018). Automated
competitive analysis of real time scheduling with graph games. Real-Time Systems.
Springer. https://doi.org/10.1007/s11241-017-9293-4
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich
Schmid. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.”
Real-Time Systems. Springer, 2018. https://doi.org/10.1007/s11241-017-9293-4.
ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “Automated competitive
analysis of real time scheduling with graph games,” Real-Time Systems,
vol. 54, no. 1. Springer, pp. 166–207, 2018.
ista: Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2018. Automated competitive
analysis of real time scheduling with graph games. Real-Time Systems. 54(1), 166–207.
mla: Chatterjee, Krishnendu, et al. “Automated Competitive Analysis of Real Time
Scheduling with Graph Games.” Real-Time Systems, vol. 54, no. 1, Springer,
2018, pp. 166–207, doi:10.1007/s11241-017-9293-4.
short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, Real-Time Systems 54
(2018) 166–207.
date_created: 2018-12-11T11:48:14Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-27T12:52:38Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/s11241-017-9293-4
ec_funded: 1
external_id:
isi:
- '000419955500006'
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creator: system
date_created: 2018-12-12T10:17:14Z
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language:
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month: '01'
oa: 1
oa_version: Published Version
page: 166 - 207
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Real-Time Systems
publication_status: published
publisher: Springer
publist_id: '6929'
pubrep_id: '960'
quality_controlled: '1'
related_material:
record:
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scopus_import: '1'
status: public
title: Automated competitive analysis of real time scheduling with graph games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2018'
...
---
_id: '52'
abstract:
- lang: eng
text: In this thesis we will discuss systems of point interacting fermions, their
stability and other spectral properties. Whereas for bosons a point interacting
system is always unstable this ques- tion is more subtle for a gas of two species
of fermions. In particular the answer depends on the mass ratio between these
two species. Most of this work will be focused on the N + M model which consists
of two species of fermions with N, M particles respectively which interact via
point interactions. We will introduce this model using a formal limit and discuss
the N + 1 system in more detail. In particular, we will show that for mass ratios
above a critical one, which does not depend on the particle number, the N + 1
system is stable. In the context of this model we will prove rigorous versions
of Tan relations which relate various quantities of the point-interacting model.
By restricting the N + 1 system to a box we define a finite density model with
point in- teractions. In the context of this system we will discuss the energy
change when introducing a point-interacting impurity into a system of non-interacting
fermions. We will see that this change in energy is bounded independently of the
particle number and in particular the bound only depends on the density and the
scattering length. As another special case of the N + M model we will show stability
of the 2 + 2 model for mass ratios in an interval around one. Further we will
investigate a different model of point interactions which was discussed before
in the literature and which is, contrary to the N + M model, not given by a limiting
procedure but is based on a Dirichlet form. We will show that this system behaves
trivially in the thermodynamic limit, i.e. the free energy per particle is the
same as the one of the non-interacting system.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
citation:
ama: Moser T. Point interactions in systems of fermions. 2018. doi:10.15479/AT:ISTA:th_1043
apa: Moser, T. (2018). Point interactions in systems of fermions. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1043
chicago: Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of
Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1043.
ieee: T. Moser, “Point interactions in systems of fermions,” Institute of Science
and Technology Austria, 2018.
ista: Moser T. 2018. Point interactions in systems of fermions. Institute of Science
and Technology Austria.
mla: Moser, Thomas. Point Interactions in Systems of Fermions. Institute
of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1043.
short: T. Moser, Point Interactions in Systems of Fermions, Institute of Science
and Technology Austria, 2018.
date_created: 2018-12-11T11:44:22Z
date_published: 2018-09-04T00:00:00Z
date_updated: 2023-09-27T12:34:14Z
day: '04'
ddc:
- '515'
- '530'
- '519'
degree_awarded: PhD
department:
- _id: RoSe
doi: 10.15479/AT:ISTA:th_1043
file:
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checksum: fbd8c747d148b468a21213b7cf175225
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creator: dernst
date_created: 2019-04-09T07:45:38Z
date_updated: 2020-07-14T12:46:37Z
file_id: '6256'
file_name: 2018_Thesis_Moser.pdf
file_size: 851164
relation: main_file
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checksum: c28e16ecfc1126d3ce324ec96493c01e
content_type: application/zip
creator: dernst
date_created: 2019-04-09T07:45:38Z
date_updated: 2020-07-14T12:46:37Z
file_id: '6257'
file_name: 2018_Thesis_Moser_Source.zip
file_size: 1531516
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file_date_updated: 2020-07-14T12:46:37Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '115'
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8002'
pubrep_id: '1043'
related_material:
record:
- id: '5856'
relation: part_of_dissertation
status: public
- id: '154'
relation: part_of_dissertation
status: public
- id: '1198'
relation: part_of_dissertation
status: public
- id: '741'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: Point interactions in systems of fermions
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '913'
abstract:
- lang: eng
text: Coordinated cell polarization in developing tissues is a recurrent theme in
multicellular organisms. In plants, a directional distribution of the plant hormone
auxin is at the core of many developmental programs. A feedback regulation of
auxin on the polarized localization of PIN auxin transporters in individual cells
has been proposed as a self-organizing mechanism for coordinated tissue polarization,
but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport
remain unknown. We performed a microarray-based approach to find regulators of
the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified
a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs
(PATL). Here, we show that PATLs are expressed in partially overlapping cells
types in different tissues going through mitosis or initiating differentiation
programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis
embryos, primary roots, lateral root primordia, and developing stomata. Higher
order patl mutants display reduced PIN1 repolarization in response to auxin, shorter
root apical meristem, and drastic defects in embryo and seedling development.
This suggests PATLs redundantly play a crucial role in polarity and patterning
in Arabidopsis.
article_number: jcs.204198
article_processing_charge: No
author:
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Cecilia
full_name: Rodríguez Furlán, Cecilia
last_name: Rodríguez Furlán
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Lorena
full_name: Norambuena, Lorena
last_name: Norambuena
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS
are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis
thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198
apa: Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L.,
& Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation
and plant development in Arabidopsis thaliana. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.204198
chicago: Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer,
Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated
PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.
ieee: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and
J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant
development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131,
no. 2. Company of Biologists, 2018.
ista: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J.
2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.
mla: Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation
and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198.
short: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J.
Friml, Journal of Cell Science 131 (2018).
date_created: 2018-12-11T11:49:10Z
date_published: 2018-01-29T00:00:00Z
date_updated: 2023-09-26T15:47:50Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1242/jcs.204198
ec_funded: 1
external_id:
isi:
- '000424842400019'
file:
- access_level: open_access
checksum: bf156c20a4f117b4b932370d54cbac8c
content_type: application/pdf
creator: dernst
date_created: 2019-04-12T08:46:32Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6299'
file_name: 2017_adamowski_PATELLINS_are.pdf
file_size: 14925985
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 131'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
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: Journal of Cell Science
publication_identifier:
issn:
- '00219533'
publication_status: published
publisher: Company of Biologists
publist_id: '6530'
pubrep_id: '988'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 131
year: '2018'
...
---
_id: '69'
abstract:
- lang: eng
text: 'A qubit, a unit of quantum information, is essentially any quantum mechanical
two-level system which can be coherently controlled. Still, to be used for computation,
it has to fulfill criteria. Qubits, regardless of the system in which they are
realized, suffer from decoherence. This leads to loss of the information stored
in the qubit. The upper bound of the time scale on which decoherence happens is
set by the spin relaxation time. In this thesis I studied a two-level system consisting
of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire.
Such Ge hut wires have emerged as a promising material system for the realization
of spin qubits, due to the combination of two significant properties: long spin
coherence time as expected for group IV semiconductors due to the low hyperfine
interaction and a strong valence band spin-orbit coupling. Here, I present how
to fabricate quantum dot devices suitable for electrical transport measurements.
Coupled quantum dot devices allowed the realization of a charge sensor, which
is electrostatically and tunnel coupled to a quantum dot. By integrating the charge
sensor into a radio-frequency reflectometry setup, I performed for the first time
single-shot readout measurements of hole spins and extracted the hole spin relaxation
times in Ge hut wires.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
citation:
ama: Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires.
2018. doi:10.15479/AT:ISTA:TH_1047
apa: Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in
Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047
chicago: Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge
Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047.
ieee: L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,”
Institute of Science and Technology Austria, 2018.
ista: Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut
wires. Institute of Science and Technology Austria.
mla: Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut
Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047.
short: L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '01'
ddc:
- '530'
- '600'
degree_awarded: PhD
department:
- _id: GeKa
- _id: GradSch
doi: 10.15479/AT:ISTA:TH_1047
file:
- access_level: open_access
checksum: c570b656e30749cd65b1c7e13a9ce0a8
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:00:40Z
date_updated: 2020-07-14T12:47:44Z
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language:
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publication_identifier:
issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7985'
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related_material:
record:
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relation: part_of_dissertation
status: public
- id: '840'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Charge sensing and spin relaxation times of holes in Ge 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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '324'
abstract:
- lang: eng
text: Neuronal networks in the brain consist of two main types of neuron, glutamatergic
principal neurons and GABAergic interneurons. Although these interneurons only
represent 10–20% of the whole population, they mediate feedback and feedforward
inhibition and are involved in the generation of high-frequency network oscillations.
A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing
(PV+) subtypes, is the speed of signaling at their output synapse across species
and brain regions. Several molecular and subcellular factors may underlie the
submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q
type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors
of exocytosis. However, whether the molecular identity of the release sensor contributes
to these signaling properties remains unclear. Besides, these interneurons are
mainly show depression in response to train of stimuli. How could they keep sufficient
release to control the activity of postsynaptic principal neurons during high
network activity, is largely elusive. For my Ph.D. work, we firstly examined the
Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC)
synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively
expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched
in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked
release to ~10% compared to the wild-type control, identifying Syt2 as the major
Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed
Syt2 triggered release with shorter latency and higher temporal precision, and
mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of
Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber
stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse
ensures fast feedforward inhibition in cerebellar microcircuits. Additionally,
we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic
transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates
asynchronous transmitter release and facilitation at synapses. However, it is
strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output
synapses of these neurons produce only minimal asynchronous release and show depression
rather than facilitation. How could Syt7, a facilitation sensor, contribute to
the depressed inhibitory synaptic transmission needs to be further investigated
and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes
to asynchronous release, pool replenishment and facilitation. In combination,
these three effects ensure efficient transmitter release during high‑frequency
activity and guarantee frequency independence of inhibition. Taken together, our
results confirmed that Syt2, which has the fastest kinetic properties among all
synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic
transmission, contributing to the speed and temporal precision of transmitter
release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin
member in the output synapses of cerebellar BCs, is used for ensuring efficient
inhibitor synaptic transmission during high activity.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter
release. 2018. doi:10.15479/AT:ISTA:th_997
apa: Chen, C. (2018). Synaptotagmins ensure speed and efficiency of inhibitory
neurotransmitter release. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_997
chicago: Chen, Chong. “Synaptotagmins Ensure Speed and Efficiency of Inhibitory
Neurotransmitter Release.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:th_997.
ieee: C. Chen, “Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter
release,” Institute of Science and Technology Austria, 2018.
ista: Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter
release. Institute of Science and Technology Austria.
mla: Chen, Chong. Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter
Release. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_997.
short: C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter
Release, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:49Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-27T12:26:03Z
day: '01'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: PeJo
doi: 10.15479/AT:ISTA:th_997
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creator: system
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page: '110'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7541'
pubrep_id: '997'
related_material:
record:
- id: '1117'
relation: part_of_dissertation
status: public
- id: '749'
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: Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release
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: '2018'
...
