---
_id: '9871'
abstract:
- lang: eng
text: The positional information in a discrete morphogen field with Gaussian noise
is computed.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in
a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional
information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of
Positional Information in a Discrete Morphogen Field.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pone.0163628.s003.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information
in a discrete morphogen field.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information
in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.
mla: Hillenbrand, Patrick, et al. Computation of Positional Information in a
Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T09:27:35Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s003
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Computation of positional information in a discrete morphogen field
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9873'
article_processing_charge: No
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification
of the growth rate reduction as a consequence of age-specific mortality. 2016.
doi:10.1371/journal.pgen.1005974.s015
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Quantification of the growth rate reduction as a consequence of age-specific
mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as
a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Quantification of the growth rate reduction as a consequence of age-specific
mortality.” Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Quantification of the growth rate reduction as a consequence of age-specific mortality,
Public Library of Science, 10.1371/journal.pgen.1005974.s015.
mla: Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence
of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
(2016).
date_created: 2021-08-10T09:42:34Z
date_updated: 2023-02-21T16:50:13Z
day: '19'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974.s015
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1250'
relation: used_in_publication
status: public
status: public
title: Quantification of the growth rate reduction as a consequence of age-specific
mortality
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '10794'
abstract:
- lang: eng
text: Mathematical models are of fundamental importance in the understanding of
complex population dynamics. For instance, they can be used to predict the population
evolution starting from different initial conditions or to test how a system responds
to external perturbations. For this analysis to be meaningful in real applications,
however, it is of paramount importance to choose an appropriate model structure
and to infer the model parameters from measured data. While many parameter inference
methods are available for models based on deterministic ordinary differential
equations, the same does not hold for more detailed individual-based models. Here
we consider, in particular, stochastic models in which the time evolution of the
species abundances is described by a continuous-time Markov chain. These models
are governed by a master equation that is typically difficult to solve. Consequently,
traditional inference methods that rely on iterative evaluation of parameter likelihoods
are computationally intractable. The aim of this paper is to present recent advances
in parameter inference for continuous-time Markov chain models, based on a moment
closure approximation of the parameter likelihood, and to investigate how these
results can help in understanding, and ultimately controlling, complex systems
in ecology. Specifically, we illustrate through an agricultural pest case study
how parameters of a stochastic individual-based model can be identified from measured
data and how the resulting model can be used to solve an optimal control problem
in a stochastic setting. In particular, we show how the matter of determining
the optimal combination of two different pest control methods can be formulated
as a chance constrained optimization problem where the control action is modeled
as a state reset, leading to a hybrid system formulation.
acknowledgement: "The authors would like to acknowledge contributions from Baptiste
Mottet who performed preliminary analysis regarding parameter inference for the
considered case study in a student project (Mottet, 2014/2015).\r\nThe research
leading to these results has received funding from the People Programme (Marie Curie
Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement No. [291734] and from SystemsX under the project SignalX."
article_number: '42'
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in
Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042'
apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic
individual-based models of ecological systems: a pest control simulation study.
Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042'
chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference
for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation
Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.'
ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study,” Frontiers in
Environmental Science, vol. 3. Frontiers, 2015.'
ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in Environmental
Science. 3, 42.'
mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based
Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in
Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.'
short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
date_created: 2022-02-25T11:42:25Z
date_published: 2015-06-10T00:00:00Z
date_updated: 2022-02-25T11:59:23Z
day: '10'
ddc:
- '000'
- '570'
department:
- _id: ToHe
- _id: GaTk
doi: 10.3389/fenvs.2015.00042
ec_funded: 1
file:
- access_level: open_access
checksum: 26c222487564e1be02a11d688d6f769d
content_type: application/pdf
creator: dernst
date_created: 2022-02-25T11:55:26Z
date_updated: 2022-02-25T11:55:26Z
file_id: '10795'
file_name: 2015_FrontiersEnvironmScience_Parise.pdf
file_size: 1371201
relation: main_file
success: 1
file_date_updated: 2022-02-25T11:55:26Z
has_accepted_license: '1'
intvolume: ' 3'
keyword:
- General Environmental Science
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Environmental Science
publication_identifier:
issn:
- 2296-665X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bayesian inference for stochastic individual-based models of ecological systems:
a pest control simulation study'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2015'
...
