---
_id: '1874'
abstract:
- lang: eng
text: 'The hippocampal region, comprising the hippocampal formation and the parahippocampal
region, has been one of the most intensively studied parts of the brain for decades.
Better understanding of its functional diversity and complexity has led to an
increased demand for specificity in experimental procedures and manipulations.
In view of the complex 3D structure of the hippocampal region, precisely positioned
experimental approaches require a fine-grained architectural description that
is available and readable to experimentalists lacking detailed anatomical experience.
In this paper, we provide the first cyto- and chemoarchitectural description of
the hippocampal formation and parahippocampal region in the rat at high resolution
and in the three standard sectional planes: coronal, horizontal and sagittal.
The atlas uses a series of adjacent sections stained for neurons and for a number
of chemical marker substances, particularly parvalbumin and calbindin. All the
borders defined in one plane have been cross-checked against their counterparts
in the other two planes. The entire dataset will be made available as a web-based
interactive application through the Rodent Brain WorkBench (http://www.rbwb.org)
which, together with this paper, provides a unique atlas resource.'
author:
- first_name: Charlotte
full_name: Boccara, Charlotte
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Lisa
full_name: Kjønigsen, Lisa
last_name: Kjønigsen
- first_name: Ingvild
full_name: Hammer, Ingvild
last_name: Hammer
- first_name: Jan
full_name: Bjaalie, Jan
last_name: Bjaalie
- first_name: Trygve
full_name: Leergaard, Trygve
last_name: Leergaard
- first_name: Menno
full_name: Witter, Menno
last_name: Witter
citation:
ama: Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane
architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857.
doi:10.1002/hipo.22407
apa: Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., &
Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region.
Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407
chicago: Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve
Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal
Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407.
ieee: C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter,
“A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus,
vol. 25, no. 7. Wiley, pp. 838–857, 2015.
ista: Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015.
A three-plane architectonic atlas of the rat hippocampal region. Hippocampus.
25(7), 838–857.
mla: Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat
Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57,
doi:10.1002/hipo.22407.
short: C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter,
Hippocampus 25 (2015) 838–857.
date_created: 2018-12-11T11:54:29Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:46Z
day: '01'
department:
- _id: JoCs
doi: 10.1002/hipo.22407
intvolume: ' 25'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 838 - 857
publication: Hippocampus
publication_status: published
publisher: Wiley
publist_id: '5222'
quality_controlled: '1'
scopus_import: 1
status: public
title: A three-plane architectonic atlas of the rat hippocampal region
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '1873'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
limit-average payoff, where a reward value in the interval [0,1] is associated
with every transition, and the payoff of an infinite path is the long-run average
of the rewards. We consider two types of path constraints: (i) a quantitative
constraint defines the set of paths where the payoff is at least a given threshold
λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative
constraint with λ1=1. We consider the computation of the almost-sure winning set,
where the controller needs to ensure that the path constraint is satisfied with
probability 1. Our main results for qualitative path constraints are as follows:
(i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete;
and (ii) the problem of deciding the existence of an infinite-memory controller
is undecidable. For quantitative path constraints we show that the problem of
deciding the existence of a finite-memory controller is undecidable. We also present
a prototype implementation of our EXPTIME algorithm and experimental results on
several examples.'
author:
- 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: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
citation:
ama: Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial
Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009
apa: Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics.
Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009
chicago: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic
Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.
ieee: K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial
Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.
ista: Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial
Intelligence. 221, 46–72.
mla: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.”
Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009.
short: K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.
date_created: 2018-12-11T11:54:28Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:46Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2014.12.009
external_id:
arxiv:
- '1408.2058'
intvolume: ' 221'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.2058
month: '04'
oa: 1
oa_version: Preprint
page: 46 - 72
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5224'
quality_controlled: '1'
scopus_import: 1
status: public
title: POMDPs under probabilistic semantics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2015'
...
