---
_id: '1690'
abstract:
- lang: eng
text: A number of powerful and scalable hybrid systems model checkers have recently
emerged. Although all of them honor roughly the same hybrid systems semantics,
they have drastically different model description languages. This situation (a)
makes it difficult to quickly evaluate a specific hybrid automaton model using
the different tools, (b) obstructs comparisons of reachability approaches, and
(c) impedes the widespread application of research results that perform model
modification and could benefit many of the tools. In this paper, we present Hyst,
a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently
taking input in the SpaceEx model format, and translating to the formats of HyCreate,
Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation
passes that serve to both ease the translation and potentially improve reachability
results for the supported tools. Although these model transformation passes could
be implemented within each tool, the Hyst approach provides a single place for
model modification, generating modified input sources for the unmodified target
tools. Our evaluation demonstrates Hyst is capable of automatically translating
benchmarks in several classes (including affine and nonlinear hybrid automata)
to the input formats of several tools. Additionally, we illustrate a general model
transformation pass based on pseudo-invariants implemented in Hyst that illustrates
the reachability improvement.
acknowledgement: The material presented in this paper is based upon work sup-ported
by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through
the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115
and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings,
and conclusions or recommendations expressed in this publication are those of the
authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work
was also partly supported in part by the German Research Foundation (DFG) as part
of the Transregional Collaborative Research Center “Automatic Verification and Analysis
of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), by the European Research
Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF)
under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).
author:
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
citation:
ama: 'Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation
tool for hybrid automaton models. In: Springer; 2015:128-133. doi:10.1145/2728606.2728630'
apa: 'Bak, S., Bogomolov, S., & Johnson, T. (2015). HYST: A source transformation
and translation tool for hybrid automaton models (pp. 128–133). Presented at the
HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer.
https://doi.org/10.1145/2728606.2728630'
chicago: 'Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation
and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. https://doi.org/10.1145/2728606.2728630.'
ieee: 'S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and
translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems
- Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.'
ista: 'Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation
tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control,
128–133.'
mla: 'Bak, Stanley, et al. HYST: A Source Transformation and Translation Tool
for Hybrid Automaton Models. Springer, 2015, pp. 128–33, doi:10.1145/2728606.2728630.'
short: S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133.
conference:
end_date: 2015-04-16
location: Seattle, WA, United States
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2015-04-14
date_created: 2018-12-11T11:53:29Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2021-01-12T06:52:33Z
day: '14'
department:
- _id: ToHe
doi: 10.1145/2728606.2728630
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 128 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5454'
quality_controlled: '1'
status: public
title: 'HYST: A source transformation and translation tool for hybrid automaton models'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1691'
abstract:
- lang: eng
text: We consider a case study of the problem of deploying an autonomous air vehicle
in a partially observable, dynamic, indoor environment from a specification given
as a linear temporal logic (LTL) formula over regions of interest. We model the
motion and sensing capabilities of the vehicle as a partially observable Markov
decision process (POMDP). We adapt recent results for solving POMDPs with parity
objectives to generate a control policy. We also extend the existing framework
with a policy minimization technique to obtain a better implementable policy,
while preserving its correctness. The proposed techniques are illustrated in an
experimental setup involving an autonomous quadrotor performing surveillance in
a dynamic environment.
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Kevin
full_name: Leahy, Kevin
last_name: Leahy
- first_name: Hasan
full_name: Eniser, Hasan
last_name: Eniser
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Chmelik M, Leahy K, et al. Temporal logic motion planning using
POMDPs with parity objectives: Case study paper. In: Proceedings of the 18th
International Conference on Hybrid Systems: Computation and Control. ACM;
2015:233-238. doi:10.1145/2728606.2728617'
apa: 'Svoreňová, M., Chmelik, M., Leahy, K., Eniser, H., Chatterjee, K., Cěrná,
I., & Belta, C. (2015). Temporal logic motion planning using POMDPs with parity
objectives: Case study paper. In Proceedings of the 18th International Conference
on Hybrid Systems: Computation and Control (pp. 233–238). Seattle, WA, United
States: ACM. https://doi.org/10.1145/2728606.2728617'
chicago: 'Svoreňová, Mária, Martin Chmelik, Kevin Leahy, Hasan Eniser, Krishnendu
Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Motion Planning Using
POMDPs with Parity Objectives: Case Study Paper.” In Proceedings of the 18th
International Conference on Hybrid Systems: Computation and Control, 233–38.
ACM, 2015. https://doi.org/10.1145/2728606.2728617.'
ieee: 'M. Svoreňová et al., “Temporal logic motion planning using POMDPs
with parity objectives: Case study paper,” in Proceedings of the 18th International
Conference on Hybrid Systems: Computation and Control, Seattle, WA, United
States, 2015, pp. 233–238.'
ista: 'Svoreňová M, Chmelik M, Leahy K, Eniser H, Chatterjee K, Cěrná I, Belta C.
2015. Temporal logic motion planning using POMDPs with parity objectives: Case
study paper. Proceedings of the 18th International Conference on Hybrid Systems:
Computation and Control. HSCC: Hybrid Systems - Computation and Control, 233–238.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Motion Planning Using POMDPs with
Parity Objectives: Case Study Paper.” Proceedings of the 18th International
Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–38,
doi:10.1145/2728606.2728617.'
short: 'M. Svoreňová, M. Chmelik, K. Leahy, H. Eniser, K. Chatterjee, I. Cěrná,
C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems:
Computation and Control, ACM, 2015, pp. 233–238.'
conference:
end_date: 2015-04-16
location: Seattle, WA, United States
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2015-04-14
date_created: 2018-12-11T11:53:29Z
date_published: 2015-04-14T00:00:00Z
date_updated: 2021-01-12T06:52:33Z
day: '14'
department:
- _id: KrCh
doi: 10.1145/2728606.2728617
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 233 - 238
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 'Proceedings of the 18th International Conference on Hybrid Systems:
Computation and Control'
publication_status: published
publisher: ACM
publist_id: '5453'
scopus_import: 1
status: public
title: 'Temporal logic motion planning using POMDPs with parity objectives: Case study
paper'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1694'
abstract:
- lang: eng
text: "\r\nWe introduce quantitative timed refinement and timed simulation (directed)
metrics, incorporating zenoness checks, for timed systems. These metrics assign
positive real numbers which quantify the timing mismatches between two timed systems,
amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal
timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches,
where initial transient timing mismatches are ignored; and (3) the (long-run)
average timing mismatches amongst two systems. These three kinds of mismatches
constitute three important types of timing differences. Our event times are the
global times, measured from the start of the system execution, not just the time
durations of individual steps. We present algorithms over timed automata for computing
the three quantitative simulation distances to within any desired degree of accuracy.