---
_id: '10796'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
acknowledgement: "The research was partly supported by FWF Grant No P 23499-N23, FWF
NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies
for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029.
doi:10.1137/1.9781611973730.69'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029).
San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings
of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29.
SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.
ieee: K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory
strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States,
2015, vol. 2015, no. 1, pp. 1018–1029.
ista: 'Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms
vol. 2015, 1018–1029.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of
the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015,
no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.
conference:
end_date: 2015-01-06
location: San Diego, CA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2015-01-04
date_created: 2022-02-25T12:18:43Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-02-25T12:33:32Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973730.69
ec_funded: 1
external_id:
arxiv:
- '1409.6690'
intvolume: ' 2015'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 1018-1029
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete
Algorithms
publication_identifier:
isbn:
- 978-161197374-7
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: The value 1 problem under finite-memory strategies for concurrent mean-payoff
games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '8183'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex $K$ can be mapped
to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding
is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint
simplices of $K$ do not have a common point. We show that if $r$ is not a prime
power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg
conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex
in $\\mathbb R^d$. This improves on previous constructions of counterexamples
(for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P.
Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors.
The counterexamples are obtained by proving the following algebraic criterion
in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there
exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists
a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection
number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero.
This result can be restated in terms of cohomological obstructions or equivariant
maps, and extends an analogous codimension 3 criterion by the second and fourth
authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup
S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M.
Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is
false. We prove a lemma on singular higher-dimensional Borromean rings, yielding
an elementary proof of the counterexample."
acknowledgement: We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M.
Tancer, P. Teichner and anonymous referees for helpful discussions.
article_number: '1511.03501'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: A.
full_name: Skopenkov, A.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv.
apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating
higher-multiplicity intersections, III. Codimension 2. arXiv.
chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.
ieee: S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections, III. Codimension 2,” arXiv. .
ista: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv, 1511.03501.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III.
Codimension 2.” ArXiv, 1511.03501.
short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).
date_created: 2020-07-30T10:45:19Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '15'
department:
- _id: UlWa
external_id:
arxiv:
- '1511.03501'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9308'
relation: later_version
status: public
- id: '10220'
relation: later_version
status: public
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Eliminating higher-multiplicity intersections, III. Codimension 2
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1615'
abstract:
- lang: eng
text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are
among the most common genetic abnormalities associated with autism spectrum disorders,
but little is known about the function of Neuroligin-4 and the consequences of
its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout
mice, focusing on the hippocampus as a model brain region with a critical role
in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects
of the protein composition and function of GABAergic synapses in the hippocampal
CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced
perturbations of γ-oscillatory network activity, which has been implicated in
cognitive function and is altered in multiple psychiatric and neurodevelopmental
disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent
GABAergic synapses may contribute to autism phenotypes and indicate new strategies
for therapeutic approaches.
acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.),
the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.),
the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von
Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen
Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular
Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody.
We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler
for valuable advice and excellent technical support. We are grateful to the staff
at the animal facility of the Max Planck Institute of Experimental Medicine for
mouse husbandry.
author:
- first_name: Matthieu
full_name: Hammer, Matthieu
last_name: Hammer
- first_name: Dilja
full_name: Krueger Burg, Dilja
last_name: Krueger Burg
- first_name: Liam
full_name: Tuffy, Liam
last_name: Tuffy
- first_name: Benjamin
full_name: Cooper, Benjamin
last_name: Cooper
- first_name: Holger
full_name: Taschenberger, Holger
last_name: Taschenberger
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Hannelore
full_name: Ehrenreich, Hannelore
last_name: Ehrenreich
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Frederique
full_name: Varoqueaux, Frederique
last_name: Varoqueaux
- first_name: Jeong
full_name: Rhee, Jeong
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
citation:
ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition
and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports.
2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011
apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami,
S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press.
https://doi.org/10.1016/j.celrep.2015.09.011
chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger
Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal
Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model
of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.
ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13,
no. 3. Cell Press, pp. 516–523, 2015.
ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich
H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic
inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism.
Cell Reports. 13(3), 516–523.
mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations
in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13,
no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.
short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami,
H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015)
516–523.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-10-20T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '20'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2015.09.011
file:
- access_level: open_access
checksum: 44d30fbb543774b076b4938bd36af9d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:23Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5005'
file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf
file_size: 2314406
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 516 - 523
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5551'
pubrep_id: '470'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4
knockout mouse model of autism
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: 13
year: '2015'
...