---
_id: '742'
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 (Formula presented.) there
exists a point (Formula presented.) that is contained in the images of a positive
fraction (Formula presented.) of the d-cells of X. More generally, the conclusion
holds if (Formula presented.) is replaced by any d-dimensional piecewise-linear
manifold M, with a constant (Formula presented.) that depends only on d and on
the expansion properties of X, but not on M.'
article_processing_charge: Yes (via OA deal)
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. Geometriae
Dedicata. 2018;195(1):307–317. doi:10.1007/s10711-017-0291-4
apa: Dotterrer, D., Kaufman, T., & Wagner, U. (2018). On expansion and topological
overlap. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0291-4
chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological
Overlap.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0291-4.
ieee: D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,”
Geometriae Dedicata, vol. 195, no. 1. Springer, pp. 307–317, 2018.
ista: Dotterrer D, Kaufman T, Wagner U. 2018. On expansion and topological overlap.
Geometriae Dedicata. 195(1), 307–317.
mla: Dotterrer, Dominic, et al. “On Expansion and Topological Overlap.” Geometriae
Dedicata, vol. 195, no. 1, Springer, 2018, pp. 307–317, doi:10.1007/s10711-017-0291-4.
short: D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.
date_created: 2018-12-11T11:48:16Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-27T12:29:57Z
day: '01'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.1007/s10711-017-0291-4
external_id:
isi:
- '000437122700017'
file:
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checksum: d2f70fc132156504aa4c626aa378a7ab
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date_updated: 2020-07-14T12:47:58Z
file_id: '5835'
file_name: s10711-017-0291-4.pdf
file_size: 412486
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file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 195'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 307–317
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '6925'
pubrep_id: '912'
quality_controlled: '1'
related_material:
record:
- id: '1378'
relation: earlier_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: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 195
year: '2018'
...
---
_id: '70'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process in a critical
scaling parametrized by a≥0, which creates a shock in the particle density of
order aT−1/3, T the observation time. When starting from step initial data, we
provide bounds on the limiting law which in particular imply that in the double
limit lima→∞limT→∞ one recovers the product limit law and the degeneration of
the correlation length observed at shocks of order 1. This result is shown to
apply to a general last-passage percolation model. We also obtain bounds on the
two-point functions of several airy processes.
article_processing_charge: No
article_type: original
author:
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Nejjar P. Transition to shocks in TASEP and decoupling of last passage times.
Latin American Journal of Probability and Mathematical Statistics. 2018;15(2):1311-1334.
doi:10.30757/ALEA.v15-49
apa: Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v15-49
chicago: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada, 2018. https://doi.org/10.30757/ALEA.v15-49.
ieee: P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,”
Latin American Journal of Probability and Mathematical Statistics, vol.
15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.
ista: Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics. 15(2),
1311–1334.
mla: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics,
vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34,
doi:10.30757/ALEA.v15-49.
short: P. Nejjar, Latin American Journal of Probability and Mathematical Statistics
15 (2018) 1311–1334.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-10-10T13:11:29Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
- _id: JaMa
doi: 10.30757/ALEA.v15-49
ec_funded: 1
external_id:
arxiv:
- '1705.08836'
isi:
- '000460475800022'
file:
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checksum: 2ded46aa284a836a8cbb34133a64f1cb
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T09:44:10Z
date_updated: 2020-07-14T12:47:46Z
file_id: '5981'
file_name: 2018_ALEA_Nejjar.pdf
file_size: 394851
relation: main_file
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has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1311-1334
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Latin American Journal of Probability and Mathematical Statistics
publication_identifier:
issn:
- 1980-0436
publication_status: published
publisher: Instituto Nacional de Matematica Pura e Aplicada
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to shocks in TASEP and decoupling of last passage times
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '44'
abstract:
- lang: eng
text: 'Recent realization of a kinetically constrained chain of Rydberg atoms by
Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation
of unusual revivals in the many-body quantum dynamics. In our previous work [C.
J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to
the existence of “quantum scarred” eigenstates in the many-body spectrum of the
experimentally realized model. Here, we present a detailed study of the eigenstate
properties of the same model. We find that the majority of the eigenstates exhibit
anomalous thermalization: the observable expectation values converge to their
Gibbs ensemble values, but parametrically slower compared to the predictions of
the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum,
we identify nonergodic eigenstates that strongly violate the ETH, whose number
grows polynomially with system size. Previously, the same eigenstates were identified
via large overlaps with certain product states, and were used to explain the revivals
observed in experiment. Here, we find that these eigenstates, in addition to highly
atypical expectation values of local observables, also exhibit subthermal entanglement
entropy that scales logarithmically with the system size. Moreover, we identify
an additional class of quantum scarred eigenstates, and discuss their manifestations
in the dynamics starting from initial product states. We use forward scattering
approximation to describe the structure and physical properties of quantum scarred
eigenstates. Finally, we discuss the stability of quantum scars to various perturbations.
We observe that quantum scars remain robust when the introduced perturbation is
compatible with the forward scattering approximation. In contrast, the perturbations
which most efficiently destroy quantum scars also lead to the restoration of “canonical”
thermalization.'
acknowledged_ssus:
- _id: ScienComp
article_number: '155134'
article_processing_charge: No
author:
- first_name: C J
full_name: Turner, C J
last_name: Turner
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: D A
full_name: Abanin, D A
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Z
full_name: Papić, Z
last_name: Papić
citation:
ama: 'Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates
in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability
to perturbations. Physical Review B. 2018;98(15). doi:10.1103/PhysRevB.98.155134'
apa: 'Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., & Papić, Z.
(2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown
of thermalization, and stability to perturbations. Physical Review B. American
Physical Society. https://doi.org/10.1103/PhysRevB.98.155134'
chicago: 'Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić.
“Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown
of Thermalization, and Stability to Perturbations.” Physical Review B.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.155134.'
ieee: 'C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum
scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization,
and stability to perturbations,” Physical Review B, vol. 98, no. 15. American
Physical Society, 2018.'
ista: 'Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred
eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization,
and stability to perturbations. Physical Review B. 98(15), 155134.'
mla: 'Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain:
Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical
Review B, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:10.1103/PhysRevB.98.155134.'
short: C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review
B 98 (2018).
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-22T00:00:00Z
date_updated: 2023-10-10T13:28:49Z
day: '22'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.98.155134
external_id:
arxiv:
- '1806.10933'
isi:
- '000447919100001'
intvolume: ' 98'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10933
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '8010'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown
of thermalization, and stability to perturbations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '328'
abstract:
- lang: eng
text: The drag of turbulent flows can be drastically decreased by adding small amounts
of high molecular weight polymers. While drag reduction initially increases with
polymer concentration, it eventually saturates to what is known as the maximum
drag reduction (MDR) asymptote; this asymptote is generally attributed to the
dynamics being reduced to a marginal yet persistent state of subdued turbulent
motion. Contrary to this accepted view, we show that, for an appropriate choice
of parameters, polymers can reduce the drag beyond the suggested asymptotic limit,
eliminating turbulence and giving way to laminar flow. At higher polymer concentrations,
however, the laminar state becomes unstable, resulting in a fluctuating flow with
the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic
state is hence dynamically disconnected from ordinary turbulence. © 2018 American
Physical Society.
acknowledged_ssus:
- _id: SSU
acknowledgement: The authors thank Philipp Maier and the IST Austria workshop for
their dedicated technical support.
article_number: '124501'
article_processing_charge: No
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer
drag reduction. Physical Review Letters. 2018;120(12). doi:10.1103/PhysRevLett.120.124501
apa: Choueiri, G. H., Lopez Alonso, J. M., & Hof, B. (2018). Exceeding the asymptotic
limit of polymer drag reduction. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.120.124501
chicago: Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the
Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters. American
Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.124501.
ieee: G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic
limit of polymer drag reduction,” Physical Review Letters, vol. 120, no.
12. American Physical Society, 2018.
ista: Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit
of polymer drag reduction. Physical Review Letters. 120(12), 124501.
mla: Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag
Reduction.” Physical Review Letters, vol. 120, no. 12, 124501, American
Physical Society, 2018, doi:10.1103/PhysRevLett.120.124501.
short: G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).
date_created: 2018-12-11T11:45:51Z
date_published: 2018-03-19T00:00:00Z
date_updated: 2023-10-10T13:27:44Z
day: '19'
department:
- _id: BjHo
doi: 10.1103/PhysRevLett.120.124501
ec_funded: 1
external_id:
isi:
- '000427804000005'
intvolume: ' 120'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.06271
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7537'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exceeding the asymptotic limit of polymer drag reduction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2018'
...
---
_id: '136'
abstract:
- lang: eng
text: Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes
equation may provide deep insights into fluid turbulence. In this article, we
present a combined experimental and numerical study exploring the dynamical role
of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent,
electromagnetically driven, shallow fluid layer. Identifying instants when turbulent
evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional
model of the flow. We establish the dynamical relevance of these unstable equilibria
by showing that they are closely visited by the turbulent flow. We also establish
the dynamical relevance of unstable manifolds by verifying that they are shadowed
by turbulent trajectories departing from the neighborhoods of unstable equilibria
over large distances in state space.
article_processing_charge: No
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jeffrey
full_name: Tithof, Jeffrey
last_name: Tithof
- first_name: Roman
full_name: Grigoriev, Roman
last_name: Grigoriev
- first_name: Michael
full_name: Schatz, Michael
last_name: Schatz
citation:
ama: Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E.