In order to compute the values of the quantitative simulation distances, we use
a game theoretic formulation. We introduce two new kinds of objectives for two
player games on finite-state game graphs: (1) eventual debit-sum level objectives,
and (2) average debit-sum level objectives. We present algorithms for computing
the optimal values for these objectives in graph games, and then use these algorithms
to compute the values of the timed simulation distances over timed automata.\r\n"
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vinayak
full_name: Prabhu, Vinayak
last_name: Prabhu
citation:
ama: Chatterjee K, Prabhu V. Quantitative temporal simulation and refinement distances
for timed systems. IEEE Transactions on Automatic Control. 2015;60(9):2291-2306.
doi:10.1109/TAC.2015.2404612
apa: Chatterjee, K., & Prabhu, V. (2015). Quantitative temporal simulation and
refinement distances for timed systems. IEEE Transactions on Automatic Control.
IEEE. https://doi.org/10.1109/TAC.2015.2404612
chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation
and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic
Control. IEEE, 2015. https://doi.org/10.1109/TAC.2015.2404612.
ieee: K. Chatterjee and V. Prabhu, “Quantitative temporal simulation and refinement
distances for timed systems,” IEEE Transactions on Automatic Control, vol.
60, no. 9. IEEE, pp. 2291–2306, 2015.
ista: Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement
distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306.
mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation
and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic
Control, vol. 60, no. 9, IEEE, 2015, pp. 2291–306, doi:10.1109/TAC.2015.2404612.
short: K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015)
2291–2306.
date_created: 2018-12-11T11:53:30Z
date_published: 2015-02-24T00:00:00Z
date_updated: 2021-01-12T06:52:34Z
day: '24'
department:
- _id: KrCh
doi: 10.1109/TAC.2015.2404612
ec_funded: 1
intvolume: ' 60'
issue: '9'
language:
- iso: eng
month: '02'
oa_version: None
page: 2291 - 2306
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: IEEE Transactions on Automatic Control
publication_status: published
publisher: IEEE
publist_id: '5450'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative temporal simulation and refinement distances for timed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2015'
...
---
_id: '1695'
abstract:
- lang: eng
text: We give a comprehensive introduction into a diagrammatic method that allows
for the evaluation of Gutzwiller wave functions in finite spatial dimensions.
We discuss in detail some numerical schemes that turned out to be useful in the
real-space evaluation of the diagrams. The method is applied to the problem of
d-wave superconductivity in a two-dimensional single-band Hubbard model. Here,
we discuss in particular the role of long-range contributions in our diagrammatic
expansion. We further reconsider our previous analysis on the kinetic energy gain
in the superconducting state.
author:
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Tobias
full_name: Schickling, Tobias
last_name: Schickling
- first_name: Jörg
full_name: Bünemann, Jörg
last_name: Bünemann
citation:
ama: 'Kaczmarczyk J, Schickling T, Bünemann J. Evaluation techniques for Gutzwiller
wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid
State Physics. 2015;252(9):2059-2071. doi:10.1002/pssb.201552082'
apa: 'Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2015). Evaluation techniques
for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B):
Basic Solid State Physics. Wiley. https://doi.org/10.1002/pssb.201552082'
chicago: 'Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Evaluation Techniques
for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi
(B): Basic Solid State Physics. Wiley, 2015. https://doi.org/10.1002/pssb.201552082.'
ieee: 'J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Evaluation techniques for
Gutzwiller wave functions in finite dimensions,” Physica Status Solidi (B):
Basic Solid State Physics, vol. 252, no. 9. Wiley, pp. 2059–2071, 2015.'
ista: 'Kaczmarczyk J, Schickling T, Bünemann J. 2015. Evaluation techniques for
Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic
Solid State Physics. 252(9), 2059–2071.'
mla: 'Kaczmarczyk, Jan, et al. “Evaluation Techniques for Gutzwiller Wave Functions
in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics,
vol. 252, no. 9, Wiley, 2015, pp. 2059–71, doi:10.1002/pssb.201552082.'
short: 'J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic
Solid State Physics 252 (2015) 2059–2071.'
date_created: 2018-12-11T11:53:31Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:34Z
day: '01'
department:
- _id: MiLe
doi: 10.1002/pssb.201552082
ec_funded: 1
intvolume: ' 252'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1503.03738
month: '09'
oa: 1
oa_version: Preprint
page: 2059 - 2071
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Physica Status Solidi (B): Basic Solid State Physics'
publication_status: published
publisher: Wiley
publist_id: '5449'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evaluation techniques for Gutzwiller wave functions in finite dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 252
year: '2015'
...
---
_id: '1697'
abstract:
- lang: eng
text: Motion tracking is a challenge the visual system has to solve by reading out
the retinal population. It is still unclear how the information from different
neurons can be combined together to estimate the position of an object. Here we
recorded a large population of ganglion cells in a dense patch of salamander and
guinea pig retinas while displaying a bar moving diffusively. We show that the
bar’s position can be reconstructed from retinal activity with a precision in
the hyperacuity regime using a linear decoder acting on 100+ cells. We then took
advantage of this unprecedented precision to explore the spatial structure of
the retina’s population code. The classical view would have suggested that the
firing rates of the cells form a moving hill of activity tracking the bar’s position.