---
_id: '1618'
abstract:
- lang: eng
text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells,
particularly within the lymphatic system, through activation of CCR7. Concurrent
expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells
to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of
CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping
shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19
and binding is competitive. Implications for the mechanism of PSGL-1's enhancement
of resting T-cell recruitment are discussed.
article_processing_charge: No
author:
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Skylar
full_name: Gabel Eissens, Skylar
last_name: Gabel Eissens
- first_name: Miranda
full_name: Gillitzer, Miranda
last_name: Gillitzer
- first_name: David
full_name: Lippner, David
last_name: Lippner
- first_name: Frank
full_name: Disilvio, Frank
last_name: Disilvio
- first_name: Casey
full_name: Mueller, Casey
last_name: Mueller
- first_name: Paeton
full_name: Wantuch, Paeton
last_name: Wantuch
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Michael
full_name: Famiglietti, Michael
last_name: Famiglietti
- first_name: Danielle
full_name: Zgoba, Danielle
last_name: Zgoba
- first_name: Asha
full_name: Bailey, Asha
last_name: Bailey
- first_name: Yaya
full_name: Bah, Yaya
last_name: Bah
- first_name: Samantha
full_name: Engebretson, Samantha
last_name: Engebretson
- first_name: David
full_name: Graupner, David
last_name: Graupner
- first_name: Emily
full_name: Lackner, Emily
last_name: Lackner
- first_name: Vincent
full_name: Larosa, Vincent
last_name: Larosa
- first_name: Tysha
full_name: Medeiros, Tysha
last_name: Medeiros
- first_name: Michael
full_name: Olson, Michael
last_name: Olson
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Harley
full_name: Pyles, Harley
last_name: Pyles
- first_name: Amanda
full_name: Richard, Amanda
last_name: Richard
- first_name: Scott
full_name: Schoeller, Scott
last_name: Schoeller
- first_name: Boris
full_name: Touzeau, Boris
last_name: Touzeau
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Francis
full_name: Peterson, Francis
last_name: Peterson
citation:
ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19
and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry.
2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560
apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D.,
Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical
Society. https://doi.org/10.1021/acs.biochem.5b00560
chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer,
David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19
and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry.
American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.
ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no.
27. American Chemical Society, pp. 4163–4166, 2015.
ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio
F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson
S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H,
Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution
structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites.
Biochemistry. 54(27), 4163–4166.
mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification
of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no.
27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.
short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F.
Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey,
Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson,
A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K.
Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.
date_created: 2018-12-11T11:53:03Z
date_published: 2015-06-26T00:00:00Z
date_updated: 2023-03-30T11:32:57Z
day: '26'
department:
- _id: MiSi
doi: 10.1021/acs.biochem.5b00560
ec_funded: 1
external_id:
pmid:
- '26115234'
intvolume: ' 54'
issue: '27'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/
month: '06'
oa: 1
oa_version: Submitted Version
page: 4163 - 4166
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Biochemistry
publication_status: published
publisher: American Chemical Society
publist_id: '5548'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1
binding sites
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '1619'
abstract:
- lang: eng
text: The emergence of drug resistant pathogens is a serious public health problem.
It is a long-standing goal to predict rates of resistance evolution and design
optimal treatment strategies accordingly. To this end, it is crucial to reveal
the underlying causes of drug-specific differences in the evolutionary dynamics
leading to resistance. However, it remains largely unknown why the rates of resistance
evolution via spontaneous mutations and the diversity of mutational paths vary
substantially between drugs. Here we comprehensively quantify the distribution
of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics,
in the presence of eight antibiotics representing the main modes of action. Using
precise high-throughput fitness measurements for genome-wide Escherichia coli
gene deletion strains, we find that the width of the DFE varies dramatically between
antibiotics and, contrary to conventional wisdom, for some drugs the DFE width
is lower than in the absence of stress. We show that this previously underappreciated
divergence in DFE width among antibiotics is largely caused by their distinct
drug-specific dose-response characteristics. Unlike the DFE, the magnitude of
the changes in tolerated drug concentration resulting from genome-wide mutations
is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin,
i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin
than for other drugs. A population genetics model predicts that resistance evolution
for drugs with this property is severely limited and confined to reproducible
mutational paths. We tested this prediction in laboratory evolution experiments
using the “morbidostat”, a device for evolving bacteria in well-controlled drug
environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible
mutations—an almost paradoxical behavior since this drug causes DNA damage and
increases the mutation rate. Overall, we identified novel quantitative characteristics
of the evolutionary landscape that provide the conceptual foundation for predicting
the dynamics of drug resistance evolution.