---
_id: '1879'
abstract:
- lang: eng
text: When electron microscopy (EM) was introduced in the 1930s it gave scientists
their first look into the nanoworld of cells. Over the last 80 years EM has vastly
increased our understanding of the complex cellular structures that underlie the
diverse functions that cells need to maintain life. One drawback that has been
difficult to overcome was the inherent lack of volume information, mainly due
to the limit on the thickness of sections that could be viewed in a transmission
electron microscope (TEM). For many years scientists struggled to achieve three-dimensional
(3D) EM using serial section reconstructions, TEM tomography, and scanning EM
(SEM) techniques such as freeze-fracture. Although each technique yielded some
special information, they required a significant amount of time and specialist
expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists
began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning
of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and
subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists
were able to collect large volumes of 3D EM information at resolutions that could
address many important biological questions, and do so in an efficient manner.
We present here some examples of 3D EM taken from the many diverse specimens that
have been imaged in our core facility. We propose that the next major step forward
will be to efficiently correlate functional information obtained using light microscopy
(LM) with 3D EM datasets to more completely investigate the important links between
cell structures and their functions.
acknowledgement: The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired
through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel
Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds
Wetenschappelijk Onderzoek) of Flanders.
author:
- first_name: A
full_name: Kremer, A
last_name: Kremer
- first_name: Stefaan
full_name: Lippens, Stefaan
last_name: Lippens
- first_name: Sonia
full_name: Bartunkova, Sonia
last_name: Bartunkova
- first_name: Bob
full_name: Asselbergh, Bob
last_name: Asselbergh
- first_name: Cendric
full_name: Blanpain, Cendric
last_name: Blanpain
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: A
full_name: Goossens, A
last_name: Goossens
- first_name: Matthew
full_name: Holt, Matthew
last_name: Holt
- first_name: Sophie
full_name: Janssens, Sophie
last_name: Janssens
- first_name: Michiel
full_name: Krols, Michiel
last_name: Krols
- first_name: Jean
full_name: Larsimont, Jean
last_name: Larsimont
- first_name: Conor
full_name: Mc Guire, Conor
last_name: Mc Guire
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Xavier
full_name: Saelens, Xavier
last_name: Saelens
- first_name: Andreas
full_name: Schertel, Andreas
last_name: Schertel
- first_name: B
full_name: Schepens, B
last_name: Schepens
- first_name: M
full_name: Slezak, M
last_name: Slezak
- first_name: Vincent
full_name: Timmerman, Vincent
last_name: Timmerman
- first_name: Clara
full_name: Theunis, Clara
last_name: Theunis
- first_name: Ronald
full_name: Van Brempt, Ronald
last_name: Van Brempt
- first_name: Y
full_name: Visser, Y
last_name: Visser
- first_name: Christophe
full_name: Guérin, Christophe
last_name: Guérin
citation:
ama: Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological
context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211
apa: Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych,
M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal
of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211
chicago: Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain,
Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.”
Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.
ieee: A. Kremer et al., “Developing 3D SEM in a broad biological context,”
Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.
ista: Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens
A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X,
Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser
Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of
Microscopy. 259(2), 80–96.
mla: Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal
of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.
short: A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych,
A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack,
X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R.
Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.
date_created: 2018-12-11T11:54:30Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1111/jmi.12211
file:
- access_level: open_access
checksum: 3649c5372d1644062d728ea9287e367f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:19Z
date_updated: 2020-07-14T12:45:19Z
file_id: '4872'
file_name: IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf
file_size: 2899898
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 259'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 80 - 96
publication: Journal of Microscopy
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5218'
pubrep_id: '459'
quality_controlled: '1'
scopus_import: 1
status: public
title: Developing 3D SEM in a broad biological context
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: 259
year: '2015'
...