Instead, we found that most ganglion cells in the salamander fired sparsely and
idiosyncratically, so that their neural image did not track the bar. Furthermore,
ganglion cell activity spanned an area much larger than predicted by their receptive
fields, with cells coding for motion far in their surround. As a result, population
redundancy was high, and we could find multiple, disjoint subsets of neurons that
encoded the trajectory with high precision. This organization allows for diverse
collections of ganglion cells to represent high-accuracy motion information in
a form easily read out by downstream neural circuits.
acknowledgement: 'This work was supported by grants EY 014196 and EY 017934 to MJB,
ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence
Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the
Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to
VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010-
22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).'
article_number: e1004304
author:
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Kristina
full_name: Simmons, Kristina
last_name: Simmons
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy
decoding of dynamical motion from a large retinal population. PLoS Computational
Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304
apa: Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry,
M. (2015). High accuracy decoding of dynamical motion from a large retinal population.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304
chicago: Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora,
Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion
from a Large Retinal Population.” PLoS Computational Biology. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304.
ieee: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry,
“High accuracy decoding of dynamical motion from a large retinal population,”
PLoS Computational Biology, vol. 11, no. 7. Public Library of Science,
2015.
ista: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High
accuracy decoding of dynamical motion from a large retinal population. PLoS Computational
Biology. 11(7), e1004304.
mla: Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large
Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304,
Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
short: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS
Computational Biology 11 (2015).
date_created: 2018-12-11T11:53:31Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:52:35Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004304
file:
- access_level: open_access
checksum: 472b979f3f1cffb37b3e503f085115ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:25Z
date_updated: 2020-07-14T12:45:12Z
file_id: '5212'
file_name: IST-2016-455-v1+1_journal.pcbi.1004304.pdf
file_size: 4673930
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
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
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5447'
pubrep_id: '455'
quality_controlled: '1'
scopus_import: 1
status: public
title: High accuracy decoding of dynamical motion from a large retinal population
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: 11
year: '2015'
...
---
_id: '1699'
abstract:
- lang: eng
text: By hybridization and backcrossing, alleles can surmount species boundaries
and be incorporated into the genome of a related species. This introgression of
genes is of particular evolutionary relevance if it involves the transfer of adaptations
between populations. However, any beneficial allele will typically be associated
with other alien alleles that are often deleterious and hamper the introgression
process. In order to describe the introgression of an adaptive allele, we set
up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious
alleles. Based on the theory of reducible multitype branching processes, we derive
a recursive expression for the establishment probability of the beneficial allele
after a single hybridization event. We furthermore study the probability that
slightly deleterious alleles hitchhike to fixation. The key to the analysis is
a split of the process into a stochastic phase in which the advantageous alleles
establishes and a deterministic phase in which it sweeps to fixation. We thereafter
apply the theory to a set of biologically relevant scenarios such as introgression
in the presence of many unlinked or few closely linked deleterious alleles. A
comparison to computer simulations shows that the approximations work well over
a large parameter range.
acknowledgement: This work was made possible with financial support by the Vienna
Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG),
Research Unit 1078 Natural selection in structured populations, by the Austrian
Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics,
and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with
the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial
support from the Federal Ministry for Science and Research Austria).
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Derek
full_name: Setter, Derek
last_name: Setter
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y
apa: Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression
after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y
chicago: Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene
Introgression after Secondary Contact.” Journal of Mathematical Biology.
Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.
ieee: H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after
secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer,
pp. 1523–1580, 2015.
ista: Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 70(7), 1523–1580.
mla: Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.”
Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80,
doi:10.1007/s00285-014-0802-y.
short: H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015)
1523–1580.
date_created: 2018-12-11T11:53:32Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:10:36Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1007/s00285-014-0802-y
file:
- access_level: open_access
checksum: 00e3a67bda05d4cc165b3a48b41ef9ad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:27Z
date_updated: 2020-07-14T12:45:12Z
file_id: '5079'
file_name: IST-2016-458-v1+1_s00285-014-0802-y.pdf
file_size: 1321527
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1523 - 1580
project:
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: L'OREAL Fellowship
publication: Journal of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '5442'
pubrep_id: '458'
quality_controlled: '1'
scopus_import: 1
status: public
title: Adaptive gene introgression after secondary contact
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: 70
year: '2015'
...
---
_id: '1696'
abstract:
- lang: eng
text: The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller
wave function (GWF) is applied to the Anderson lattice model. This approach allows
for a systematic evaluation of the expectation values with full Gutzwiller wave
function in finite-dimensional systems. It introduces results extending in an
essential manner those obtained by means of the standard Gutzwiller approximation
(GA), which is variationally exact only in infinite dimensions. Within the DE-GWF
approach we discuss the principal paramagnetic properties and their relevance
to heavy-fermion systems. We demonstrate the formation of an effective, narrow
f band originating from atomic f-electron states and subsequently interpret this
behavior as a direct itineracy of f electrons; it represents a combined effect
of both the hybridization and the correlations induced by the Coulomb repulsive
interaction. Such a feature is absent on the level of GA, which is equivalent
to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent
narrow f band rationalizes the common assumption of such dispersion of f levels
in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it
is shown that the emerging f-electron direct itineracy leads in a natural manner
to three physically distinct regimes within a single model that are frequently
discussed for 4f- or 5f-electron compounds as separate model situations. We identify
these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating
regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very
close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging
correlated quantum liquid state are stressed.
acknowledgement: The work was partly supported by the National Science Centre (NCN)
under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality
of the Institute of Science and Technology Austria during the final stage of development
of the present work, as well as partial financial support from the Society-Environment-Technology
project of the Jagiellonian University for that stay. J.K. acknowledges support
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007-2013) under REA Grant Agreement No. [291734 ].
article_number: '125135'
author:
- first_name: Marcin
full_name: Wysokiński, Marcin
last_name: Wysokiński
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Jozef
full_name: Spałek, Jozef
last_name: Spałek
citation:
ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for
Anderson lattice model: Emerging universal regimes of heavy quasiparticle states.
Physical Review B. 2015;92(12). doi:10.1103/PhysRevB.92.125135'
apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2015). Gutzwiller wave
function solution for Anderson lattice model: Emerging universal regimes of heavy
quasiparticle states. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.125135'
chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave
Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy
Quasiparticle States.” Physical Review B. American Physical Society, 2015.
https://doi.org/10.1103/PhysRevB.92.125135.'
ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution
for Anderson lattice model: Emerging universal regimes of heavy quasiparticle
states,” Physical Review B, vol. 92, no. 12. American Physical Society,
2015.'
ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution
for Anderson lattice model: Emerging universal regimes of heavy quasiparticle
states. Physical Review B. 92(12), 125135.'
mla: 'Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson
Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical
Review B, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:10.1103/PhysRevB.92.125135.'
short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015).
date_created: 2018-12-11T11:53:31Z
date_published: 2015-09-18T00:00:00Z
date_updated: 2021-01-12T06:52:35Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.92.125135
ec_funded: 1
intvolume: ' 92'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1505.07003
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '5448'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Gutzwiller wave function solution for Anderson lattice model: Emerging universal
regimes of heavy quasiparticle states'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '1701'
abstract:
- lang: eng
text: 'The activity of a neural network is defined by patterns of spiking and silence
from the individual neurons. Because spikes are (relatively) sparse, patterns
of activity with increasing numbers of spikes are less probable, but, with more
spikes, the number of possible patterns increases. This tradeoff between probability
and numerosity is mathematically equivalent to the relationship between entropy
and energy in statistical physics. We construct this relationship for populations
of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination
of direct and model-based analyses of experiments on the response of this network
to naturalistic movies. We see signs of a thermodynamic limit, where the entropy
per neuron approaches a smooth function of the energy per neuron as N increases.
The form of this function corresponds to the distribution of activity being poised
near an unusual kind of critical point. We suggest further tests of criticality,
and give a brief discussion of its functional significance. '
acknowledgement: "Research was supported in part by National Science Foundation Grants
PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant
R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support
was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation,
by the W. M. Keck Foundation, and by the Simons Foundation."
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Stephanie
full_name: Palmer, Stephanie
last_name: Palmer
- first_name: Michael
full_name: Berry Ii, Michael
last_name: Berry Ii
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality
in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112
apa: Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., &
Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of
neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112
chicago: Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer,
Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality
in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112.
ieee: G. Tkačik et al., “Thermodynamics and signatures of criticality in
a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences,
pp. 11508–11513, 2015.
ista: Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015.
Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37),
11508–11513.
mla: Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network
of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015,
pp. 11508–13, doi:10.1073/pnas.1514188112.
short: G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek,
PNAS 112 (2015) 11508–11513.
date_created: 2018-12-11T11:53:33Z
date_published: 2015-09-15T00:00:00Z
date_updated: 2021-01-12T06:52:37Z
day: '15'
department:
- _id: GaTk
doi: 10.1073/pnas.1514188112
external_id:
pmid:
- '26330611'
intvolume: ' 112'
issue: '37'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/
month: '09'
oa: 1
oa_version: Submitted Version
page: 11508 - 11513
pmid: 1
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5440'
quality_controlled: '1'
scopus_import: 1
status: public
title: Thermodynamics and signatures of criticality in a network of neurons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1698'
abstract:
- lang: eng
text: 'In mean-payoff games, the objective of the protagonist is to ensure that
the limit average of an infinite sequence of numeric weights is nonnegative. In
energy games, the objective is to ensure that the running sum of weights is always
nonnegative. Multi-mean-payoff and multi-energy games replace individual weights
by tuples, and the limit average (resp., running sum) of each coordinate must
be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy
games and show inter-reducibility of multi-mean-payoff and multi-energy games
for finite-memory strategies. We improve the computational complexity for solving
both classes with finite-memory strategies: we prove coNP-completeness improving
the previous known EXPSPACE bound. For memoryless strategies, we show that deciding
the existence of a winning strategy for the protagonist is NP-complete. We present
the first solution of multi-mean-payoff games with infinite-memory strategies:
we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf
objectives are coNP-complete.'
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start
grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant
QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148),
ERC Start grant (279499: inVEST).'
author:
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- 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: Alexander
full_name: Rabinovich, Alexander
last_name: Rabinovich
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
citation:
ama: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The
complexity of multi-mean-payoff and multi-energy games. Information and Computation.
2015;241(4):177-196. doi:10.1016/j.ic.2015.03.001
apa: Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., &
Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games.
Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.001
chicago: Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger,
Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and
Multi-Energy Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.001.
ieee: Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J.
Raskin, “The complexity of multi-mean-payoff and multi-energy games,” Information
and Computation, vol. 241, no. 4. Elsevier, pp. 177–196, 2015.
ista: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015.
The complexity of multi-mean-payoff and multi-energy games. Information and Computation.
241(4), 177–196.
mla: Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy
Games.” Information and Computation, vol. 241, no. 4, Elsevier, 2015, pp.
177–96, doi:10.1016/j.ic.2015.03.001.
short: Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin,
Information and Computation 241 (2015) 177–196.
date_created: 2018-12-11T11:53:32Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:36Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2015.03.001
ec_funded: 1
intvolume: ' 241'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.3234
month: '04'
oa: 1
oa_version: Preprint
page: 177 - 196
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '5443'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of multi-mean-payoff and multi-energy games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 241
year: '2015'
...
---
_id: '1700'
abstract:
- lang: eng
text: We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard
model with long-range dipole-dipole interactions. By using a large-scale finite-temperature
calculation on a 64×64 square lattice we demonstrate the existence of a novel
phase, possessing an "ultralong-range" order. The fingerprint of this
phase - the density correlation function - features a nontrivial behavior on a
scale of tens of lattice sites. We study the properties and the stability of the
ultralong-range-ordered phase, and show that it is accessible in modern experiments
with ultracold polar molecules and magnetic atoms.
acknowledgement: The work is supported by European Research Council (ERC) Advanced
Grant No. 338957 FEMTO/NANO.
article_number: '081106'
author:
- first_name: Erik
full_name: Van Loon, Erik
last_name: Van Loon
- first_name: Mikhail
full_name: Katsnelson, Mikhail
last_name: Katsnelson
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard
model with long-range interactions. Physical Review B. 2015;92(8). doi:10.1103/PhysRevB.92.081106
apa: Van Loon, E., Katsnelson, M., & Lemeshko, M. (2015). Ultralong-range order
in the Fermi-Hubbard model with long-range interactions. Physical Review B.
American Physical Society. https://doi.org/10.1103/PhysRevB.92.081106
chicago: Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range
Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review
B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.081106.
ieee: E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the
Fermi-Hubbard model with long-range interactions,” Physical Review B, vol.