2018;98(2). doi:10.1103/PhysRevE.98.023105
apa: Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria
and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical
Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105
chicago: Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz.
“Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like
Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.
ieee: B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and
invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical
Review E, vol. 98, no. 2. American Physical Society, 2018.
ista: Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).
mla: Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional
Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical
Society, 2018, doi:10.1103/PhysRevE.98.023105.
short: B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).
date_created: 2018-12-11T11:44:49Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2023-10-10T13:29:10Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.98.023105
external_id:
arxiv:
- '1808.02088'
isi:
- '000441466800010'
intvolume: ' 98'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.02088
month: '08'
oa: 1
oa_version: Submitted Version
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like
flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
that regulates membrane trafficking through the Golgi apparatus. The clinical
phenotype associated with mutations in various TRAPP subunits has allowed elucidation
of their functions in specific tissues. The role of some subunits in human disease,
however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
We aimed to expand the range of neurodevelopmental disorders associated with mutations
in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
Linkage and homozygosity mapping and candidate gene analysis were used to identify
homozygous mutations in families. Patient fibroblasts were used to study splicing
defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
disorder characterised by microcephaly, epilepsy and autistic features, and showed
splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
displaying decreased head size and neuronal hyperexcitability, leading to a lower
seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
full_name: Marin Valencia, Isaac
last_name: Marin Valencia
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Gifty
full_name: Bhat, Gifty
last_name: Bhat
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Valentina
full_name: Stanley, Valentina
last_name: Stanley
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Jeremy
full_name: Gleeson, Jeremy
last_name: Gleeson
- first_name: Farhad
full_name: Imam, Farhad
last_name: Imam
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54.
doi:10.1136/jmedgenet-2017-104627
apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
with a neurodevelopmental disorder characterised by microcephaly epilepsy and
autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627
chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group,
2018. https://doi.org/10.1136/jmedgenet-2017-104627.
ieee: I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B
associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ
Publishing Group, pp. 48–54, 2018.
ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features. Journal
of Medical Genetics. 55(1), 48–54.
mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing
Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.
short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-10-16T09:55:43Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
isi:
- '000418199800007'
pmid:
- '28626029'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
issn:
- 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...
---
_id: '284'
abstract:
- lang: eng
text: "Borel probability measures living on metric spaces are fundamental\r\nmathematical
objects. There are several meaningful distance functions that make the collection
of the probability measures living on a certain space a metric space. We are interested
in the description of the structure of the isometries of such metric spaces. We
overview some of the recent results of the topic and we also provide some new
ones concerning the Wasserstein distance. More specifically, we consider the space
of all Borel probability measures on the unit sphere of a Euclidean space endowed
with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the
action of a Wasserstein isometry on the set of Dirac measures is induced by an
isometry of the underlying unit sphere."
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office, NKFIH (grant
no. K124152).
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Maps on probability measures preserving certain distances - a
survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80.
doi:10.14232/actasm-018-753-y
apa: Virosztek, D. (2018). Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. Springer
Nature. https://doi.org/10.14232/actasm-018-753-y
chicago: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer
Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.
ieee: D. Virosztek, “Maps on probability measures preserving certain distances -
a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84,
no. 1–2. Springer Nature, pp. 65–80, 2018.
ista: Virosztek D. 2018. Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.
mla: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol.
84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.
short: D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-04T00:00:00Z
date_updated: 2023-10-16T10:29:22Z
day: '04'
department:
- _id: LaEr
doi: 10.14232/actasm-018-753-y
ec_funded: 1
external_id:
arxiv:
- '1802.03305'
intvolume: ' 84'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.03305
month: '06'
oa: 1
oa_version: Preprint
page: 65 - 80
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Acta Scientiarum Mathematicarum
publication_identifier:
eissn:
- 2064-8316
issn:
- 0001-6969
publication_status: published
publisher: Springer Nature
publist_id: '7615'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maps on probability measures preserving certain distances - a survey and some
new results
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...
---
_id: '180'
abstract:
- lang: eng
text: In this paper we define and study the classical Uniform Electron Gas (UEG),
a system of infinitely many electrons whose density is constant everywhere in
space. The UEG is defined differently from Jellium, which has a positive constant
background but no constraint on the density. We prove that the UEG arises in Density
Functional Theory in the limit of a slowly varying density, minimizing the indirect
Coulomb energy. We also construct the quantum UEG and compare it to the classical
UEG at low density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme
(grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by
the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National
Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged."
article_processing_charge: No
article_type: original
author:
- first_name: Mathieu
full_name: Lewi, Mathieu
last_name: Lewi
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64
apa: Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the
uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique. https://doi.org/10.5802/jep.64
chicago: Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics
of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.
ieee: M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform
electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5.
Ecole Polytechnique, pp. 79–116, 2018.
ista: Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.
mla: Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.”
Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique,
2018, pp. 79–116, doi:10.5802/jep.64.
short: M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques
5 (2018) 79–116.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-10-17T08:05:28Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.5802/jep.64
ec_funded: 1
external_id:
arxiv:
- '1705.10676'
file:
- access_level: open_access
checksum: 1ba7cccdf3900f42c4f715ae75d6813c
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:38:18Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5726'
file_name: 2018_JournaldeLecoleMath_Lewi.pdf
file_size: 843938
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 116
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_identifier:
eissn:
- 2270-518X
issn:
- 2429-7100
publication_status: published
publisher: Ecole Polytechnique
publist_id: '7741'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics of the uniform electron gas
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '163'
abstract:
- lang: eng
text: For ultrafast fixation of biological samples to avoid artifacts, high-pressure
freezing (HPF) followed by freeze substitution (FS) is preferred over chemical
fixation at room temperature. After HPF, samples are maintained at low temperature
during dehydration and fixation, while avoiding damaging recrystallization. This
is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample
agitation during FS dramatically reduces the necessary time. Then, in 2015, we
(H.G. and S.R.) introduced an agitation module into the cryochamber of an automated
FS unit and demonstrated that the preparation of algae could be shortened from
days to a couple of hours. We argued that variability in the processing, reproducibility,
and safety issues are better addressed using automated FS units. For dissemination,
we started low-cost manufacturing of agitation modules for two of the most widely
used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from
Leica Microsystems, using three dimensional (3D)-printing of the major components.
To test them, several labs independently used the modules on a wide variety of
specimens that had previously been processed by manual agitation, or without agitation.
We demonstrate that automated processing with sample agitation saves time, increases
flexibility with respect to sample requirements and protocols, and produces data
of at least as good quality as other approaches.
article_processing_charge: No
article_type: original
author:
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Helmuth
full_name: Goldammer, Helmuth
last_name: Goldammer
- first_name: Christine
full_name: Richardson, Christine
last_name: Richardson
- first_name: Martin
full_name: Goldberg, Martin
last_name: Goldberg
- first_name: Timothy
full_name: Hawkins, Timothy
last_name: Hawkins
- first_name: Elena
full_name: Hollergschwandtner, Elena
id: 3C054040-F248-11E8-B48F-1D18A9856A87
last_name: Hollergschwandtner
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Sebastian
full_name: Antreich, Sebastian
last_name: Antreich
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
citation:
ama: 'Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means
to accelerate automated freeze substitution. Journal of Histochemistry and
Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698'
apa: 'Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl,
E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated
freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE
Publications. https://doi.org/10.1369/0022155418786698'
chicago: 'Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg,
Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof.
“Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.”
Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.'
ieee: 'S. Reipert et al., “Agitation modules: Flexible means to accelerate
automated freeze substitution,” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.'
ista: 'Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann
W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate
automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12),
903–921.'
mla: 'Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate
Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.'
short: S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl,
W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry
66 (2018) 903–921.
date_created: 2018-12-11T11:44:57Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-10-17T08:42:24Z
day: '01'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1369/0022155418786698
external_id:
isi:
- '000452277700005'
pmid:
- '29969056'
intvolume: ' 66'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1369/0022155418786698
month: '12'
oa: 1
oa_version: Published Version
page: 903-921
pmid: 1
publication: Journal of Histochemistry and Cytochemistry
publication_identifier:
issn:
- 0022-1554
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Agitation modules: Flexible means to accelerate automated freeze substitution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2018'
...
---
_id: '6012'
abstract:
- lang: eng
text: We present an approach to identify concise equations from data using a shallow
neural network approach. In contrast to ordinary black-box regression, this approach
allows understanding functional relations and generalizing them from observed
data to unseen parts of the parameter space. We show how to extend the class of
learnable equations for a recently proposed equation learning network to include
divisions, and we improve the learning and model selection strategy to be useful
for challenging real-world data. For systems governed by analytical expressions,
our method can in many cases identify the true underlying equation and extrapolate
to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum
system, where only 2 random rollouts are required to learn the forward dynamics
and successfully achieve the swing-up task.
article_processing_charge: No
author:
- first_name: Subham
full_name: Sahoo, Subham
last_name: Sahoo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: 'Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control.
In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:4442-4450.'
apa: 'Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for
extrapolation and control. In Proceedings of the 35th International Conference
on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research
Press.'
chicago: Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations
for Extrapolation and Control.” In Proceedings of the 35th International Conference
on Machine Learning, 80:4442–50. ML Research Press, 2018.
ieee: S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation
and control,” in Proceedings of the 35th International Conference on Machine
Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.
ista: 'Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation
and control. Proceedings of the 35th International Conference on Machine Learning.
ICML: International Conference on Machine Learning vol. 80, 4442–4450.'
mla: Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings
of the 35th International Conference on Machine Learning, vol. 80, ML Research
Press, 2018, pp. 4442–50.
short: S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International
Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2019-02-14T15:21:07Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T09:50:53Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1806.07259'
isi:
- '000683379204058'
intvolume: ' 80'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.07259
month: '02'
oa: 1
oa_version: Preprint
page: 4442-4450
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/
scopus_import: '1'
status: public
title: Learning equations for extrapolation and control
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '6011'
abstract:
- lang: eng
text: 'We establish a data-dependent notion of algorithmic stability for Stochastic
Gradient Descent (SGD), and employ it to develop novel generalization bounds.
This is in contrast to previous distribution-free algorithmic stability results
for SGD which depend on the worst-case constants. By virtue of the data-dependent
argument, our bounds provide new insights into learning with SGD on convex and
non-convex problems. In the convex case, we show that the bound on the generalization
error depends on the risk at the initialization point. In the non-convex case,
we prove that the expected curvature of the objective function around the initialization
point has crucial influence on the generalization error. In both cases, our results
suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization.