article_number: e1002299
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Dravecka, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Dravecka
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay
full_name: Ayhan, Dilay
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of
evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11).
doi:10.1371/journal.pbio.1002299
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak,
E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary
dynamics leading to drug resistance. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants
of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.
ieee: G. Chevereau et al., “Quantifying the determinants of evolutionary
dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public
Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach
MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug
resistance. PLoS Biology. 13(11), e1002299.
mla: Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary
Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299,
Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak,
M.T. Bollenbach, PLoS Biology 13 (2015).
date_created: 2018-12-11T11:53:04Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '18'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299
ec_funded: 1
file:
- access_level: open_access
checksum: 0e82e3279f50b15c6c170c042627802b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:00Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4723'
file_name: IST-2016-468-v1+1_journal.pbio.1002299.pdf
file_size: 1387760
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5547'
pubrep_id: '468'
quality_controlled: '1'
related_material:
record:
- id: '9711'
relation: research_data
status: public
- id: '9765'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantifying the determinants of evolutionary dynamics leading to drug resistance
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: 13
year: '2015'
...
---
_id: '1623'
abstract:
- lang: eng
text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of
biotechnological applications including biofuel production. However, due to slow
growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe
present a method for high-throughput, single-cell analysis and sorting of genetically
engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic
device is used to encapsulate single cells in picoliter droplets, assay the droplets
for l-lactate production, and sort strains with high productivity. We demonstrate
the separation of low- and high-producing reference strains, as well as enrichment
of a more productive l-lactate-synthesizing population after UV-induced mutagenesis.
The droplet platform also revealed population heterogeneity in photosynthetic
growth and lactate production, as well as the presence of metabolically stalled
cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and
directed evolution studies and will be useful in studies of cyanobacteria biochemistry
and physiology.\r\n"
article_number: '193'
author:
- first_name: Petter
full_name: Hammar, Petter
last_name: Hammar
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Staffan
full_name: Sjostrom, Staffan
last_name: Sjostrom
- first_name: Josefin
full_name: Van Der Meer, Josefin
last_name: Van Der Meer
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Elton
full_name: Hudson, Elton
last_name: Hudson
- first_name: Hakaan
full_name: Joensson, Hakaan
last_name: Joensson
citation:
ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
2015;8(1). doi:10.1186/s13068-015-0380-2
apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K.,
Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
BioMed Central. https://doi.org/10.1186/s13068-015-0380-2
chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer,
Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of
Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology
for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.
ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and
lactate production by cyanobacteria,” Biotechnology for Biofuels, vol.
8, no. 1. BioMed Central, 2015.
ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E,
Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production
by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.
mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and
Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol.
8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.
short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E.
Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).
date_created: 2018-12-11T11:53:05Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '25'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1186/s13068-015-0380-2
file:
- access_level: open_access
checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:11Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4796'
file_name: IST-2016-467-v1+1_s13068-015-0380-2.pdf
file_size: 2914089
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Biotechnology for Biofuels
publication_status: published
publisher: BioMed Central
publist_id: '5537'
pubrep_id: '467'
quality_controlled: '1'
scopus_import: 1
status: public
title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria
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: 8
year: '2015'
...
---
_id: '1624'
abstract:
- lang: eng
text: Population structure can facilitate evolution of cooperation. In a structured
population, cooperators can form clusters which resist exploitation by defectors.
Recently, it was observed that a shift update rule is an extremely strong amplifier
of cooperation in a one dimensional spatial model. For the shift update rule,
an individual is chosen for reproduction proportional to fecundity; the offspring
is placed next to the parent; a random individual dies. Subsequently, the population
is rearranged (shifted) until all individual cells are again evenly spaced out.
For large population size and a one dimensional population structure, the shift
update rule favors cooperation for any benefit-to-cost ratio greater than one.
But every attempt to generalize shift updating to higher dimensions while maintaining
its strong effect has failed. The reason is that in two dimensions the clusters
are fragmented by the movements caused by rearranging the cells. Here we introduce
the natural phenomenon of a repulsive force between cells of different types.