92, no. 8. American Physical Society, 2015.
ista: Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard
model with long-range interactions. Physical Review B. 92(8), 081106.
mla: Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with
Long-Range Interactions.” Physical Review B, vol. 92, no. 8, 081106, American
Physical Society, 2015, doi:10.1103/PhysRevB.92.081106.
short: E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015).
date_created: 2018-12-11T11:53:32Z
date_published: 2015-08-10T00:00:00Z
date_updated: 2021-01-12T06:52:37Z
day: '10'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.92.081106
intvolume: ' 92'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1506.06007
month: '08'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '5441'
scopus_import: 1
status: public
title: Ultralong-range order in the Fermi-Hubbard model with long-range interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '1704'
abstract:
- lang: eng
text: Given a convex function (Formula presented.) and two hermitian matrices A
and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative
entropy defined by (Formula presented.). Among other things, they prove that the
so-defined quantity is monotone if and only if (Formula presented.) is operator
monotone. The monotonicity is then used to properly define (Formula presented.)
for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space
by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional
projections (Formula presented.) with (Formula presented.) strongly, the limit
(Formula presented.) is shown to exist and to be independent of the sequence of
projections (Formula presented.). The question whether this sequence converges
to its "obvious" limit, namely (Formula presented.), has been left open.
We answer this question in principle affirmatively and show that (Formula presented.).
If the operators A and B are regular enough, that is (A − B), (Formula presented.)
and (Formula presented.) are trace-class, the identity (Formula presented.) holds.
author:
- first_name: Andreas
full_name: Deuchert, Andreas
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative
entropies. Letters in Mathematical Physics. 2015;105(10):1449-1466. doi:10.1007/s11005-015-0787-5
apa: Deuchert, A., Hainzl, C., & Seiringer, R. (2015). Note on a family of monotone
quantum relative entropies. Letters in Mathematical Physics. Springer.
https://doi.org/10.1007/s11005-015-0787-5
chicago: Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family
of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics.
Springer, 2015. https://doi.org/10.1007/s11005-015-0787-5.
ieee: A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum
relative entropies,” Letters in Mathematical Physics, vol. 105, no. 10.
Springer, pp. 1449–1466, 2015.
ista: Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum
relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466.
mla: Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.”
Letters in Mathematical Physics, vol. 105, no. 10, Springer, 2015, pp.
1449–66, doi:10.1007/s11005-015-0787-5.
short: A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105
(2015) 1449–1466.
date_created: 2018-12-11T11:53:34Z
date_published: 2015-08-05T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '05'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-015-0787-5
file:
- access_level: open_access
checksum: fd7307282a314cc1fbbaef77b187516b
content_type: application/pdf
creator: dernst
date_created: 2019-01-15T14:42:07Z
date_updated: 2020-07-14T12:45:13Z
file_id: '5836'
file_name: 2015_LettersMathPhys_Deuchert.pdf
file_size: 484967
relation: main_file
file_date_updated: 2020-07-14T12:45:13Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.07205
month: '08'
oa: 1
oa_version: Preprint
page: 1449 - 1466
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5432'
quality_controlled: '1'
scopus_import: 1
status: public
title: Note on a family of monotone quantum relative entropies
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2015'
...
---
_id: '1703'
abstract:
- lang: eng
text: Vegetation clearing and land-use change have depleted many natural plant communities
to the point where restoration is required. A major impediment to the success
of rebuilding complex vegetation communities is having regular access to sufficient
quantities of high-quality seed. Seed-production areas (SPAs) can help generate
this seed, but these must be underpinned by a broad genetic base to maximise the
evolutionary potential of restored populations. However, genetic bottlenecks can
occur at the collection, establishment and production stages in SPAs, requiring
genetic evaluation. This is especially relevant for species that may take many
years before a return on SPA investment is realised. Two recently established
yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated
to determine whether genetic bottlenecks had occurred between seed collection
and SPA establishment. No evidence was found to suggest that a significant loss
of genetic diversity had occurred at this stage, although there was a significant
difference in diversity between the two SPAs. Complex population genetic structure
was also observed in the seed used to source the SPAs, with up to eight groups
identified. Plant survival in the SPAs was influenced by seed collection location
but not by SPA location and was not associated with genetic diversity. There were
also no associations between genetic diversity and plant growth. These data highlighted
the importance of chance events when establishing SPAs and indicated that the
two yellow box SPAs are likely to provide genetically diverse seed sources for
future restoration projects, especially by pooling seed from both SPAs.
author:
- first_name: Linda
full_name: Broadhurst, Linda
last_name: Broadhurst
- first_name: Graham
full_name: Fifield, Graham
last_name: Fifield
- first_name: Bindi
full_name: Vanzella, Bindi
last_name: Vanzella
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic
structure of seed sources and the maintenance of genetic diversity during establishment
of two yellow box (Eucalyptus melliodora) seed-production areas. Australian
Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023
apa: Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation
of the genetic structure of seed sources and the maintenance of genetic diversity
during establishment of two yellow box (Eucalyptus melliodora) seed-production
areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023
chicago: Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup.
“An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of
Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora)
Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023.
ieee: L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas,”
Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.
ista: Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas.
Australian Journal of Botany. 63(5), 455–466.
mla: Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources
and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box
(Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany,
vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.
short: L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of
Botany 63 (2015) 455–466.
date_created: 2018-12-11T11:53:34Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '26'
department:
- _id: NiBa
doi: 10.1071/BT15023
intvolume: ' 63'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 455 - 466
publication: Australian Journal of Botany
publication_status: published
publisher: CSIRO
publist_id: '5434'
quality_controlled: '1'
scopus_import: 1
status: public
title: An evaluation of the genetic structure of seed sources and the maintenance
of genetic diversity during establishment of two yellow box (Eucalyptus melliodora)
seed-production areas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2015'
...
---
_id: '1706'
abstract:
- lang: eng
text: We consider a problem of learning kernels for use in SVM classification in
the multi-task and lifelong scenarios and provide generalization bounds on the
error of a large margin classifier. Our results show that, under mild conditions
on the family of kernels used for learning, solving several related tasks simultaneously
is beneficial over single task learning. In particular, as the number of observed
tasks grows, assuming that in the considered family of kernels there exists one
that yields low approximation error on all tasks, the overhead associated with
learning such a kernel vanishes and the complexity converges to that of learning
when this good kernel is given to the learner.
alternative_title:
- LNCS
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Shai
full_name: Ben David, Shai
last_name: Ben David
citation:
ama: 'Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol
9355. Springer; 2015:194-208. doi:10.1007/978-3-319-24486-0_13'
apa: 'Pentina, A., & Ben David, S. (2015). Multi-task and lifelong learning
of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning
Theory, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-319-24486-0_13'
chicago: Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning
of Kernels,” 9355:194–208. Springer, 2015. https://doi.org/10.1007/978-3-319-24486-0_13.
ieee: 'A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,”
presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol.
