---
_id: '136'
abstract:
- lang: eng
text: Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes
equation may provide deep insights into fluid turbulence. In this article, we
present a combined experimental and numerical study exploring the dynamical role
of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent,
electromagnetically driven, shallow fluid layer. Identifying instants when turbulent
evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional
model of the flow. We establish the dynamical relevance of these unstable equilibria
by showing that they are closely visited by the turbulent flow. We also establish
the dynamical relevance of unstable manifolds by verifying that they are shadowed
by turbulent trajectories departing from the neighborhoods of unstable equilibria
over large distances in state space.
article_processing_charge: No
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jeffrey
full_name: Tithof, Jeffrey
last_name: Tithof
- first_name: Roman
full_name: Grigoriev, Roman
last_name: Grigoriev
- first_name: Michael
full_name: Schatz, Michael
last_name: Schatz
citation:
ama: Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E.
2018;98(2). doi:10.1103/PhysRevE.98.023105
apa: Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria
and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical
Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105
chicago: Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz.
“Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like
Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.
ieee: B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and
invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical
Review E, vol. 98, no. 2. American Physical Society, 2018.
ista: Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant
manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).
mla: Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional
Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical
Society, 2018, doi:10.1103/PhysRevE.98.023105.
short: B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).
date_created: 2018-12-11T11:44:49Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2023-10-10T13:29:10Z
day: '13'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.98.023105
external_id:
arxiv:
- '1808.02088'
isi:
- '000441466800010'
intvolume: ' 98'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.02088
month: '08'
oa: 1
oa_version: Submitted Version
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like
flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
that regulates membrane trafficking through the Golgi apparatus. The clinical
phenotype associated with mutations in various TRAPP subunits has allowed elucidation
of their functions in specific tissues. The role of some subunits in human disease,
however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
We aimed to expand the range of neurodevelopmental disorders associated with mutations
in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
Linkage and homozygosity mapping and candidate gene analysis were used to identify
homozygous mutations in families. Patient fibroblasts were used to study splicing
defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
disorder characterised by microcephaly, epilepsy and autistic features, and showed
splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
displaying decreased head size and neuronal hyperexcitability, leading to a lower
seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
full_name: Marin Valencia, Isaac
last_name: Marin Valencia
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Gifty
full_name: Bhat, Gifty
last_name: Bhat
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Valentina
full_name: Stanley, Valentina
last_name: Stanley
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Jeremy
full_name: Gleeson, Jeremy
last_name: Gleeson
- first_name: Farhad
full_name: Imam, Farhad
last_name: Imam
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54.
doi:10.1136/jmedgenet-2017-104627
apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
with a neurodevelopmental disorder characterised by microcephaly epilepsy and
autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627
chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group,
2018. https://doi.org/10.1136/jmedgenet-2017-104627.
ieee: I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B
associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ
Publishing Group, pp. 48–54, 2018.
ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features. Journal
of Medical Genetics. 55(1), 48–54.
mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing
Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.
short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-10-16T09:55:43Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
isi:
- '000418199800007'
pmid:
- '28626029'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
issn:
- 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...
---
_id: '284'
abstract:
- lang: eng
text: "Borel probability measures living on metric spaces are fundamental\r\nmathematical
objects. There are several meaningful distance functions that make the collection
of the probability measures living on a certain space a metric space. We are interested
in the description of the structure of the isometries of such metric spaces. We
overview some of the recent results of the topic and we also provide some new
ones concerning the Wasserstein distance. More specifically, we consider the space
of all Borel probability measures on the unit sphere of a Euclidean space endowed
with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the
action of a Wasserstein isometry on the set of Dirac measures is induced by an
isometry of the underlying unit sphere."
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office, NKFIH (grant
no. K124152).
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Maps on probability measures preserving certain distances - a
survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80.
doi:10.14232/actasm-018-753-y
apa: Virosztek, D. (2018). Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. Springer
Nature. https://doi.org/10.14232/actasm-018-753-y
chicago: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer
Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.
ieee: D. Virosztek, “Maps on probability measures preserving certain distances -
a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84,
no. 1–2. Springer Nature, pp. 65–80, 2018.
ista: Virosztek D. 2018. Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.
mla: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol.
84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.
short: D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-04T00:00:00Z
date_updated: 2023-10-16T10:29:22Z
day: '04'
department:
- _id: LaEr
doi: 10.14232/actasm-018-753-y
ec_funded: 1
external_id:
arxiv:
- '1802.03305'
intvolume: ' 84'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.03305
month: '06'
oa: 1
oa_version: Preprint
page: 65 - 80
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Acta Scientiarum Mathematicarum
publication_identifier:
eissn:
- 2064-8316
issn:
- 0001-6969
publication_status: published
publisher: Springer Nature
publist_id: '7615'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maps on probability measures preserving certain distances - a survey and some
new results
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...