After a birth and death event, the cells are being rearranged minimizing the overall
energy expenditure. If the repulsive force is sufficiently high, shift becomes
a strong promoter of cooperation in two dimensions.
acknowledgement: 'The research was supported by the Austrian Science Fund (FWF) Grant
No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:
Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton
foundation is gratefully acknowledged.'
article_number: '17147'
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift
updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147
apa: Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular
cooperation with shift updating and repulsion. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep17147
chicago: Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak.
“Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports.
Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147.
ieee: A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation
with shift updating and repulsion,” Scientific Reports, vol. 5. Nature
Publishing Group, 2015.
ista: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation
with shift updating and repulsion. Scientific Reports. 5, 17147.
mla: Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and
Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group,
2015, doi:10.1038/srep17147.
short: A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5
(2015).
date_created: 2018-12-11T11:53:06Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '25'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/srep17147
ec_funded: 1
file:
- access_level: open_access
checksum: 38e06d8310d2087cae5f6d4d4bfe082b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:29Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4947'
file_name: IST-2016-466-v1+1_srep17147.pdf
file_size: 1021931
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5536'
pubrep_id: '466'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cellular cooperation with shift updating and repulsion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2015'
...
---
_id: '1625'
abstract:
- lang: eng
text: In recent years we have seen numerous improvements on 3D scanning and tracking
of human faces, greatly advancing the creation of digital doubles for film and
video games. However, despite the high-resolution quality of the reconstruction
approaches available, current methods are unable to capture one of the most important
regions of the face - the eye region. In this work we present the first method
for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing
eyelids is extremely challenging, as this region exhibits very complex and unique
skin deformation where skin is folded under while opening the eye. Furthermore,
eyelids are often only partially visible and obstructed due to selfocclusion and
eyelashes. Our approach is to combine a geometric deformation model with image
data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle
detection from local skin appearance. Our deformation model serves as a prior
that enables reconstruction of eyelids even under strong self-occlusions caused
by rolling and folding skin as the eye opens and closes. The output is a person-specific,
time-varying eyelid reconstruction with anatomically plausible deformations. Our
high-resolution detailed eyelids couple naturally with current facial performance
capture approaches. As a result, our method can largely increase the fidelity
of facial capture and the creation of digital doubles.
article_number: '44'
author:
- first_name: Amit
full_name: Bermano, Amit
last_name: Bermano
- first_name: Thabo
full_name: Beeler, Thabo
last_name: Beeler
- first_name: Yeara
full_name: Kozlov, Yeara
last_name: Kozlov
- first_name: Derek
full_name: Bradley, Derek
last_name: Bradley
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal
reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:10.1145/2766924'
apa: 'Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., & Gross,
M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766924'
chicago: Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel,
and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34.
ACM, 2015. https://doi.org/10.1145/2766924.
ieee: 'A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed
spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special
Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA,
United States, 2015, vol. 34, no. 4.'
ista: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed
spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on
Computer Graphics and Interactive Techniques vol. 34, 44.'
mla: Bermano, Amit, et al. Detailed Spatio-Temporal Reconstruction of Eyelids.
Vol. 34, no. 4, 44, ACM, 2015, doi:10.1145/2766924.
short: A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM,
2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:06Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766924
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5535'
quality_controlled: '1'
scopus_import: 1
status: public
title: Detailed spatio-temporal reconstruction of eyelids
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1626'
abstract:
- lang: eng
text: This paper introduces "OmniAD," a novel data-driven pipeline to
model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally,
aerodynamics are examined through elaborate wind tunnel experiments or expensive
fluid dynamics computations, and are only measured for a small number of discrete
wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag
and lift, for any incoming wind direction using a novel representation based on
spherical harmonics. Our datadriven technique acquires the aerodynamic properties
of an object simply by capturing its falling motion using a single camera. Once
model parameters are estimated, OmniAD enables realistic realtime simulation of
rigid bodies, such as the tumbling and gliding of leaves, without simulating the
surrounding air. In addition, we propose an intuitive user interface based on
OmniAD to interactively design three-dimensional kites that actually fly. Various
nontraditional kites were designed to demonstrate the physical validity of our
model.
alternative_title:
- ACM Transactions on Graphics
article_number: '113'
author:
- first_name: Tobias
full_name: Martin, Tobias
last_name: Martin
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics.