As a corollary, our results allow us to show optimistic generalization bounds
that exhibit fast convergence rates for SGD subject to a vanishing empirical risk
and low noise of stochastic gradient. '
article_processing_charge: No
author:
- first_name: Ilja
full_name: Kuzborskij, Ilja
last_name: Kuzborskij
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent.
In: Proceedings of the 35 Th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:2815-2824.'
apa: 'Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic
gradient descent. In Proceedings of the 35 th International Conference on Machine
Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.'
chicago: Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic
Gradient Descent.” In Proceedings of the 35 Th International Conference on
Machine Learning, 80:2815–24. ML Research Press, 2018.
ieee: I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient
descent,” in Proceedings of the 35 th International Conference on Machine Learning,
Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.
ista: 'Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient
descent. Proceedings of the 35 th International Conference on Machine Learning.
ICML: International Conference on Machine Learning vol. 80, 2815–2824.'
mla: Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic
Gradient Descent.” Proceedings of the 35 Th International Conference on Machine
Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.
short: I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference
on Machine Learning, ML Research Press, 2018, pp. 2815–2824.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2019-02-14T14:51:57Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T09:51:13Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1703.01678'
isi:
- '000683379202095'
intvolume: ' 80'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.01678
month: '02'
oa: 1
oa_version: Preprint
page: 2815-2824
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the 35 th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Data-dependent stability of stochastic gradient descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '6589'
abstract:
- lang: eng
text: Distributed training of massive machine learning models, in particular deep
neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace.
Several families of communication-reduction methods, such as quantization, large-batch
methods, and gradient sparsification, have been proposed. To date, gradient sparsification
methods--where each node sorts gradients by magnitude, and only communicates a
subset of the components, accumulating the rest locally--are known to yield some
of the largest practical gains. Such methods can reduce the amount of communication
per step by up to \emph{three orders of magnitude}, while preserving model accuracy.
Yet, this family of methods currently has no theoretical justification. This is
the question we address in this paper. We prove that, under analytic assumptions,
sparsifying gradients by magnitude with local error correction provides convergence
guarantees, for both convex and non-convex smooth objectives, for data-parallel
SGD. The main insight is that sparsification methods implicitly maintain bounds
on the maximum impact of stale updates, thanks to selection by magnitude. Our
analysis and empirical validation also reveal that these methods do require analytical
conditions to converge well, justifying existing heuristics.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
citation:
ama: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. The convergence of sparsified gradient methods. In: Advances in Neural Information
Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems
Foundation; 2018:5973-5983.'
apa: 'Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat,
S., & Renggli, C. (2018). The convergence of sparsified gradient methods.
In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018,
pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.'
chicago: Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov,
Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.”
In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83.
Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat,
and C. Renggli, “The convergence of sparsified gradient methods,” in Advances
in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol.
Volume 2018, pp. 5973–5983.
ista: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information
Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems
vol. Volume 2018, 5973–5983.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.”
Advances in Neural Information Processing Systems 31, vol. Volume 2018,
Neural Information Processing Systems Foundation, 2018, pp. 5973–83.
short: D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat,
C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural
Information Processing Systems Foundation, 2018, pp. 5973–5983.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-27T09:32:55Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:20Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1809.10505'
isi:
- '000461852000047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.10505
month: '12'
oa: 1
oa_version: Preprint
page: 5973-5983
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Neural Information Processing Systems 31
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of sparsified gradient methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: Volume 2018
year: '2018'
...
---
_id: '7'
abstract:
- lang: eng
text: Animal social networks are shaped by multiple selection pressures, including
the need to ensure efficient communication and functioning while simultaneously
limiting disease transmission. Social animals could potentially further reduce
epidemic risk by altering their social networks in the presence of pathogens,
yet there is currently no evidence for such pathogen-triggered responses. We tested
this hypothesis experimentally in the ant Lasius niger using a combination of
automated tracking, controlled pathogen exposure, transmission quantification,
and temporally explicit simulations. Pathogen exposure induced behavioral changes
in both exposed ants and their nestmates, which helped contain the disease by
reinforcing key transmission-inhibitory properties of the colony's contact network.
This suggests that social network plasticity in response to pathogens is an effective
strategy for mitigating the effects of disease in social groups.
acknowledgement: This project was funded by two European Research Council Advanced
Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science
Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research
Council Starting Grant (SocialVaccines, 243071) to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. Science.
2018;362(6417):941-945. doi:10.1126/science.aat4793
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Science. AAAS. https://doi.org/10.1126/science.aat4793
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect,”
Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect. Science.
362(6417), 941–945.
mla: Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission
in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45,
doi:10.1126/science.aat4793.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science
362 (2018) 941–945.
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-23T00:00:00Z
date_updated: 2023-10-17T11:50:05Z
day: '23'
department:
- _id: SyCr
doi: 10.1126/science.aat4793
ec_funded: 1
external_id:
isi:
- '000451124500041'
intvolume: ' 362'
isi: 1
issue: '6417'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 941 - 945
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Science
publication_identifier:
issn:
- 1095-9203
publication_status: published
publisher: AAAS
publist_id: '8049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/
record:
- id: '13055'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 362
year: '2018'
...
---
_id: '19'
abstract:
- lang: eng
text: Bacteria regulate genes to survive antibiotic stress, but regulation can be
far from perfect. When regulation is not optimal, mutations that change gene expression
can contribute to antibiotic resistance. It is not systematically understood to
what extent natural gene regulation is or is not optimal for distinct antibiotics,
and how changes in expression of specific genes quantitatively affect antibiotic
resistance. Here we discover a simple quantitative relation between fitness, gene
expression, and antibiotic potency, which rationalizes our observation that a
multitude of genes and even innate antibiotic defense mechanisms have expression
that is critically nonoptimal under antibiotic treatment. First, we developed
a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression
and knockout libraries, finding that resistance to a range of 31 antibiotics could
result from changing expression of a large and functionally diverse set of genes,
in a primarily but not exclusively drug-specific manner. Second, by synthetically
controlling the expression of single-drug and multidrug resistance genes, we observed
that their fitness-expression functions changed dramatically under antibiotic
treatment in accordance with a log-sensitivity relation. Thus, because many genes
are nonoptimally expressed under antibiotic treatment, many regulatory mutations
can contribute to resistance by altering expression and by activating latent defenses.
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Palmer, Adam
last_name: Palmer
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential
for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684.
doi:10.1093/molbev/msy163
apa: Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression
creates latent potential for antibiotic resistance. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msy163
chicago: Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression
Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and
Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.
ieee: A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates
latent potential for antibiotic resistance,” Molecular Biology and Evolution,
vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.
ista: Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent
potential for antibiotic resistance. Molecular Biology and Evolution. 35(11),
2669–2684.
mla: Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for
Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11,
Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.
short: A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018)
2669–2684.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-10-17T11:51:06Z
day: '28'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/molbev/msy163
external_id:
isi:
- '000452567200006'
pmid:
- '30169679'
intvolume: ' 35'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30169679
month: '08'
oa: 1
oa_version: Submitted Version
page: 2669 - 2684
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '8036'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonoptimal gene expression creates latent potential for antibiotic resistance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2018'
...
---
_id: '6'
abstract:
- lang: eng
text: Lesion and electrode location verification are traditionally done via histological
examination of stained brain slices, a time-consuming procedure that requires
manual estimation. Here, we describe a simple, straightforward method for quantifying
lesions and locating electrodes in the brain that is less laborious and yields
more detailed results. Whole brains are stained with osmium tetroxide, embedded
in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes
of the brains with resolutions and virtual section thicknesses dependent on the
sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively).
Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays,
electrolytic lesions, and silicon probes can also be localized. Free and proprietary
software allows experimenters to examine the sample volume from any plane and
segment the volume manually or automatically. Because this method generates whole
brain volume, lesions and electrodes can be quantified to a much higher degree
than in current methods, which will help standardize comparisons within and across
studies.
article_processing_charge: No
author:
- first_name: Javier
full_name: Masís, Javier
last_name: Masís
- first_name: David
full_name: Mankus, David
last_name: Mankus
- first_name: Steffen
full_name: Wolff, Steffen
last_name: Wolff
- first_name: Grigori
full_name: Guitchounts, Grigori
last_name: Guitchounts
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: David
full_name: Cox, David
last_name: Cox
citation:
ama: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based
method for characterising lesions and locating electrodes in small animal brains.
Journal of visualized experiments. 2018;141. doi:10.3791/58585
apa: Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox,
D. (2018). A micro-CT-based method for characterising lesions and locating electrodes
in small animal brains. Journal of Visualized Experiments. MyJove Corporation.
https://doi.org/10.3791/58585
chicago: Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian
A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and
Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments.
MyJove Corporation, 2018. https://doi.org/10.3791/58585.
ieee: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A
micro-CT-based method for characterising lesions and locating electrodes in small
animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation,
2018.
ista: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based
method for characterising lesions and locating electrodes in small animal brains.
Journal of visualized experiments. 141.
mla: Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and
Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments,
vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.
short: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal
of Visualized Experiments 141 (2018).
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-08T00:00:00Z
date_updated: 2023-10-17T11:49:25Z
day: '08'
department:
- _id: MaJö
doi: 10.3791/58585
external_id:
isi:
- '000456469400103'
intvolume: ' 141'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
publication: Journal of visualized experiments
publication_status: published
publisher: MyJove Corporation
publist_id: '8050'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A micro-CT-based method for characterising lesions and locating electrodes
in small animal brains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2018'
...
---
_id: '13055'
abstract:
- lang: eng
text: "Dataset for manuscript 'Social network plasticity decreases disease transmission
in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n
\ - correction of URLs within
README.txt file\r\n"
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect.”
Zenodo, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect, Zenodo,
10.5281/ZENODO.1322669.
mla: Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).
date_created: 2023-05-23T13:24:51Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-10-17T11:50:04Z
day: '23'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.5281/ZENODO.1322669
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.1480665
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '7'
relation: used_in_publication
status: public
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '22'
abstract:
- lang: eng
text: Conventional ultra-high sensitivity detectors in the millimeter-wave range
are usually cooled as their own thermal noise at room temperature would mask the
weak received radiation. The need for cryogenic systems increases the cost and
complexity of the instruments, hindering the development of, among others, airborne
and space applications. In this work, the nonlinear parametric upconversion of
millimeter-wave radiation to the optical domain inside high-quality (Q) lithium
niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise
detection. We experimentally demonstrate coherent upconversion of millimeter-wave
signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing
the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows
that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling
the millimeter-wave WGM, effectively cooling the upconverted mode and allowing
ultra-low noise detection. By theoretically estimating the sensitivity of a correlation
radiometer based on the presented scheme, it is found that room-temperature radiometers
with better sensitivity than state-of-the-art high-electron-mobility transistor
(HEMT)-based radiometers can be designed. This detection paradigm can be used
to develop room-temperature instrumentation for radio astronomy, earth observation,
planetary missions, and imaging systems.