9355, pp. 194–208.'
ista: 'Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels.
ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.'
mla: Pentina, Anastasia, and Shai Ben David. Multi-Task and Lifelong Learning
of Kernels. Vol. 9355, Springer, 2015, pp. 194–208, doi:10.1007/978-3-319-24486-0_13.
short: A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208.
conference:
end_date: 2015-10-06
location: Banff, AB, Canada
name: 'ALT: Algorithmic Learning Theory'
start_date: 2015-10-04
date_created: 2018-12-11T11:53:35Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:39Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-319-24486-0_13
ec_funded: 1
intvolume: ' 9355'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1602.06531
month: '01'
oa: 1
oa_version: Preprint
page: 194 - 208
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Springer
publist_id: '5430'
quality_controlled: '1'
scopus_import: 1
status: public
title: Multi-task and lifelong learning of kernels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9355
year: '2015'
...
---
_id: '1712'
abstract:
- lang: eng
text: The majority of immune cells in Drosophila melanogaster are plasmatocytes;
they carry out similar functions to vertebrate macrophages, influencing development
as well as protecting against infection and cancer. Plasmatocytes, sometimes referred
to with the broader term of hemocytes, migrate widely during embryonic development
and cycle in the larvae between sessile and circulating positions. Here we discuss
the similarities of plasmatocyte developmental migration and its functions to
that of vertebrate macrophages, considering the recent controversy regarding the
functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings
on the significance of adhesion for plasmatocyte migration in the embryo, as well
as proliferation, trans-differentiation, and tumor responses in the larva. We
spotlight parallels throughout to vertebrate immune responses.
author:
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion
during embryonic development and larval immune responses. Current Opinion in
Cell Biology. 2015;36(10):71-79. doi:10.1016/j.ceb.2015.07.003
apa: Ratheesh, A., Belyaeva, V., & Siekhaus, D. E. (2015). Drosophila immune
cell migration and adhesion during embryonic development and larval immune responses.
Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.07.003
chicago: Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune
Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.”
Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.07.003.
ieee: A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration
and adhesion during embryonic development and larval immune responses,” Current
Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 71–79, 2015.
ista: Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration
and adhesion during embryonic development and larval immune responses. Current
Opinion in Cell Biology. 36(10), 71–79.
mla: Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during
Embryonic Development and Larval Immune Responses.” Current Opinion in Cell
Biology, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:10.1016/j.ceb.2015.07.003.
short: A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology
36 (2015) 71–79.
date_created: 2018-12-11T11:53:36Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:52:41Z
day: '01'
ddc:
- '573'
department:
- _id: DaSi
doi: 10.1016/j.ceb.2015.07.003
ec_funded: 1
file:
- access_level: open_access
checksum: bbb1ee39ca52929aefe4f48752b166ee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:44Z
date_updated: 2020-07-14T12:45:13Z
file_id: '5098'
file_name: IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf
file_size: 1023680
relation: main_file
file_date_updated: 2020-07-14T12:45:13Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 71 - 79
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '5421'
pubrep_id: '346'
quality_controlled: '1'
scopus_import: 1
status: public
title: Drosophila immune cell migration and adhesion during embryonic development
and larval immune responses
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2015'
...
---
_id: '1710'
abstract:
- lang: eng
text: 'We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by
a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles
incident on the hollow. It is assumed that u satisfies the so-called single impact
condition (SIC): each incident particle is elastically reflected by graph(u) and
goes away without hitting the graph of u anymore. We solve the problem: find the
function u minimizing the force of resistance created by the flow. We show that
the graph of the minimizer is formed by two arcs of parabolas symmetric to each
other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals
1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This
result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014),
pp. 2730-2742] stating in particular that the minimal resistance of a hollow in
higher dimensions equals 0.5. We additionally consider a similar problem of minimal
resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1
is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x =
(x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow
is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides
with 0.6435 when d = 1) and converges to 0.5 as d → ∞.'
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexander
full_name: Plakhov, Alexander
last_name: Plakhov
citation:
ama: Akopyan A, Plakhov A. Minimal resistance of curves under the single impact
assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769.
doi:10.1137/140993843
apa: Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the
single impact assumption. Society for Industrial and Applied Mathematics.
SIAM. https://doi.org/10.1137/140993843
chicago: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves
under the Single Impact Assumption.” Society for Industrial and Applied Mathematics.
SIAM, 2015. https://doi.org/10.1137/140993843.
ieee: A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single
impact assumption,” Society for Industrial and Applied Mathematics, vol.
47, no. 4. SIAM, pp. 2754–2769, 2015.
ista: Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single
impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769.
mla: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under
the Single Impact Assumption.” Society for Industrial and Applied Mathematics,
vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843.
short: A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47
(2015) 2754–2769.
date_created: 2018-12-11T11:53:36Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T06:52:41Z
day: '14'
department:
- _id: HeEd
doi: 10.1137/140993843
ec_funded: 1
intvolume: ' 47'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.3736
month: '07'
oa: 1
oa_version: Preprint
page: 2754 - 2769
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Society for Industrial and Applied Mathematics
publication_status: published
publisher: SIAM
publist_id: '5423'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimal resistance of curves under the single impact assumption
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '1730'
abstract:
- lang: eng
text: How much cutting is needed to simplify the topology of a surface? We provide
bounds for several instances of this question, for the minimum length of topologically
non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial
map in triangulated combinatorial surfaces (or their dual cross-metric counterpart).
Our work builds upon Riemannian systolic inequalities, which bound the minimum
length of non-trivial closed curves in terms of the genus and the area of the
surface. We first describe a systematic way to translate Riemannian systolic inequalities
to a discrete setting, and vice-versa. This implies a conjecture by Przytycka
and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993),
a number of new systolic inequalities in the discrete setting, and the fact that
a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s
systolic inequality for surfaces are essentially equivalent. We also discuss how
these proofs generalize to higher dimensions. Then we focus on topological decompositions
of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions
of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus
g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition.