In: Vol 34. ACM; 2015. doi:10.1145/2766919'
apa: 'Martin, T., Umetani, N., & Bickel, B. (2015). OmniAD: Data-driven omni-directional
aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766919'
chicago: 'Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven
Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766919.'
ieee: 'T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional
aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no.
4.'
ista: 'Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional
aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, ACM Transactions on Graphics, vol. 34, 113.'
mla: 'Martin, Tobias, et al. OmniAD: Data-Driven Omni-Directional Aerodynamics.
Vol. 34, no. 4, 113, ACM, 2015, doi:10.1145/2766919.'
short: T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:06Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:05Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766919
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5532'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'OmniAD: Data-driven omni-directional aerodynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1627'
abstract:
- lang: eng
text: We present a computational tool for fabrication-oriented design of flexible
rod meshes. Given a deformable surface and a set of deformed poses as input, our
method automatically computes a printable rod mesh that, once manufactured, closely
matches the input poses under the same boundary conditions. The core of our method
is formed by an optimization scheme that adjusts the cross-sectional profiles
of the rods and their rest centerline in order to best approximate the target
deformations. This approach allows us to locally control the bending and stretching
resistance of the surface with a single material, yielding high design flexibility
and low fabrication cost.
acknowledgement: This work was supported in part by grants from the Spanish Ministry
of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant
no. 280135 Animetrics).
article_number: '138'
author:
- first_name: Jesús
full_name: Pérez, Jesús
last_name: Pérez
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: Stelian
full_name: Coros, Stelian
last_name: Coros
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: José
full_name: Canabal, José
last_name: Canabal
- first_name: Robert
full_name: Sumner, Robert
last_name: Sumner
- first_name: Miguel
full_name: Otaduy, Miguel
last_name: Otaduy
citation:
ama: 'Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible
rod meshes. In: Vol 34. ACM; 2015. doi:10.1145/2766998'
apa: 'Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R.,
& Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34).
Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766998'
chicago: Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José
Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible
Rod Meshes,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766998.
ieee: 'J. Pérez et al., “Design and fabrication of flexible rod meshes,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.'
ista: 'Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M.
2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques vol. 34, 138.'
mla: Pérez, Jesús, et al. Design and Fabrication of Flexible Rod Meshes.
Vol. 34, no. 4, 138, ACM, 2015, doi:10.1145/2766998.
short: J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M.
Otaduy, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:07Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '27'
department:
- _id: BeBi
doi: 10.1145/2766998
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '5530'
quality_controlled: '1'
scopus_import: 1
status: public
title: Design and fabrication of flexible rod meshes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1628'
abstract:
- lang: eng
text: We propose a method for fabricating deformable objects with spatially varying
elasticity using 3D printing. Using a single, relatively stiff printer material,
our method designs an assembly of smallscale microstructures that have the effect
of a softer material at the object scale, with properties depending on the microstructure
used in each part of the object. We build on work in the area of metamaterials,
using numerical optimization to design tiled microstructures with desired properties,
but with the key difference that our method designs families of related structures
that can be interpolated to smoothly vary the material properties over a wide
range. To create an object with spatially varying elastic properties, we tile
the object's interior with microstructures drawn from these families, generating
a different microstructure for each cell using an efficient algorithm to select
compatible structures for neighboring cells. We show results computed for both
2D and 3D objects, validating several 2D and 3D printed structures using standard
material tests as well as demonstrating various example applications.
article_number: '136'
article_processing_charge: No
author:
- first_name: Christian
full_name: Schumacher, Christian
last_name: Schumacher
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Jan
full_name: Rys, Jan
last_name: Rys
- first_name: Steve
full_name: Marschner, Steve
last_name: Marschner
- first_name: Chiara
full_name: Daraio, Chiara
last_name: Daraio
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures
to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926'
apa: 'Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross,
M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926'
chicago: Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio,
and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol.