---
_id: '1880'
abstract:
- lang: eng
text: We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity
in the ground state of a one-dimensional model of interacting bosons in a strong
random potential. We prove rigorously that in a certain parameter regime the superfluid
fraction can be arbitrarily small while complete BEC prevails. In another regime
there is both complete BEC and complete superfluidity, despite the strong disorder
acknowledgement: Support from the Natural Sciences and Engineering Research Council
of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project
P 22929-N16) is gratefully acknowledged
article_number: '013022'
author:
- first_name: Martin
full_name: Könenberg, Martin
last_name: Könenberg
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein
condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022
apa: Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid
behavior of a Bose-Einstein condensate in a random potential. New Journal of
Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022
chicago: Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason.
“Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New
Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.
ieee: M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior
of a Bose-Einstein condensate in a random potential,” New Journal of Physics,
vol. 17. IOP Publishing Ltd., 2015.
ista: Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of
a Bose-Einstein condensate in a random potential. New Journal of Physics. 17,
013022.
mla: Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate
in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing
Ltd., 2015, doi:10.1088/1367-2630/17/1/013022.
short: M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics
17 (2015).
date_created: 2018-12-11T11:54:30Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '15'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1088/1367-2630/17/1/013022
file:
- access_level: open_access
checksum: 38fdf2b5ac30445e26a5d613abd84b16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:44Z
date_updated: 2020-07-14T12:45:20Z
file_id: '4963'
file_name: IST-2016-447-v1+1_document_1_.pdf
file_size: 768108
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5214'
pubrep_id: '447'
quality_controlled: '1'
scopus_import: 1
status: public
title: Superfluid behavior of a Bose-Einstein condensate in a random potential
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: 17
year: '2015'
...
---
_id: '1882'
abstract:
- lang: eng
text: We provide a framework for compositional and iterative design and verification
of systems with quantitative information, such as rewards, time or energy. It
is based on disjunctive modal transition systems where we allow actions to bear
various types of quantitative information. Throughout the design process the actions
can be further refined and the information made more precise. We show how to compute
the results of standard operations on the systems, including the quotient (residual),
which has not been previously considered for quantitative non-deterministic systems.
Our quantitative framework has close connections to the modal nu-calculus and
is compositional with respect to general notions of distances between systems
and the standard operations.
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.
alternative_title:
- LNCS
author:
- first_name: Uli
full_name: Fahrenberg, Uli
last_name: Fahrenberg
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Louis
full_name: Traonouez, Louis
last_name: Traonouez
citation:
ama: 'Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative
specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19'
apa: 'Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality
for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS:
Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19'
chicago: Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality
for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.
ieee: 'U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality
for quantitative specifications,” presented at the FACS: Formal Aspects of Component
Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.'
ista: 'Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for
quantitative specifications. FACS: Formal Aspects of Component Software, LNCS,
vol. 8997, 306–324.'
mla: Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications.
Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19.
short: U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015,
pp. 306–324.
conference:
end_date: 2014-09-12
location: Bertinoro, Italy
name: 'FACS: Formal Aspects of Component Software'
start_date: 2014-09-10
date_created: 2018-12-11T11:54:31Z
date_published: 2015-01-30T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '30'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-319-15317-9_19
ec_funded: 1
intvolume: ' 8997'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.1256
month: '01'
oa: 1
oa_version: Preprint
page: 306 - 324
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5216'
quality_controlled: '1'
scopus_import: 1
status: public
title: Compositionality for quantitative specifications
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8997
year: '2015'
...