---
_id: '180'
abstract:
- lang: eng
text: In this paper we define and study the classical Uniform Electron Gas (UEG),
a system of infinitely many electrons whose density is constant everywhere in
space. The UEG is defined differently from Jellium, which has a positive constant
background but no constraint on the density. We prove that the UEG arises in Density
Functional Theory in the limit of a slowly varying density, minimizing the indirect
Coulomb energy. We also construct the quantum UEG and compare it to the classical
UEG at low density.
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme
(grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by
the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National
Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged."
article_processing_charge: No
article_type: original
author:
- first_name: Mathieu
full_name: Lewi, Mathieu
last_name: Lewi
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64
apa: Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the
uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique. https://doi.org/10.5802/jep.64
chicago: Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics
of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques.
Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.
ieee: M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform
electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5.
Ecole Polytechnique, pp. 79–116, 2018.
ista: Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron
gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.
mla: Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.”
Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique,
2018, pp. 79–116, doi:10.5802/jep.64.
short: M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques
5 (2018) 79–116.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-10-17T08:05:28Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.5802/jep.64
ec_funded: 1
external_id:
arxiv:
- '1705.10676'
file:
- access_level: open_access
checksum: 1ba7cccdf3900f42c4f715ae75d6813c
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:38:18Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5726'
file_name: 2018_JournaldeLecoleMath_Lewi.pdf
file_size: 843938
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 116
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_identifier:
eissn:
- 2270-518X
issn:
- 2429-7100
publication_status: published
publisher: Ecole Polytechnique
publist_id: '7741'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics of the uniform electron gas
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '163'
abstract:
- lang: eng
text: For ultrafast fixation of biological samples to avoid artifacts, high-pressure
freezing (HPF) followed by freeze substitution (FS) is preferred over chemical
fixation at room temperature. After HPF, samples are maintained at low temperature
during dehydration and fixation, while avoiding damaging recrystallization. This
is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample
agitation during FS dramatically reduces the necessary time. Then, in 2015, we
(H.G. and S.R.) introduced an agitation module into the cryochamber of an automated
FS unit and demonstrated that the preparation of algae could be shortened from
days to a couple of hours. We argued that variability in the processing, reproducibility,
and safety issues are better addressed using automated FS units. For dissemination,
we started low-cost manufacturing of agitation modules for two of the most widely
used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from
Leica Microsystems, using three dimensional (3D)-printing of the major components.
To test them, several labs independently used the modules on a wide variety of
specimens that had previously been processed by manual agitation, or without agitation.
We demonstrate that automated processing with sample agitation saves time, increases
flexibility with respect to sample requirements and protocols, and produces data
of at least as good quality as other approaches.
article_processing_charge: No
article_type: original
author:
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Helmuth
full_name: Goldammer, Helmuth
last_name: Goldammer
- first_name: Christine
full_name: Richardson, Christine
last_name: Richardson
- first_name: Martin
full_name: Goldberg, Martin
last_name: Goldberg
- first_name: Timothy
full_name: Hawkins, Timothy
last_name: Hawkins
- first_name: Elena
full_name: Hollergschwandtner, Elena
id: 3C054040-F248-11E8-B48F-1D18A9856A87
last_name: Hollergschwandtner
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Sebastian
full_name: Antreich, Sebastian
last_name: Antreich
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
citation:
ama: 'Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means
to accelerate automated freeze substitution. Journal of Histochemistry and
Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698'
apa: 'Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl,
E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated
freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE
Publications. https://doi.org/10.1369/0022155418786698'
chicago: 'Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg,
Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof.
“Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.”
Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.'
ieee: 'S. Reipert et al., “Agitation modules: Flexible means to accelerate
automated freeze substitution,” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.'
ista: 'Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann
W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate
automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12),
903–921.'
mla: 'Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate
Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.'
short: S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl,
W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry
66 (2018) 903–921.
date_created: 2018-12-11T11:44:57Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-10-17T08:42:24Z
day: '01'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1369/0022155418786698
external_id:
isi:
- '000452277700005'
pmid:
- '29969056'
intvolume: ' 66'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1369/0022155418786698
month: '12'
oa: 1
oa_version: Published Version
page: 903-921
pmid: 1
publication: Journal of Histochemistry and Cytochemistry
publication_identifier:
issn:
- 0022-1554
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Agitation modules: Flexible means to accelerate automated freeze substitution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2018'
...