34. ACM, 2015. https://doi.org/10.1145/2766926.
ieee: 'C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross,
“Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, USA, 2015, vol. 34, no. 4.'
ista: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures
to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques vol. 34, 136.'
mla: Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D
Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926.
short: C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:,
ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:07Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:06Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/2766926
intvolume: ' 34'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/2766926
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '5529'
quality_controlled: '1'
scopus_import: 1
status: public
title: Microstructures to control elasticity in 3D printing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1630'
abstract:
- lang: eng
text: We present a method to learn and propagate shape placements in 2D polygonal
scenes from a few examples provided by a user. The placement of a shape is modeled
as an oriented bounding box. Simple geometric relationships between this bounding
box and nearby scene polygons define a feature set for the placement. The feature
sets of all example placements are then used to learn a probabilistic model over
all possible placements and scenes. With this model, we can generate a new set
of placements with similar geometric relationships in any given scene. We introduce
extensions that enable propagation and generation of shapes in 3D scenes, as
well as the application of a learned modeling session to large scenes without
additional user interaction. These concepts allow us to generate complex scenes
with thousands of objects with relatively little user interaction.
acknowledgement: This publication is based upon work supported by the KAUST Office
of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual
Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no.
P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23).
article_number: '108'
author:
- first_name: Paul
full_name: Guerrero, Paul
last_name: Guerrero
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
- first_name: Peter
full_name: Wonka, Peter
last_name: Wonka
citation:
ama: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example.
In: Vol 34. ACM; 2015. doi:10.1145/2766933'
apa: 'Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape
placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States:
ACM. https://doi.org/10.1145/2766933'
chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning
Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933.
ieee: 'P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements
by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no.
4.'
ista: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements
by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 108.'
mla: Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34,
no. 4, 108, ACM, 2015, doi:10.1145/2766933.
short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:08Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766933
file:
- access_level: open_access
checksum: 8b05a51e372c9b0b5af9a00098a9538b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:49Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4647'
file_name: IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf
file_size: 11902290
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
publication_status: published
publisher: ACM
publist_id: '5525'
pubrep_id: '576'
quality_controlled: '1'
scopus_import: 1
status: public
title: Learning shape placements by example
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1632'
abstract:
- lang: eng
text: "This paper presents a liquid simulation technique that enforces the incompressibility
condition using a stream function solve instead of a pressure projection. Previous
methods have used stream function techniques for the simulation of detailed single-phase
flows, but a formulation for liquid simulation has proved elusive in part due
to the free surface boundary conditions. In this paper, we introduce a stream
function approach to liquid simulations with novel boundary conditions for free
surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach
increases the dimension of the linear system necessary to enforce incompressibility,
it provides interesting and surprising benefits. First, the resulting flow is
guaranteed to be divergence-free regardless of the accuracy of the solve. Second,
our free-surface boundary conditions guarantee divergence-free motion even in
the un-simulated air phase, which enables two-phase flow simulation by only computing
a single phase. We implemented this method using a variant of FLIP simulation
which only samples particles within a narrow band of the liquid surface, and we
illustrate the effectiveness of our method for detailed two-phase flow simulations
with complex boundaries, detailed bubble interactions, and two-way solid-fluid
coupling."
acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship
for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014
realFlow and ERC-2014- StG-638176 BigSplash.
alternative_title:
- ACM Transactions on Graphics
article_number: '53'
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- 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, Thuerey N, Wojtan C. A stream function solver for liquid simulations.
In: Vol 34. ACM; 2015. doi:10.1145/2766935'
apa: 'Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for
liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935'
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver
for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935.
ieee: 'R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid
simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics
and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.'
ista: 'Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations.
SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
ACM Transactions on Graphics, vol. 34, 53.'
mla: Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations.
Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935.
short: R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, USA
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:37Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766935
file:
- access_level: open_access
checksum: 7a9afdfaba9209157ce19376e15bc90b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:52Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4909'
file_name: IST-2016-610-v1+1_vecpotential.pdf
file_size: 21831121
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: ACM
publist_id: '5523'
pubrep_id: '610'
quality_controlled: '1'
scopus_import: 1
status: public
title: A stream function solver for liquid simulations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1633'
abstract:
- lang: eng
text: "We present a method for simulating brittle fracture under the assumptions
of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element
method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture
surfaces. The computational cost of the BEM is alleviated by using a low-resolution
mesh and interpolating the resulting stress intensity factors when propagating
the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture
surfaces with high spatial and temporal resolution, taking spatial variation of
material toughness and/or strength into account. It also allows for crack initiation
to be handled separately from crack propagation, which is not only more reasonable
from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating
the resolution of the crack-front from the resolution of the computational mesh
increases the efficiency and therefore the amount of visual detail on the resulting
fracture surfaces. The BEM also allows us to re-use previously computed blocks
of the system matrix."
article_number: '151'
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary
elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896'
apa: 'Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation
with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States: ACM. https://doi.org/10.1145/2766896'
chicago: Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation
with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.
ieee: 'D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with
boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol.