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
full_name: Botello, Gabriel
last_name: Botello
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Kerlos
full_name: Abdalmalak, Kerlos
last_name: Abdalmalak
- first_name: Elliott
full_name: Brown, Elliott
last_name: Brown
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Sascha
full_name: Preu, Sascha
last_name: Preu
- first_name: Daniel
full_name: Segovia Vargas, Daniel
last_name: Segovia Vargas
- first_name: Dmitry
full_name: Strekalov, Dmitry
last_name: Strekalov
- first_name: Luis
full_name: Munoz, Luis
last_name: Munoz
- first_name: Harald
full_name: Schwefel, Harald
last_name: Schwefel
citation:
ama: Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave
photonic radiometers based on efficient electro-optic upconverters. Optica.
2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210
apa: Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E.,
Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic
radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210
chicago: Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak,
Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave
Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica,
2018. https://doi.org/10.1364/OPTICA.5.001210.
ieee: G. Botello et al., “Sensitivity limits of millimeter-wave photonic
radiometers based on efficient electro-optic upconverters,” Optica, vol.
5, no. 10. pp. 1210–1219, 2018.
ista: Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G,
Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity
limits of millimeter-wave photonic radiometers based on efficient electro-optic
upconverters. Optica. 5(10), 1210–1219.
mla: Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers
Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10,
2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.
short: G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G.
Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica
5 (2018) 1210–1219.
date_created: 2018-12-11T11:44:12Z
date_published: 2018-10-20T00:00:00Z
date_updated: 2023-10-17T12:12:40Z
day: '20'
department:
- _id: JoFi
doi: 10.1364/OPTICA.5.001210
external_id:
isi:
- '000447853100007'
intvolume: ' 5'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'www.doi.org/10.1364/OPTICA.5.001210 '
month: '10'
oa: 1
oa_version: Published Version
page: 1210 - 1219
publication: Optica
publication_identifier:
issn:
- '23342536'
publication_status: published
publist_id: '8033'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensitivity limits of millimeter-wave photonic radiometers based on efficient
electro-optic upconverters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '5677'
abstract:
- lang: eng
text: 'Recently, contract-based design has been proposed as an “orthogonal” approach
that complements system design methodologies proposed so far to cope with the
complexity of system design. Contract-based design provides a rigorous scaffolding
for verification, analysis, abstraction/refinement, and even synthesis. A number
of results have been obtained in this domain but a unified treatment of the topic
that can help put contract-based design in perspective was missing. This monograph
intends to provide such a treatment where contracts are precisely defined and
characterized so that they can be used in design methodologies with no ambiguity.
In particular, this monograph identifies the essence of complex system design
using contracts through a mathematical “meta-theory”, where all the properties
of the methodology are derived from a very abstract and generic notion of contract.
We show that the meta-theory provides deep and illuminating links with existing
contract and interface theories, as well as guidelines for designing new theories.
Our study encompasses contracts for both software and systems, with emphasis on
the latter. We illustrate the use of contracts with two examples: requirement
engineering for a parking garage management, and the development of contracts
for timing and scheduling in the context of the Autosar methodology in use in
the automotive sector.'
article_processing_charge: No
article_type: original
author:
- first_name: Albert
full_name: Benveniste, Albert
last_name: Benveniste
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
- first_name: Benoît
full_name: Caillaud, Benoît
last_name: Caillaud
- first_name: Roberto
full_name: Passerone, Roberto
last_name: Passerone
- first_name: Jean Baptiste
full_name: Raclet, Jean Baptiste
last_name: Raclet
- first_name: Philipp
full_name: Reinkemeier, Philipp
last_name: Reinkemeier
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni-Vincentelli
- first_name: Werner
full_name: Damm, Werner
last_name: Damm
- 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: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
citation:
ama: Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations
and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053
apa: Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier,
P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends
in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053
chicago: Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone,
Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner
Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations
and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.
ieee: A. Benveniste et al., “Contracts for system design,” Foundations
and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers,
pp. 124–400, 2018.
ista: Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier
P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts
for system design. Foundations and Trends in Electronic Design Automation. 12(2–3),
124–400.
mla: Benveniste, Albert, et al. “Contracts for System Design.” Foundations and
Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers,
2018, pp. 124–400, doi:10.1561/1000000053.
short: A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier,
A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations
and Trends in Electronic Design Automation 12 (2018) 124–400.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-10-17T11:53:09Z
day: '01'
department:
- _id: ToHe
doi: 10.1561/1000000053
intvolume: ' 12'
issue: 2-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-00757488/
month: '05'
oa: 1
oa_version: Submitted Version
page: 124-400
publication: Foundations and Trends in Electronic Design Automation
publication_identifier:
issn:
- 1551-3939
publication_status: published
publisher: Now Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contracts for system design
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2018'
...
---
_id: '435'
abstract:
- lang: eng
text: It is shown that two fundamentally different phenomena, the bound states in
continuum and the spectral singularity (or time-reversed spectral singularity),
can occur simultaneously. This can be achieved in a rectangular core dielectric
waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional
bound state in a continuum is created in the plane of a waveguide cross section,
and it is emitted or absorbed along the waveguide core. The idea can be used for
experimental implementation of a laser or a coherent-perfect-absorber for a photonic
bound state that resides in a continuous spectrum.
acknowledgement: 'Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE)
(291734). B. M. acknowledges the financial support by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013)
under REA.'
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. Coherent-perfect-absorber and laser for bound states in
a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607
apa: Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for
bound states in a continuum. Optics Letters. Optica Publishing Group.
https://doi.org/10.1364/OL.43.000607
chicago: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and
Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing
Group, 2018. https://doi.org/10.1364/OL.43.000607.
ieee: B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states
in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group,
pp. 607–610, 2018.
ista: Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states
in a continuum. Optics Letters. 43(3), 607–610.
mla: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser
for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica
Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.
short: B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.
date_created: 2018-12-11T11:46:27Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T12:15:06Z
day: '01'
department:
- _id: MiLe
doi: 10.1364/OL.43.000607
ec_funded: 1
external_id:
arxiv:
- '1711.01986'
isi:
- '000423776600066'
intvolume: ' 43'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.01986
month: '02'
oa: 1
oa_version: Preprint
page: 607 - 610
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: '7388'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coherent-perfect-absorber and laser for bound states in a continuum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2018'
...
---
_id: '139'
abstract:
- lang: eng
text: 'Genome-scale diversity data are increasingly available in a variety of biological
systems, and can be used to reconstruct the past evolutionary history of species
divergence. However, extracting the full demographic information from these data
is not trivial, and requires inferential methods that account for the diversity
of coalescent histories throughout the genome. Here, we evaluate the potential
and limitations of one such approach. We reexamine a well-known system of mussel
sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations
computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation
(ABC) framework. We first assess the best sampling strategy (number of: individuals,
loci, and bins in the jSFS), and show that model selection is robust to variation
in the number of individuals and loci. In contrast, different binning choices
when summarizing the jSFS, strongly affect the results: including classes of low
and high frequency shared polymorphisms can more effectively reveal recent migration
events. We then take advantage of the flexibility of ABC to compare more realistic
models of speciation, including variation in migration rates through time (i.e.,
periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration
rates). We show that these models were consistently selected as the most probable,
suggesting that mussels have experienced a complex history of gene flow during
divergence and that the species boundary is semi-permeable. Our work provides
a comprehensive evaluation of ABC demographic inference in mussels based on the
coding jSFS, and supplies guidelines for employing different sequencing techniques
and sampling strategies. We emphasize, perhaps surprisingly, that inferences are
less limited by the volume of data, than by the way in which they are analyzed.'
article_number: '30083438'
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Pierre
full_name: Gagnaire, Pierre
last_name: Gagnaire
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Nicolas
full_name: Faivre, Nicolas
last_name: Faivre
- first_name: John
full_name: Welch, John
last_name: Welch
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: 'Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue
mussel species reconstructed from Approximate Bayesian Computation: The effects
of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7).
doi:10.7717/peerj.5198'
apa: 'Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J.,
& Bierne, N. (2018). The divergence history of European blue mussel species
reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198'
chicago: 'Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier,
Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European
Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects
of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018.
https://doi.org/10.7717/peerj.5198.'
ieee: 'C. Fraisse et al., “The divergence history of European blue mussel
species reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.'
ista: 'Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N.
2018. The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies. PeerJ. 2018(7), 30083438.'
mla: 'Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel
Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing
Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438,
PeerJ, 2018, doi:10.7717/peerj.5198.'
short: C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne,
PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-10-17T12:25:28Z
day: '30'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.7717/peerj.5198
external_id:
isi:
- '000440484800002'
file:
- access_level: open_access
checksum: 7d55ae22598a1c70759cd671600cff53
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:42:11Z
date_updated: 2020-07-14T12:44:48Z
file_id: '5739'
file_name: 2018_PeerJ_Fraisse.pdf
file_size: 1480792
relation: main_file
file_date_updated: 2020-07-14T12:44:48Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '7784'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies'
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: 2018
year: '2018'
...
---
_id: '33'
abstract:
- lang: eng
text: Secondary contact is the reestablishment of gene flow between sister populations
that have diverged. For instance, at the end of the Quaternary glaciations in
Europe, secondary contact occurred during the northward expansion of the populations
which had found refugia in the southern peninsulas. With the advent of multi-locus
markers, secondary contact can be investigated using various molecular signatures
including gradients of allele frequency, admixture clines, and local increase
of genetic differentiation. We use coalescent simulations to investigate if molecular
data provide enough information to distinguish between secondary contact following
range expansion and an alternative evolutionary scenario consisting of a barrier
to gene flow in an isolation-by-distance model. We find that an excess of linkage
disequilibrium and of genetic diversity at the suture zone is a unique signature
of secondary contact. We also find that the directionality index ψ, which was
proposed to study range expansion, is informative to distinguish between the two
hypotheses. However, although evidence for secondary contact is usually conveyed
by statistics related to admixture coefficients, we find that they can be confounded
by isolation-by-distance. We recommend to account for the spatial repartition
of individuals when investigating secondary contact in order to better reflect
the complex spatio-temporal evolution of populations and species.
acknowledgement: 'Johanna Bertl was supported by the Vienna Graduate School of Population
Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while
employed at the Department of Statistics and Operations Research, University of
Vienna, Austria. This article was developed in the framework of the Grenoble Alpes
Data Institute, which is supported by the French National Research Agency under
the “Investissments d’avenir” program (ANR-15-IDEX-02).'
article_number: e5325
article_processing_charge: No
author:
- first_name: Johanna
full_name: Bertl, Johanna
last_name: Bertl
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Michaël
full_name: Blum, Michaël
last_name: Blum
citation:
ama: Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion
be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325
apa: Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following
range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ.
https://doi.org/10.7717/peerj.5325
chicago: Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact
Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ.