---
_id: '6012'
abstract:
- lang: eng
text: We present an approach to identify concise equations from data using a shallow
neural network approach. In contrast to ordinary black-box regression, this approach
allows understanding functional relations and generalizing them from observed
data to unseen parts of the parameter space. We show how to extend the class of
learnable equations for a recently proposed equation learning network to include
divisions, and we improve the learning and model selection strategy to be useful
for challenging real-world data. For systems governed by analytical expressions,
our method can in many cases identify the true underlying equation and extrapolate
to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum
system, where only 2 random rollouts are required to learn the forward dynamics
and successfully achieve the swing-up task.
article_processing_charge: No
author:
- first_name: Subham
full_name: Sahoo, Subham
last_name: Sahoo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: 'Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control.
In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:4442-4450.'
apa: 'Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for
extrapolation and control. In Proceedings of the 35th International Conference
on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research
Press.'
chicago: Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations
for Extrapolation and Control.” In Proceedings of the 35th International Conference
on Machine Learning, 80:4442–50. ML Research Press, 2018.
ieee: S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation
and control,” in Proceedings of the 35th International Conference on Machine
Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.
ista: 'Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation
and control. Proceedings of the 35th International Conference on Machine Learning.
ICML: International Conference on Machine Learning vol. 80, 4442–4450.'
mla: Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings
of the 35th International Conference on Machine Learning, vol. 80, ML Research
Press, 2018, pp. 4442–50.
short: S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International
Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2019-02-14T15:21:07Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T09:50:53Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1806.07259'
isi:
- '000683379204058'
intvolume: ' 80'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.07259
month: '02'
oa: 1
oa_version: Preprint
page: 4442-4450
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/
scopus_import: '1'
status: public
title: Learning equations for extrapolation and control
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '6011'
abstract:
- lang: eng
text: 'We establish a data-dependent notion of algorithmic stability for Stochastic
Gradient Descent (SGD), and employ it to develop novel generalization bounds.
This is in contrast to previous distribution-free algorithmic stability results
for SGD which depend on the worst-case constants. By virtue of the data-dependent
argument, our bounds provide new insights into learning with SGD on convex and
non-convex problems. In the convex case, we show that the bound on the generalization
error depends on the risk at the initialization point. In the non-convex case,
we prove that the expected curvature of the objective function around the initialization
point has crucial influence on the generalization error. In both cases, our results
suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization.
As a corollary, our results allow us to show optimistic generalization bounds
that exhibit fast convergence rates for SGD subject to a vanishing empirical risk
and low noise of stochastic gradient. '
article_processing_charge: No
author:
- first_name: Ilja
full_name: Kuzborskij, Ilja
last_name: Kuzborskij
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent.
In: Proceedings of the 35 Th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:2815-2824.'
apa: 'Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic
gradient descent. In Proceedings of the 35 th International Conference on Machine
Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.'
chicago: Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic
Gradient Descent.” In Proceedings of the 35 Th International Conference on
Machine Learning, 80:2815–24. ML Research Press, 2018.
ieee: I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient
descent,” in Proceedings of the 35 th International Conference on Machine Learning,
Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.
ista: 'Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient
descent. Proceedings of the 35 th International Conference on Machine Learning.
ICML: International Conference on Machine Learning vol. 80, 2815–2824.'
mla: Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic
Gradient Descent.” Proceedings of the 35 Th International Conference on Machine
Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.
short: I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference
on Machine Learning, ML Research Press, 2018, pp. 2815–2824.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2019-02-14T14:51:57Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T09:51:13Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1703.01678'
isi:
- '000683379202095'
intvolume: ' 80'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.01678
month: '02'
oa: 1
oa_version: Preprint
page: 2815-2824
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the 35 th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Data-dependent stability of stochastic gradient descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '6589'
abstract:
- lang: eng
text: Distributed training of massive machine learning models, in particular deep
neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace.
Several families of communication-reduction methods, such as quantization, large-batch
methods, and gradient sparsification, have been proposed. To date, gradient sparsification
methods--where each node sorts gradients by magnitude, and only communicates a
subset of the components, accumulating the rest locally--are known to yield some
of the largest practical gains. Such methods can reduce the amount of communication
per step by up to \emph{three orders of magnitude}, while preserving model accuracy.