34, no. 4.'
ista: 'Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with
boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 151.'
mla: Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation
with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896.
short: D. Hahn, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-09-07T12:02:56Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766896
ec_funded: 1
file:
- access_level: open_access
checksum: 955aee971983f6b6152bcc1c9b4a7c20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:13Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5131'
file_name: IST-2016-609-v1+1_FractureBEM.pdf
file_size: 20154270
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5522'
pubrep_id: '609'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: High-resolution brittle fracture simulation with boundary elements
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1634'
abstract:
- lang: eng
text: Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally
required the use of a fully three-dimensional many-phase Navier-Stokes solver,
even though their visual appearance is completely dominated by the thin liquid
surface. We depart from earlier work on soap bubbles and foams by noting that
their dynamics are naturally described by a Lagrangian vortex sheet model in which
circulation is the primary variable. This leads us to derive a novel circulation-preserving
surface-only discretization of foam dynamics driven by surface tension on a non-manifold
triangle mesh. We represent the surface using a mesh-based multimaterial surface
tracker which supports complex bubble topology changes, and evolve the surface
according to the ambient air flow induced by a scalar circulation field stored
on the mesh. Surface tension forces give rise to a simple update rule for circulation,
even at non-manifold Plateau borders, based on a discrete measure of signed scalar
mean curvature. We further incorporate vertex constraints to enable the interaction
of soap films with wires. The result is a method that is at once simple, robust,
and efficient, yet able to capture an array of soap films behaviors including
foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being
pulled apart.
article_number: '149'
author:
- first_name: Fang
full_name: Da, Fang
last_name: Da
- first_name: Christopher
full_name: Batty, Christopher
last_name: Batty
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Eitan
full_name: Grinspun, Eitan
last_name: Grinspun
citation:
ama: 'Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. In: Vol
34. ACM; 2015. doi:10.1145/2767003'
apa: 'Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans
toil and trouble: discrete circulation-preserving vortex sheets for soap films
and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003'
chicago: 'Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double
Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for
Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.'
ieee: 'F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and
trouble: discrete circulation-preserving vortex sheets for soap films and foams,”
presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.'
ista: 'Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble:
discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques vol. 34,
149.'
mla: 'Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving
Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.'
short: F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-02-23T10:07:42Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2767003
ec_funded: 1
file:
- access_level: open_access
checksum: 57b07d78d2d612a8052744b37d4a71fa
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:14Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4867'
file_name: IST-2016-608-v1+1_doublebubbles.pdf
file_size: 8973215
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5521'
pubrep_id: '608'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Double bubbles sans toil and trouble: discrete circulation-preserving vortex
sheets for soap films and foams'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1635'
abstract:
- lang: eng
text: We calculate a Ricci curvature lower bound for some classical examples of
random walks, namely, a chain on a slice of the n-dimensional discrete cube (the
so-called Bernoulli-Laplace model) and the random transposition shuffle of the
symmetric group of permutations on n letters.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Prasad
full_name: Tetali, Prasad
last_name: Tetali
citation:
ama: Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models. Annales de la faculté des sciences de Toulouse.
2015;24(4):781-800. doi:10.5802/afst.1464
apa: Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds
for Bernoulli-Laplace and random transposition models. Annales de La Faculté
Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464
chicago: Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature
Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La
Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015.
https://doi.org/10.5802/afst.1464.
ieee: M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models,” Annales de la faculté des sciences de Toulouse,
vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.
ista: Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace
and random transposition models. Annales de la faculté des sciences de Toulouse.
24(4), 781–800.
mla: Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace
and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse,
vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464.
short: M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse
24 (2015) 781–800.
date_created: 2018-12-11T11:53:10Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-10-18T07:48:28Z
day: '01'
department:
- _id: JaMa
doi: 10.5802/afst.1464
external_id:
arxiv:
- '1409.8605'
intvolume: ' 24'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1409.8605
month: '01'
oa: 1
oa_version: Preprint
page: 781 - 800
publication: Annales de la faculté des sciences de Toulouse
publication_status: published
publisher: Faculté des sciences de Toulouse
publist_id: '5520'
quality_controlled: '1'
status: public
title: Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition
models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...