PeerJ, 2018. https://doi.org/10.7717/peerj.5325.
ieee: J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range
expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018,
no. 10. PeerJ, 2018.
ista: Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range
expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.
mla: Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be
Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325,
PeerJ, 2018, doi:10.7717/peerj.5325.
short: J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-10-17T12:24:43Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7717/peerj.5325
external_id:
isi:
- '000447204400001'
pmid:
- '30294507'
file:
- access_level: open_access
checksum: 3334886c4b39678db4c4b74299ca14ba
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:46:06Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5692'
file_name: 2018_PeerJ_Bertl.pdf
file_size: 1328344
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '8022'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can secondary contact following range expansion be distinguished from barriers
to gene flow?
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: 2018
year: '2018'
...
---
_id: '5673'
abstract:
- lang: eng
text: Cell polarity, manifested by the localization of proteins to distinct polar
plasma membrane domains, is a key prerequisite of multicellular life. In plants,
PIN auxin transporters are prominent polarity markers crucial for a plethora of
developmental processes. Cell polarity mechanisms in plants are distinct from
other eukaryotes and still largely elusive. In particular, how the cell polarities
are propagated and maintained following cell division remains unknown. Plant cytokinesis
is orchestrated by the cell plate—a transient centrifugally growing endomembrane
compartment ultimately forming the cross wall1. Trafficking of polar membrane
proteins is typically redirected to the cell plate, and these will consequently
have opposite polarity in at least one of the daughter cells2–5. Here, we provide
mechanistic insights into post-cytokinetic re-establishment of cell polarity as
manifested by the apical, polar localization of PIN2. We show that the apical
domain is defined in a cell-intrinsic manner and that re-establishment of PIN2
localization to this domain requires de novo protein secretion and endocytosis,
but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related
kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated
specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2
polarity re-establishment.
article_processing_charge: No
author:
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment
of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088.
doi:10.1038/s41477-018-0318-3
apa: Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for
cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature
Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3
chicago: Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework
for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature
Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.
ieee: M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division,” Nature Plants,
vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.
ista: Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.
mla: Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment
of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature
Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.
short: M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-12-03T00:00:00Z
date_updated: 2023-10-17T12:19:28Z
day: '03'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0318-3
ec_funded: 1
external_id:
isi:
- '000454576600017'
pmid:
- '30518833'
intvolume: ' 4'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30518833
month: '12'
oa: 1
oa_version: Submitted Version
page: 1082-1088
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity
after cell division
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '198'
abstract:
- lang: eng
text: We consider a class of students learning a language from a teacher. The situation
can be interpreted as a group of child learners receiving input from the linguistic
environment. The teacher provides sample sentences. The students try to learn
the grammar from the teacher. In addition to just listening to the teacher, the
students can also communicate with each other. The students hold hypotheses about
the grammar and change them if they receive counter evidence. The process stops
when all students have converged to the correct grammar. We study how the time
to convergence depends on the structure of the classroom by introducing and evaluating
various complexity measures. We find that structured communication between students,
although potentially introducing confusion, can greatly reduce some of the complexity
measures. Our theory can also be interpreted as applying to the scientific process,
where nature is the teacher and the scientists are the students.
article_number: '20180073'
article_processing_charge: No
article_type: original
author:
- 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: 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: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with
communication between learners. Journal of the Royal Society Interface.
2018;15(140). doi:10.1098/rsif.2018.0073
apa: Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language
acquisition with communication between learners. Journal of the Royal Society
Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073
chicago: Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Language Acquisition with Communication between Learners.” Journal
of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.
ieee: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition
with communication between learners,” Journal of the Royal Society Interface,
vol. 15, no. 140. The Royal Society, 2018.
ista: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition
with communication between learners. Journal of the Royal Society Interface. 15(140),
20180073.
mla: Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between
Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073,
The Royal Society, 2018, doi:10.1098/rsif.2018.0073.
short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal
Society Interface 15 (2018).
date_created: 2018-12-11T11:45:09Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-10-18T06:36:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rsif.2018.0073
ec_funded: 1
external_id:
isi:
- '000428576200023'
pmid:
- '29593089'
file:
- access_level: open_access
checksum: 444e1a9d98eb0e780671be82b13025f3
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T07:54:37Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5955'
file_name: 2018_RS_IbsenJensen.pdf
file_size: 219837
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '140'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _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
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: The Royal Society
publist_id: '7715'
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4028971
record:
- id: '9814'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Language acquisition with communication between learners
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '5859'
abstract:
- lang: eng
text: The emergence of syntax during childhood is a remarkable example of how complex
correlations unfold in nonlinear ways through development. In particular, rapid
transitions seem to occur as children reach the age of two, which seems to separate
a two-word, tree-like network of syntactic relations among words from the scale-free
graphs associated with the adult, complex grammar. Here, we explore the evolution
of syntax networks through language acquisition using the chromatic number, which
captures the transition and provides a natural link to standard theories on syntactic
structures. The data analysis is compared to a null model of network growth dynamics
which is shown to display non-trivial and sensible differences. At a more general
level, we observe that the chromatic classes define independent regions of the
graph, and thus, can be interpreted as the footprints of incompatibility relations,
somewhat as opposed to modularity considerations.
acknowledgement: This work was supported by the James McDonnell Foundation (B.C-M.,
S.V. and R.S.)
article_number: '181286'
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Martí Sànchez
full_name: Fibla, Martí Sànchez
last_name: Fibla
- first_name: Sergi
full_name: Valverde, Sergi
last_name: Valverde
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in
the emergence of syntax networks. Royal Society Open Science. 2018;5(12).
doi:10.1098/rsos.181286
apa: Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic
transitions in the emergence of syntax networks. Royal Society Open Science.
The Royal Society. https://doi.org/10.1098/rsos.181286
chicago: Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard
Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society
Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.
ieee: B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions
in the emergence of syntax networks,” Royal Society Open Science, vol.
5, no. 12. The Royal Society, 2018.
ista: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions
in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.
mla: Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of
Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The
Royal Society, 2018, doi:10.1098/rsos.181286.
short: B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open
Science 5 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-10-18T06:41:12Z
day: '12'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1098/rsos.181286
external_id:
isi:
- '000456566500027'
pmid:
- '30662738'
file:
- access_level: open_access
checksum: 9664d4417f6b792242e31eea77ce9501
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:38:09Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5924'
file_name: 2018_RoyalSocOS_Corominas.pdf
file_size: 646732
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Royal Society Open Science
publication_identifier:
issn:
- 2054-5703
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatic transitions in the emergence of syntax 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '6183'
abstract:
- lang: eng
text: "We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z
- a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq
0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element
of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$.
We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued
measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this
measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect
to the Lebesgue measure, which\r\nis supported on finitely many intervals, called
bands. In fact, the density is\r\nanalytic inside the bands with a square-root
growth at the edges and internal\r\ncubic root cusps whenever the gap between
two bands vanishes. The shape of\r\nthese singularities is universal and no other
singularity may occur. We give a\r\nprecise asymptotic description of $m$ near
the singular points. These\r\nasymptotics generalize the analysis at the regular
edges given in the companion\r\npaper on the Tracy-Widom universality for the
edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744]
and they play a key role in the\r\nproof of the Pearcey universality at the cusp
for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend
the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von
Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically
rigid under\r\ndeformations and we conclude that these masses are quantized in
some important\r\ncases."
article_number: '1804.07752'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: 'Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral
bands, edges and cusps. arXiv.'
apa: 'Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear
self-energy: Spectral bands, edges and cusps. arXiv.'
chicago: 'Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation
with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.'
ieee: 'J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy:
Spectral bands, edges and cusps,” arXiv. .'
ista: 'Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral
bands, edges and cusps. arXiv, 1804.07752.'
mla: 'Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral
Bands, Edges and Cusps.” ArXiv, 1804.07752.'
short: J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).
date_created: 2019-03-28T09:20:06Z
date_published: 2018-04-20T00:00:00Z
date_updated: 2023-12-18T10:46:08Z
day: '20'
department:
- _id: LaEr
external_id:
arxiv:
- '1804.07752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07752
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
- id: '14694'
relation: later_version
status: public
status: public
title: 'The Dyson equation with linear self-energy: Spectral bands, edges and cusps'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '75'
abstract:
- lang: eng
text: We prove that any convex body in the plane can be partitioned into m convex
parts of equal areas and perimeters for any integer m≥2; this result was previously
known for prime powers m=pk. We also give a higher-dimensional generalization.
article_number: '1804.03057'
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
citation:
ama: Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number
of pieces. 2018. doi:10.48550/arXiv.1804.03057
apa: Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions
into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057
chicago: Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions
into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057.
ieee: A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary
number of pieces.” arXiv, 2018.
ista: Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary
number of pieces. 1804.03057.
mla: Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of
Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.
short: A. Akopyan, S. Avvakumov, R. Karasev, (2018).
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-13T00:00:00Z
date_updated: 2023-12-18T10:51:02Z
day: '13'
department:
- _id: HeEd
- _id: JaMa
doi: 10.48550/arXiv.1804.03057
ec_funded: 1
external_id:
arxiv:
- '1804.03057'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.03057
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication_status: published
publisher: arXiv
related_material:
record:
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Convex fair partitions into arbitrary number of pieces
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '556'
abstract:
- lang: eng
text: 'We investigate the free boundary Schur process, a variant of the Schur process
introduced by Okounkov and Reshetikhin, where we allow the first and the last
partitions to be arbitrary (instead of empty in the original setting). The pfaffian
Schur process, previously studied by several authors, is recovered when just one
of the boundary partitions is left free. We compute the correlation functions
of the process in all generality via the free fermion formalism, which we extend
with the thorough treatment of “free boundary states.” For the case of one free
boundary, our approach yields a new proof that the process is pfaffian. For the
case of two free boundaries, we find that the process is not pfaffian, but a closely
related process is. We also study three different applications of the Schur process
with one free boundary: fluctuations of symmetrized last passage percolation models,
limit shapes and processes for symmetric plane partitions and for plane overpartitions.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dan
full_name: Betea, Dan
last_name: Betea
- first_name: Jeremie
full_name: Bouttier, Jeremie
last_name: Bouttier
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
- first_name: Mirjana
full_name: Vuletic, Mirjana
last_name: Vuletic
citation:
ama: Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and
applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1
apa: Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary
Schur process and applications I. Annales Henri Poincare. Springer Nature.
https://doi.org/10.1007/s00023-018-0723-1
chicago: Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free
Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer
Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.
ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur
process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer
Nature, pp. 3663–3742, 2018.
ista: Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process
and applications I. Annales Henri Poincare. 19(12), 3663–3742.
mla: Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales
Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1.
short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018)
3663–3742.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-11-13T00:00:00Z
date_updated: 2024-02-20T10:48:17Z
day: '13'
ddc:
- '500'
department:
- _id: LaEr
- _id: JaMa
doi: 10.1007/s00023-018-0723-1
ec_funded: 1
external_id:
arxiv:
- '1704.05809'
file:
- access_level: open_access
checksum: 0c38abe73569b7166b7487ad5d23cc68
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T15:18:55Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5866'
file_name: 2018_Annales_Betea.pdf
file_size: 3084674
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '12'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3663-3742
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Annales Henri Poincare
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
publist_id: '7258'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free boundary Schur process and applications I
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: 19
year: '2018'
...
---
_id: '5573'
abstract:
- lang: eng
text: Graph matching problems for large displacement optical flow of RGB-D images.
article_processing_charge: No
author:
- first_name: Hassan
full_name: Alhaija, Hassan
last_name: Alhaija
- first_name: Anita
full_name: Sellent, Anita
last_name: Sellent
- first_name: Daniel
full_name: Kondermann, Daniel
last_name: Kondermann
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow
– 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82
apa: Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching
problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:82
chicago: Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother.
“Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute
of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82.
ieee: H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems
for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology
Austria, 2018.
ista: Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems
for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:82.
mla: Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large
Displacement Scene Flow. Institute of Science and Technology Austria, 2018,
doi:10.15479/AT:ISTA:82.
short: H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).
contributor:
- contributor_type: researcher
first_name: Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
datarep_id: '82'
date_created: 2018-12-12T12:31:36Z
date_published: 2018-01-04T00:00:00Z
date_updated: 2024-02-21T13:41:17Z
day: '04'
ddc:
- '001'
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:82
file:
- access_level: open_access
checksum: 53c17082848e12f3c2e1b4185b578208
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:34Z
date_updated: 2020-07-14T12:47:05Z
file_id: '5600'
file_name: IST-2018-82-v1+1_GraphFlowMatchingProblems.zip
file_size: 1737958
relation: main_file
file_date_updated: 2020-07-14T12:47:05Z
has_accepted_license: '1'
keyword:
- graph matching
- quadratic assignment problem<
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: research_paper
url: https://doi.org/10.1007/978-3-319-24947-6_23
status: public
title: Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow
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: '2018'
...
---
_id: '292'
abstract:
- lang: eng
text: 'Retina is a paradigmatic system for studying sensory encoding: the transformation
of light into spiking activity of ganglion cells. The inverse problem, where stimulus
is reconstructed from spikes, has received less attention, especially for complex
stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred
neurons from a dense patch in a rat retina and decoded movies of multiple small
randomly-moving discs. We constructed nonlinear (kernelized and neural network)
decoders that improved significantly over linear results. An important contribution
to this was the ability of nonlinear decoders to reliably separate between neural
responses driven by locally fluctuating light signals, and responses at locally
constant light driven by spontaneous-like activity. This improvement crucially
depended on the precise, non-Poisson temporal structure of individual spike trains,
which originated in the spike-history dependence of neural responses. We propose
a general principle by which downstream circuitry could discriminate between spontaneous
and stimulus-driven activity based solely on higher-order statistical structure
in the incoming spike trains.'
article_number: e1006057
article_processing_charge: Yes
article_type: original
author:
- first_name: Vicent
full_name: Botella Soler, Vicent
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Georg S
full_name: Martius, Georg S
last_name: Martius
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. PLoS Computational Biology.
2018;14(5). doi:10.1371/journal.pcbi.1006057
apa: Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057
chicago: Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.
ieee: V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina,” PLoS Computational
Biology, vol. 14, no. 5. Public Library of Science, 2018.
ista: Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5),
e1006057.
mla: Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from
the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057,
Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
short: V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational
Biology 14 (2018).
date_created: 2018-12-11T11:45:39Z
date_published: 2018-05-10T00:00:00Z
date_updated: 2024-02-21T13:45:25Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1006057
ec_funded: 1
external_id:
isi:
- '000434012100002'
file:
- access_level: open_access
checksum: 3026f94d235219e15514505fdbadf34e
content_type: application/pdf
creator: dernst
date_created: 2019-02-13T11:07:15Z
date_updated: 2020-07-14T12:45:53Z
file_id: '5974'
file_name: 2018_Plos_Botella_Soler.pdf
file_size: 3460786
relation: main_file
file_date_updated: 2020-07-14T12:45:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/
record:
- id: '5584'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '438'
abstract:
- lang: eng
text: The MazF toxin sequence-specifically cleaves single-stranded RNA upon various
stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin
module in Escherichia coli. Although autoregulation of mazEF expression through
the MazE antitoxin-dependent transcriptional repression has been biochemically
characterized, less is known about post-transcriptional autoregulation, as well
as how both of these autoregulatory features affect growth of single cells during
conditions that promote MazF production. Here, we demonstrate post-transcriptional
autoregulation of mazF expression dynamics by MazF cleaving its own transcript.
Single-cell analyses of bacterial populations during ectopic MazF production indicated
that two-level autoregulation of mazEF expression influences cell-to-cell growth
rate heterogeneity. The increase in growth rate heterogeneity is governed by the
MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both
autoregulatory features grant rapid exit from the stress caused by mazF overexpression.
Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads
to increased temporal variability in length of individual cells during ectopic
mazF overexpression, as explained by a stochastic model indicating that mazEF
mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Alexandra
full_name: Vandervelde, Alexandra
last_name: Vandervelde
- first_name: Tanino
full_name: Albanese, Tanino
last_name: Albanese
- first_name: Lendert
full_name: Gelens, Lendert
last_name: Gelens
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation
of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic
Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079
apa: Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &
Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity
in bacterial populations. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gky079
chicago: Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese,
Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies
Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research.
Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.
ieee: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I.
Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University
Press, pp. 2918–2931, 2018.
ista: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018.
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations. Nucleic Acids Research. 46(6), 2918–2931.
mla: Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth
Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46,
no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.
short: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll,
Nucleic Acids Research 46 (2018) 2918–2931.
date_created: 2018-12-11T11:46:29Z
date_published: 2018-04-06T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '06'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/nar/gky079
external_id:
isi:
- '000429009500021'
file:
- access_level: open_access
checksum: 3ff4f545c27e11a4cd20ccb30778793e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5151'
file_name: IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf
file_size: 5027978
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2918-2931
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
pubrep_id: '971'
quality_controlled: '1'
related_material:
record:
- id: '5569'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2018'
...
---
_id: '131'
abstract:
- lang: eng
text: 'XY systems usually show chromosome-wide compensation of X-linked genes, while
in many ZW systems, compensation is restricted to a minority of dosage-sensitive
genes. Why such differences arose is still unclear. Here, we combine comparative
genomics, transcriptomics and proteomics to obtain a complete overview of the
evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare
the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium)
and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary
strata. We use these to assess gene expression evolution following sex-linkage.
The resulting patterns suggest a reduction in expression of Z-linked genes in
females, combined with upregulation of the Z in both sexes, in line with the first
step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics
suggest that post-transcriptional mechanisms do not play a major role in balancing
the expression of Z-linked genes. '
acknowledgement: We are grateful to Lu Dabing (Soochow University, Suzhou, China)
for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette
Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for
providing optimal environment to bioinformatic analyses, and to the Vicoso lab for
comments on the manuscript.
article_number: e35684
article_processing_charge: No
article_type: original
author:
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Celine
full_name: Cosseau, Celine
last_name: Cosseau
- first_name: Sabrina
full_name: Ferré, Sabrina
last_name: Ferré
- first_name: Thomas
full_name: Quack, Thomas
last_name: Quack
- first_name: Christoph
full_name: Grevelding, Christoph
last_name: Grevelding
- first_name: Yohann
full_name: Couté, Yohann
last_name: Couté
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome
of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684
apa: Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté,
Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome
parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684
chicago: Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph
Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the
Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications,
2018. https://doi.org/10.7554/eLife.35684.
ieee: M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome
of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications,
2018.
ista: Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B.
2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife.
7, e35684.
mla: Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome
of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications,
2018, doi:10.7554/eLife.35684.
short: M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B.
Vicoso, ELife 7 (2018).
date_created: 2018-12-11T11:44:47Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '13'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.7554/eLife.35684
external_id:
isi:
- '000441388200001'
file:
- access_level: open_access
checksum: d6331d4385b1fffd6b47b45d5949d841
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T11:55:05Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5695'
file_name: 2018_eLife_Picard.pdf
file_size: 3158125
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7792'
quality_controlled: '1'
related_material:
record:
- id: '5586'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Evolution of gene dosage on the Z-chromosome of schistosome parasites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '5584'
abstract:
- lang: eng
text: "This package contains data for the publication \"Nonlinear decoding of a
complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018).