Finally, we consider the problem of embedding a cut graph (or more generally a
cellular graph) with a given combinatorial map on a given surface. Using random
triangulations, we prove (essentially) that, for any choice of a combinatorial
map, there are some surfaces on which any cellular embedding with that combinatorial
map has length superlinear in the number of triangles of the triangulated combinatorial
surface. There is also a similar result for graphs embedded on polyhedral triangulations.
author:
- first_name: Éric
full_name: Colin De Verdière, Éric
last_name: Colin De Verdière
- first_name: Alfredo
full_name: Hubard, Alfredo
last_name: Hubard
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
citation:
ama: Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities
and decompositions of triangulated surfaces. Discrete & Computational Geometry.
2015;53(3):587-620. doi:10.1007/s00454-015-9679-9
apa: Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete
systolic inequalities and decompositions of triangulated surfaces. Discrete
& Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9
chicago: Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete
Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete
& Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9.
ieee: É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities
and decompositions of triangulated surfaces,” Discrete & Computational
Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015.
ista: Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities
and decompositions of triangulated surfaces. Discrete & Computational Geometry.
53(3), 587–620.
mla: Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions
of Triangulated Surfaces.” Discrete & Computational Geometry, vol.
53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9.
short: É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational
Geometry 53 (2015) 587–620.
date_created: 2018-12-11T11:53:42Z
date_published: 2015-04-02T00:00:00Z
date_updated: 2021-01-12T06:52:49Z
day: '02'
department:
- _id: UlWa
doi: 10.1007/s00454-015-9679-9
intvolume: ' 53'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.4036
month: '04'
oa: 1
oa_version: Preprint
page: 587 - 620
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5397'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discrete systolic inequalities and decompositions of triangulated surfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2015'
...
---
_id: '1728'
abstract:
- lang: eng
text: 'In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes
a characteristic pattern of gene expression. Here we quantify the Shh gradient
in the developing mouse neural tube and show that while the amplitude of the gradient
increases over time, the activity of the pathway transcriptional effectors, Gli
proteins, initially increases but later decreases. Computational analysis of the
pathway suggests three mechanisms that could contribute to this adaptation: transcriptional
upregulation of the inhibitory receptor Ptch1, transcriptional downregulation
of Gli and the differential stability of active and inactive Gli isoforms. Consistent
with this, Gli2 protein expression is downregulated during neural tube patterning
and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover,
the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels
from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation
of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics
of Shh signalling, resulting in different signalling dynamics in different cell
types.'
acknowledgement: C.P.B. gratefully acknowledges funding from the Wellcome Trust through
a Research Career Development Fellowship (097319/Z/11/Z). This work was supported
by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA).
author:
- first_name: Michael
full_name: Cohen, Michael H
last_name: Cohen
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Ana
full_name: Ribeiro, Ana C
last_name: Ribeiro
- first_name: Robert
full_name: Blassberg, Robert A
last_name: Blassberg
- first_name: Karen
full_name: Page, Karen M
last_name: Page
- first_name: Chris
full_name: Barnes, Chris P
last_name: Barnes
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
citation:
ama: Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling
dynamics via multiple mechanisms. Nature Communications. 2015;6. doi:10.1038/ncomms7709
apa: Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., &
Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple
mechanisms. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7709
chicago: Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page,
Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics
via Multiple Mechanisms.” Nature Communications. Nature Publishing Group,
2015. https://doi.org/10.1038/ncomms7709.
ieee: M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via
multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing
Group, 2015.
ista: Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015.
Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature
Communications. 6.
mla: Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via
Multiple Mechanisms.” Nature Communications, vol. 6, Nature Publishing
Group, 2015, doi:10.1038/ncomms7709.
short: M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe,
Nature Communications 6 (2015).
date_created: 2018-12-11T11:53:42Z
date_published: 2015-04-02T00:00:00Z
date_updated: 2021-01-12T06:52:48Z
day: '02'
doi: 10.1038/ncomms7709
extern: 1
intvolume: ' 6'
month: '04'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5399'
quality_controlled: 0
status: public
title: Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms
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
volume: 6
year: '2015'
...
---
_id: '1735'
abstract:
- lang: eng
text: This work presents a method for efficiently simplifying the pressure projection
step in a liquid simulation. We first devise a straightforward dimension reduction
technique that dramatically reduces the cost of solving the pressure projection.
Next, we introduce a novel change of basis that satisfies free-surface boundary
conditions exactly, regardless of the accuracy of the pressure solve. When combined,
these ideas greatly reduce the computational complexity of the pressure solve
without compromising free surface boundary conditions at the highest level of
detail. Our techniques are easy to parallelize, and they effectively eliminate
the computational bottleneck for large liquid simulations.
acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship
for Research Abroad
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thürey, Nils
last_name: Thürey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid
simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576
apa: Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure
solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576
chicago: Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure
Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576.
ieee: R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for
liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp.
473–480, 2015.
ista: Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for
liquid simulations. Computer Graphics Forum. 34(2), 473–480.
mla: Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.”
Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576.
short: R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.
date_created: 2018-12-11T11:53:44Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-23T10:12:11Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12576
file:
- access_level: open_access
checksum: 590752bf977855b337a80f78a9bc2404
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:30Z
date_updated: 2020-07-14T12:45:15Z
file_id: '5218'
file_name: IST-2016-607-v1+1_coarsegrid.pdf
file_size: 6312352
relation: main_file
file_date_updated: 2020-07-14T12:45:15Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 473 - 480
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley
publist_id: '5389'
pubrep_id: '607'
quality_controlled: '1'
scopus_import: 1
status: public
title: A dimension-reduced pressure solver for liquid simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1734'
abstract:
- lang: eng
text: Facial appearance capture is now firmly established within academic research
and used extensively across various application domains, perhaps most prominently
in the entertainment industry through the design of virtual characters in video
games and films. While significant progress has occurred over the last two decades,
no single survey currently exists that discusses the similarities, differences,
and practical considerations of the available appearance capture techniques as
applied to human faces. A central difficulty of facial appearance capture is the
way light interacts with skin-which has a complex multi-layered structure-and
the interactions that occur below the skin surface can, by definition, only be
observed indirectly. In this report, we distinguish between two broad strategies
for dealing with this complexity. "Image-based methods" try to exhaustively
capture the exact face appearance under different lighting and viewing conditions,
and then render the face through weighted image combinations. "Parametric
methods" instead fit the captured reflectance data to some parametric appearance
model used during rendering, allowing for a more lightweight and flexible representation
but at the cost of potentially increased rendering complexity or inexact reproduction.