---
_id: '1883'
abstract:
- lang: eng
text: "We introduce a one-parametric family of tree growth models, in which branching
probabilities decrease with branch age τ as τ-α. Depending on the exponent α,
the scaling of tree depth with tree size n displays a transition between the logarithmic
scaling of random trees and an algebraic growth. At the transition (α=1) tree
depth grows as (logn)2. This anomalous scaling is in good agreement with the trend
observed in evolution of biological species, thus providing a theoretical support
for age-dependent speciation and associating it to the occurrence of a critical
point.\r\n"
article_number: '022803'
article_processing_charge: No
article_type: original
author:
- first_name: Stephanie
full_name: Keller-Schmidt, Stephanie
last_name: Keller-Schmidt
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Víctor
full_name: Eguíluz, Víctor
last_name: Eguíluz
- first_name: Emilio
full_name: Hernandez Garcia, Emilio
last_name: Hernandez Garcia
- first_name: Konstantin
full_name: Klemm, Konstantin
last_name: Klemm
citation:
ama: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous
scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803
apa: Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm,
K. (2015). Anomalous scaling in an age-dependent branching model. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.91.022803
chicago: Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez
Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.
ieee: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm,
“Anomalous scaling in an age-dependent branching model,” Physical Review E
Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute
of Physics, 2015.
ista: Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015.
Anomalous scaling in an age-dependent branching model. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 91(2), 022803.
mla: Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching
Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.
short: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm,
Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:31Z
date_published: 2015-02-02T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '02'
department:
- _id: NiBa
doi: 10.1103/PhysRevE.91.022803
external_id:
arxiv:
- '1012.3298'
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1012.3298
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5213'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anomalous scaling in an age-dependent branching model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1878'
abstract:
- lang: eng
text: Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian
Peninsula, with some localized populations in the French Pyrenees. Within the
genus, a dozen species have been recognized based on morphological diversity,
most of them with limited distribution area, in small populations and frequently
with potential threats to their survival. To date, however, a molecular evaluation
of the current systematic treatments has not been carried out. The aim of the
present study is to infer phylogenetic relationships among its subordinate taxa
by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS)
DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis
within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by
both ITS and rps16 intron sequence analyses. Furthermore, time estimates using
BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26
Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD,
for rps16 intron).
author:
- first_name: Eduardo
full_name: Cires Rodriguez, Eduardo
id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87
last_name: Cires Rodriguez
- first_name: José
full_name: Prieto, José
last_name: Prieto
citation:
ama: Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun
ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal
of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6
apa: Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of
Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian
Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6
chicago: Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships
of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the
Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6.
ieee: E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis
A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,”
Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.
ista: Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis
A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula.
Journal of Plant Research. 128(2), 223–238.
mla: Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis
A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.”
Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38,
doi:10.1007/s10265-014-0691-6.
short: E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.
date_created: 2018-12-11T11:54:30Z
date_published: 2015-01-24T00:00:00Z
date_updated: 2021-01-12T06:53:47Z
day: '24'
department:
- _id: JiFr
doi: 10.1007/s10265-014-0691-6
intvolume: ' 128'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 223 - 238
publication: Journal of Plant Research
publication_status: published
publisher: Springer
publist_id: '5217'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae),
a discussed genus from the Iberian Peninsula
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2015'
...
---
_id: '1885'
abstract:
- lang: eng
text: 'The concept of positional information is central to our understanding of
how cells determine their location in a multicellular structure and thereby their
developmental fates. Nevertheless, positional information has neither been defined
mathematically nor quantified in a principled way. Here we provide an information-theoretic
definition in the context of developmental gene expression patterns and examine
the features of expression patterns that affect positional information quantitatively.
We connect positional information with the concept of positional error and develop
tools to directly measure information and error from experimental data. We illustrate
our framework for the case of gap gene expression patterns in the early Drosophila
embryo and show how information that is distributed among only four genes is sufficient
to determine developmental fates with nearly single-cell resolution. Our approach
can be generalized to a variety of different model systems; procedures and examples
are discussed in detail. '
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Julien
full_name: Dubuis, Julien
last_name: Dubuis
- first_name: Mariela
full_name: Petkova, Mariela
last_name: Petkova
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: 'Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
2015;199(1):39-59. doi:10.1534/genetics.114.171850'
apa: 'Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850'
chicago: 'Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional
Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical
Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.'
ieee: 'G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information,
positional error, and readout precision in morphogenesis: A mathematical framework,”
Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.'
ista: 'Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional
error, and readout precision in morphogenesis: A mathematical framework. Genetics.