\r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion
cells that pass stability and quality criteria, recorded on the multi-electrode
array, in response to the presentation of the complex movie with many randomly
moving dark discs. The responses are represented as 648000 x 91 binary matrix,
where the first index indicates the timebin of duration 12.5 ms, and the second
index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike
in the particular time bin.\r\n(ii) README file and a graphical illustration of
the structure of the experiment, specifying how the 648000 timebins are split
into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments
are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix
of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie
frame, with time that is locked to the recorded raster. The luminance traces are
produced as described in the manuscript by filtering the raw disc movie with a
small gaussian spatial kernel. "
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Vicente
full_name: Botella-Soler, Vicente
last_name: Botella-Soler
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
apa: Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98
chicago: Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
ieee: S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina.” Institute of Science and
Technology Austria, 2018.
ista: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:98.
mla: Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian
Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.
short: S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
datarep_id: '98'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2024-02-21T13:45:26Z
day: '29'
ddc:
- '570'
department:
- _id: ChLa
- _id: GaTk
doi: 10.15479/AT:ISTA:98
file:
- access_level: open_access
checksum: 6808748837b9afbbbabc2a356ca2b88a
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:24Z
date_updated: 2020-07-14T12:47:07Z
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file_name: IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat
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content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:47:07Z
file_id: '5591'
file_name: IST-2018-98-v1+2_ExperimentStructure.pdf
file_size: 702336
relation: main_file
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creator: system
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date_updated: 2020-07-14T12:47:07Z
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file_name: IST-2018-98-v1+3_GoodLocations_area2_20x20.mat
file_size: 432
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content_type: text/plain
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5593'
file_name: IST-2018-98-v1+4_README.txt
file_size: 986
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
keyword:
- retina
- decoding
- regression
- neural networks
- complex stimulus
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '292'
relation: used_in_publication
status: public
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
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: '2018'
...
---
_id: '286'
abstract:
- lang: eng
text: 'Pedigree and sibship reconstruction are important methods in quantifying
relationships and fitness of individuals in natural populations. Current methods
employ a Markov chain-based algorithm to explore plausible possible pedigrees
iteratively. This provides accurate results, but is time-consuming. Here, we develop
a method to infer sibship and paternity relationships from half-sibling arrays
of known maternity using hierarchical clustering. Given 50 or more unlinked SNP
markers and empirically derived error rates, the method performs as well as the
widely used package Colony, but is faster by two orders of magnitude. Using simulations,
we show that the method performs well across contrasting mating scenarios, even
when samples are large. We then apply the method to open-pollinated arrays of
the snapdragon Antirrhinum majus and find evidence for a high degree of multiple
mating. Although we focus on diploid SNP data, the method does not depend on marker
type and as such has broad applications in nonmodel systems. '
acknowledgement: 'ERC, Grant/Award Number: 250152'
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
- 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: Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference
given known maternity via hierarchical clustering. Molecular Ecology Resources.
2018;18(5):988-999. doi:10.1111/1755-0998.12782
apa: Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity
and sibship inference given known maternity via hierarchical clustering. Molecular
Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782
chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference
of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.”
Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.
ieee: T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and
sibship inference given known maternity via hierarchical clustering,” Molecular
Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.
ista: Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship
inference given known maternity via hierarchical clustering. Molecular Ecology
Resources. 18(5), 988–999.
mla: Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference
given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources,
vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.
short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-02-21T13:45:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/1755-0998.12782
ec_funded: 1
external_id:
isi:
- '000441753000007'
intvolume: ' 18'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 988 - 999
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology Resources
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '5583'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Efficient inference of paternity and sibship inference given known maternity
via hierarchical clustering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2018'
...
---
_id: '5586'
abstract:
- lang: eng
text: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018).
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome
of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109
apa: Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on
the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109
chicago: Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.
ieee: B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the
Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute
of Science and Technology Austria, 2018.
ista: Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on
the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute
of Science and Technology Austria, 10.15479/AT:ISTA:109.
mla: Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018).
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.
short: B. Vicoso, (2018).
contributor:
- first_name: Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
datarep_id: '109'
date_created: 2018-12-12T12:31:40Z
date_published: 2018-07-24T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '24'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:109
file:
- access_level: open_access
checksum: e60b484bd6f55c08eb66a189cb72c923
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:35Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5601'
file_name: IST-2018-109-v1+1_SupplementaryMethods.zip
file_size: 11918144
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- schistosoma
- Z-chromosome
- gene expression
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '131'
relation: research_paper
status: public
status: public
title: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018)
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: '2018'
...
---
_id: '5583'
abstract:
- lang: eng
text: "Data and scripts are provided in support of the manuscript \"Efficient inference
of paternity and sibship inference given known maternity via hierarchical clustering\",
and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation
scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison
with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe
final script covers the analysis of half-sib arrays from wild-pollinated seed
in an Antirrhinum majus hybrid zone."
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 and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95
apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95
chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.
ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute
of Science and Technology Austria, 2018.
ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:95.
mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.
short: T. Ellis, (2018).
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
datarep_id: '95'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-02-12T00:00:00Z
date_updated: 2024-02-21T13:45:01Z
day: '12'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:95
file:
- access_level: open_access
checksum: fc6aab51439f2622ba6df8632e66fd4f
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:41Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5606'
file_name: IST-2018-95-v1+1_amajus_GPS_2012.csv
file_size: 122048
relation: main_file
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checksum: 92347586ae4f8a6eb7c04354797bf314
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:42Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5607'
file_name: IST-2018-95-v1+2_offspring_SNPs_2012.csv
file_size: 235980
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checksum: 3300813645a54e6c5c39f41917228354
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creator: system
date_created: 2018-12-12T13:02:43Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5608'
file_name: IST-2018-95-v1+3_parents_SNPs_2012.csv
file_size: 311712
relation: main_file
- access_level: open_access
checksum: e739fc473567fd8f39438b445fc46147
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:44Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5609'
file_name: IST-2018-95-v1+4_faps_scripts.zip
file_size: 342090
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '286'
relation: research_paper
status: public
status: public
title: Data and Python scripts supporting Python package FAPS
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: '2018'
...
---
_id: '5569'
abstract:
- lang: eng
text: "Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese,
Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression
underlies growth heterogeneity in bacterial populations” Nucleic Acids Research,
doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image
and data analysis by Nela Nikolic."
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
citation:
ama: Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74
apa: Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74
chicago: Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute
of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.
ieee: T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science
and Technology Austria, 2018.
ista: Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:74.
mla: Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute
of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.
short: T. Bergmiller, N. Nikolic, (2018).
datarep_id: '74'
date_created: 2018-12-12T12:31:35Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '07'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:74
file:
- access_level: open_access
checksum: 61ebb92213cfffeba3ddbaff984b81af
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:39Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5637'
file_name: IST-2018-74-v1+2_15-11-05.zip
file_size: 3558703796
relation: main_file
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checksum: bf26649af310ef6892d68576515cde6d
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:55Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5638'
file_name: IST-2018-74-v1+3_15-07-31.zip
file_size: 1830422606
relation: main_file
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checksum: 8e46eedce06f22acb2be1a9b9d3f56bd
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:11Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5639'
file_name: IST-2018-74-v1+4_Images_for_analysis.zip
file_size: 2140849248
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
keyword:
- microscopy
- microfluidics
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '7385'
related_material:
record:
- id: '438'
relation: research_paper
status: public
status: public
title: Time-lapse microscopy data
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: '2018'
...
---
_id: '161'
abstract:
- lang: eng
text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
Predictive results have been obtained by flux balance analysis (FBA), by postulating
that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
of FBA to single-cell level using maximum entropy modeling, which we extend and
test experimentally. Specifically, we define for Escherichia coli metabolism a
flux distribution that yields the experimental growth rate: the model, containing
FBA as a limit, provides a better match to measured fluxes and it makes a wide
range of predictions: on flux variability, regulation, and correlations; on the
relative importance of stoichiometry vs. optimization; on scaling relations for
growth rate distributions. We validate the latter here with single-cell data at
different sub-inhibitory antibiotic concentrations. The model quantifies growth
optimization as emerging from the interplay of competitive dynamics in the population
and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Andersson Anna
full_name: Mc, Andersson Anna
last_name: Mc
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- 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: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications.
2018;9(1). doi:10.1038/s41467-018-05417-9
apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018).
Statistical mechanics for metabolic networks during steady state growth. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9
chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
mechanics for metabolic networks during steady state growth,” Nature Communications,
vol. 9, no. 1. Springer Nature, 2018.
ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications. 9(1),
2988.
mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer
Nature, 2018, doi:10.1038/s41467-018-05417-9.
short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
9 (2018).
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- id: '5587'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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year: '2018'
...
---
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abstract:
- lang: eng
text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E.
coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix
enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose
limited minimal medium, \r\nobtained from the soichiometric matrix by standard
linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John
ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in
a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter
of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli
catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with
the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input
the polytope of the feasible steady states of a metabolic network, \r\n(matrix
and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding
the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults
to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we
refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++
code file receives in input the polytope of the feasible steady states of a metabolic
network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point
inside and \r\nit gives in output a max entropy sampling at fixed average growth
rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov
chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli
network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:62
chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.
ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology
Austria, 2018.
ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:62.
mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
short: D. De Martino, G. Tkačik, (2018).
datarep_id: '111'
date_created: 2018-12-12T12:31:41Z
date_published: 2018-09-21T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
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ec_funded: 1
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file_size: 14376
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- metabolic networks
- e.coli core
- maximum entropy
- monte carlo markov chain sampling
- ellipsoidal rounding
month: '09'
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: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publisher: Institute of Science and Technology Austria
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status: public
status: public
title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE
GROWTH"
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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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...
---
_id: '542'
abstract:
- lang: eng
text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a
model for autosomal segregation distortion for close to a century, but several
questions remain regarding its biology and evolutionary history. A recently published
set of population genomics resources for wild mice includes several individuals
heterozygous for the t-haplotype, which we use to characterize this selfish element
at the genomic and transcriptomic level. Our results show that large sections
of the t-haplotype have been replaced by standard homologous sequences, possibly
due to occasional events of recombination, and that this complicates the inference
of its history. As expected for a long genomic segment of very low recombination,
the t-haplotype carries an excess of fixed nonsynonymous mutations compared to
the standard chromosome. This excess is stronger for regions that have not undergone
recent recombination, suggesting that occasional gene flow between the t and the
standard chromosome may provide a mechanism to regenerate coding sequences that
have accumulated deleterious mutations. Finally, we find that t-complex genes
with altered expression largely overlap with deleted or amplified regions, and
that carrying a t-haplotype alters the testis expression of genes outside of the
t-complex, providing new leads into the pathways involved in the biology of this
segregation distorter.
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype,
a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513
apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation
patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.117.300513
chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics
Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.
ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns
of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1.
Genetics Society of America, pp. 365–375, 2018.
ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of
the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.
mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208,
no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.
short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-02-21T13:48:27Z
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ddc:
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department:
- _id: BeVi
doi: 10.1534/genetics.117.300513
ec_funded: 1
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isi:
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issue: '1'
language:
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oa_version: Published Version
page: 365 - 375
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call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7274'
pubrep_id: '1058'
quality_controlled: '1'
related_material:
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relation: popular_science
status: public
- id: '5572'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic
driver
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
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...