The goal of this report is to provide an overview that can guide practitioners
and researchers in assessing the tradeoffs between current approaches and identifying
directions for future advances in facial appearance capture.
author:
- first_name: Oliver
full_name: Klehm, Oliver
last_name: Klehm
- first_name: Fabrice
full_name: Rousselle, Fabrice
last_name: Rousselle
- first_name: Marios
full_name: Papas, Marios
last_name: Papas
- first_name: Derek
full_name: Bradley, Derek
last_name: Bradley
- first_name: Christophe
full_name: Hery, Christophe
last_name: Hery
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Wojciech
full_name: Jarosz, Wojciech
last_name: Jarosz
- first_name: Thabo
full_name: Beeler, Thabo
last_name: Beeler
citation:
ama: Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance
capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594
apa: Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler,
T. (2015). Recent advances in facial appearance capture. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594
chicago: Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe
Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial
Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594.
ieee: O. Klehm et al., “Recent advances in facial appearance capture,” Computer
Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.
ista: Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler
T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum.
34(2), 709–733.
mla: Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer
Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594.
short: O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz,
T. Beeler, Computer Graphics Forum 34 (2015) 709–733.
date_created: 2018-12-11T11:53:43Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:52Z
day: '01'
department:
- _id: BeBi
doi: 10.1111/cgf.12594
intvolume: ' 34'
issue: '2'
language:
- iso: eng
main_file_link:
- url: https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf
month: '05'
oa_version: None
page: 709 - 733
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5391'
quality_controlled: '1'
scopus_import: 1
status: public
title: Recent advances in facial appearance capture
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1789'
abstract:
- lang: eng
text: Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its
extreme heterogeneity, the genetic basis of ID remains elusive in many cases.
Recently, whole exome sequencing (WES) studies revealed that a large proportion
of sporadic cases are caused by de novo gene variants. To identify further genes
involved in ID, we performed WES in 250 patients with unexplained ID and their
unaffected parents and included exomes of 51 previously sequenced child-parents
trios in the analysis. Exome analysis revealed de novo intragenic variants in
SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense
variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal
microarray diagnostics further identified four de novo non-recurrent microdeletions
encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants
demonstrated nonsense-mediated decay of the resulting transcripts, pointing to
a loss-of-function (LoF) and haploinsufficiency as the common disease-causing
mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions.
In silico domain prediction of SETD5, a predicted SET domain-containing histone
methyltransferase (HMT), substantiated the presence of a SET domain and identified
a novel putative PHD domain, strengthening a functional link to well-known histone-modifying
ID genes. All six patients presented with ID and certain facial dysmorphisms,
suggesting that SETD5 sequence variants contribute substantially to the microdeletion
3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients
demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent
cause of ID.
author:
- first_name: Alma
full_name: Kuechler, Alma
last_name: Kuechler
- first_name: Alexander
full_name: Zink, Alexander
last_name: Zink
- first_name: Thomas
full_name: Wieland, Thomas
last_name: Wieland
- first_name: Hermann
full_name: Lüdecke, Hermann
last_name: Lüdecke
- first_name: Kirsten
full_name: Cremer, Kirsten
last_name: Cremer
- first_name: Leonardo
full_name: Salviati, Leonardo
last_name: Salviati
- first_name: Pamela
full_name: Magini, Pamela
last_name: Magini
- first_name: Kimia
full_name: Najafi, Kimia
last_name: Najafi
- first_name: Christiane
full_name: Zweier, Christiane
last_name: Zweier
- first_name: Johanna
full_name: Czeschik, Johanna
last_name: Czeschik
- first_name: Stefan
full_name: Aretz, Stefan
last_name: Aretz
- first_name: Sabine
full_name: Endele, Sabine
last_name: Endele
- first_name: Federica
full_name: Tamburrino, Federica
last_name: Tamburrino
- first_name: Claudia
full_name: Pinato, Claudia
last_name: Pinato
- first_name: Maurizio
full_name: Clementi, Maurizio
last_name: Clementi
- first_name: Jasmin
full_name: Gundlach, Jasmin
last_name: Gundlach
- first_name: Carina
full_name: Maylahn, Carina
last_name: Maylahn
- first_name: Laura
full_name: Mazzanti, Laura
last_name: Mazzanti
- first_name: Eva
full_name: Wohlleber, Eva
last_name: Wohlleber
- first_name: Thomas
full_name: Schwarzmayr, Thomas
last_name: Schwarzmayr
- first_name: Roxana
full_name: Kariminejad, Roxana
last_name: Kariminejad
- first_name: Avner
full_name: Schlessinger, Avner
last_name: Schlessinger
- first_name: Dagmar
full_name: Wieczorek, Dagmar
last_name: Wieczorek
- first_name: Tim
full_name: Strom, Tim
last_name: Strom
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Hartmut
full_name: Engels, Hartmut
last_name: Engels
citation:
ama: Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause
intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome.
European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165
apa: Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L.,
… Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability
and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of
Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165
chicago: Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten
Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of
SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3
Syndrome.” European Journal of Human Genetics. Nature Publishing Group,
2015. https://doi.org/10.1038/ejhg.2014.165.
ieee: A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual
disability and the core phenotype of microdeletion 3p25.3 syndrome,” European
Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760,
2015.
ista: Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P,
Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi
M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad
R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function
variants of SETD5 cause intellectual disability and the core phenotype of microdeletion
3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.
mla: Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual
Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European
Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015,
pp. 753–60, doi:10.1038/ejhg.2014.165.
short: A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P.
Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino,
C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T.
Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino,
H. Engels, European Journal of Human Genetics 23 (2015) 753–760.
date_created: 2018-12-11T11:54:01Z
date_published: 2015-06-15T00:00:00Z
date_updated: 2021-01-12T06:53:12Z
day: '15'
department:
- _id: GaNo
doi: 10.1038/ejhg.2014.165
external_id:
pmid:
- '25138099'
intvolume: ' 23'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/
month: '06'
oa: 1
oa_version: Submitted Version
page: 753 - 760
pmid: 1
publication: European Journal of Human Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '5324'
quality_controlled: '1'
status: public
title: Loss-of-function variants of SETD5 cause intellectual disability and the core
phenotype of microdeletion 3p25.3 syndrome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2015'
...