199(1), 39–59.'
mla: 'Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout
Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199,
no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.'
short: G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.
date_created: 2018-12-11T11:54:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1534/genetics.114.171850
intvolume: ' 199'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.5599
month: '01'
oa: 1
oa_version: Preprint
page: 39 - 59
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5210'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Positional information, positional error, and readout precision in morphogenesis:
A mathematical framework'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2015'
...
---
_id: '1940'
abstract:
- lang: eng
text: We typically think of cells as responding to external signals independently
by regulating their gene expression levels, yet they often locally exchange information
and coordinate. Can such spatial coupling be of benefit for conveying signals
subject to gene regulatory noise? Here we extend our information-theoretic framework
for gene regulation to spatially extended systems. As an example, we consider
a lattice of nuclei responding to a concentration field of a transcriptional regulator
(the "input") by expressing a single diffusible target gene. When input
concentrations are low, diffusive coupling markedly improves information transmission;
optimal gene activation functions also systematically change. A qualitatively
new regulatory strategy emerges where individual cells respond to the input in
a nearly step-like fashion that is subsequently averaged out by strong diffusion.
While motivated by early patterning events in the Drosophila embryo, our framework
is generically applicable to spatially coupled stochastic gene expression models.
article_number: '062710'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks.
IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter
Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
apa: Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in
small genetic networks. IV. Spatial coupling. Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710
chicago: Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in
Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical
Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710.
ieee: T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic
networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and
Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.
ista: Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic
networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft
Matter Physics. 91(6), 062710.
mla: Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small
Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics,
2015, doi:10.1103/PhysRevE.91.062710.
short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft
Matter Physics 91 (2015).
date_created: 2018-12-11T11:54:49Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T06:54:13Z
day: '15'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.91.062710
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04015
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5145'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing information flow in small genetic networks. IV. Spatial coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '1938'
abstract:
- lang: eng
text: 'We numerically investigate the distribution of extrema of ''chaotic'' Laplacian
eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a)
we count extrema on grid graphs with a small number of randomly added edges and
show the behavior to coincide with the 1957 prediction of Longuet-Higgins for
the continuous case and (b) we compute the regularity of their spatial distribution
using discrepancy, which is a classical measure from the theory of Monte Carlo
integration. The first part suggests that grid graphs with randomly added edges
should behave like two-dimensional surfaces with ergodic geodesic flow; in the
second part we show that the extrema are more regularly distributed in space than
the grid Z2.'
acknowledgement: "F.P. was supported by the Graduate School of IST Austria. S.S. was
partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and
Michael Kerber for sharing their implementation of the persistence algorithm. "
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Stefan
full_name: Steinerberger, Stefan
last_name: Steinerberger
citation:
ama: Pausinger F, Steinerberger S. On the distribution of local extrema in quantum
chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010
apa: Pausinger, F., & Steinerberger, S. (2015). On the distribution of local
extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010
chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015.
https://doi.org/10.1016/j.physleta.2014.12.010.
ieee: F. Pausinger and S. Steinerberger, “On the distribution of local extrema in
quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier,
pp. 535–541, 2015.
ista: Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in
quantum chaos. Physics Letters, Section A. 379(6), 535–541.
mla: Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local
Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6,
Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.
short: F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.
date_created: 2018-12-11T11:54:49Z
date_published: 2015-03-06T00:00:00Z
date_updated: 2021-01-12T06:54:12Z
day: '06'
department:
- _id: HeEd
doi: 10.1016/j.physleta.2014.12.010
intvolume: ' 379'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 535 - 541
publication: Physics Letters, Section A
publication_status: published
publisher: Elsevier
publist_id: '5152'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the distribution of local extrema in quantum chaos
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 379
year: '2015'
...