Yet, this family of methods currently has no theoretical justification. This is
the question we address in this paper. We prove that, under analytic assumptions,
sparsifying gradients by magnitude with local error correction provides convergence
guarantees, for both convex and non-convex smooth objectives, for data-parallel
SGD. The main insight is that sparsification methods implicitly maintain bounds
on the maximum impact of stale updates, thanks to selection by magnitude. Our
analysis and empirical validation also reveal that these methods do require analytical
conditions to converge well, justifying existing heuristics.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
citation:
ama: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. The convergence of sparsified gradient methods. In: Advances in Neural Information
Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems
Foundation; 2018:5973-5983.'
apa: 'Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat,
S., & Renggli, C. (2018). The convergence of sparsified gradient methods.
In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018,
pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.'
chicago: Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov,
Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.”
In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83.
Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat,
and C. Renggli, “The convergence of sparsified gradient methods,” in Advances
in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol.
Volume 2018, pp. 5973–5983.
ista: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information
Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems
vol. Volume 2018, 5973–5983.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.”
Advances in Neural Information Processing Systems 31, vol. Volume 2018,
Neural Information Processing Systems Foundation, 2018, pp. 5973–83.
short: D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat,
C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural
Information Processing Systems Foundation, 2018, pp. 5973–5983.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-27T09:32:55Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:20Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1809.10505'
isi:
- '000461852000047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.10505
month: '12'
oa: 1
oa_version: Preprint
page: 5973-5983
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Neural Information Processing Systems 31
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of sparsified gradient methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: Volume 2018
year: '2018'
...
---
_id: '7'
abstract:
- lang: eng
text: Animal social networks are shaped by multiple selection pressures, including
the need to ensure efficient communication and functioning while simultaneously
limiting disease transmission. Social animals could potentially further reduce
epidemic risk by altering their social networks in the presence of pathogens,
yet there is currently no evidence for such pathogen-triggered responses. We tested
this hypothesis experimentally in the ant Lasius niger using a combination of
automated tracking, controlled pathogen exposure, transmission quantification,
and temporally explicit simulations. Pathogen exposure induced behavioral changes
in both exposed ants and their nestmates, which helped contain the disease by
reinforcing key transmission-inhibitory properties of the colony's contact network.
This suggests that social network plasticity in response to pathogens is an effective
strategy for mitigating the effects of disease in social groups.
acknowledgement: This project was funded by two European Research Council Advanced
Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science
Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research
Council Starting Grant (SocialVaccines, 243071) to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. Science.
2018;362(6417):941-945. doi:10.1126/science.aat4793
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Science. AAAS. https://doi.org/10.1126/science.aat4793
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect,”
Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect. Science.
362(6417), 941–945.
mla: Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission
in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45,
doi:10.1126/science.aat4793.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science
362 (2018) 941–945.
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-23T00:00:00Z
date_updated: 2023-10-17T11:50:05Z
day: '23'
department:
- _id: SyCr
doi: 10.1126/science.aat4793
ec_funded: 1
external_id:
isi:
- '000451124500041'
intvolume: ' 362'
isi: 1
issue: '6417'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 941 - 945
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Science
publication_identifier:
issn:
- 1095-9203
publication_status: published
publisher: AAAS
publist_id: '8049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/
record:
- id: '13055'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 362
year: '2018'
...
---
_id: '19'
abstract:
- lang: eng
text: Bacteria regulate genes to survive antibiotic stress, but regulation can be
far from perfect. When regulation is not optimal, mutations that change gene expression
can contribute to antibiotic resistance. It is not systematically understood to
what extent natural gene regulation is or is not optimal for distinct antibiotics,
and how changes in expression of specific genes quantitatively affect antibiotic
resistance. Here we discover a simple quantitative relation between fitness, gene
expression, and antibiotic potency, which rationalizes our observation that a
multitude of genes and even innate antibiotic defense mechanisms have expression
that is critically nonoptimal under antibiotic treatment. First, we developed
a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression
and knockout libraries, finding that resistance to a range of 31 antibiotics could
result from changing expression of a large and functionally diverse set of genes,
in a primarily but not exclusively drug-specific manner. Second, by synthetically
controlling the expression of single-drug and multidrug resistance genes, we observed
that their fitness-expression functions changed dramatically under antibiotic
treatment in accordance with a log-sensitivity relation. Thus, because many genes
are nonoptimally expressed under antibiotic treatment, many regulatory mutations
can contribute to resistance by altering expression and by activating latent defenses.
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Palmer, Adam
last_name: Palmer
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential
for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684.
doi:10.1093/molbev/msy163
apa: Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression
creates latent potential for antibiotic resistance. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msy163
chicago: Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression
Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and
Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.
ieee: A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates
latent potential for antibiotic resistance,” Molecular Biology and Evolution,
vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.
ista: Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent
potential for antibiotic resistance. Molecular Biology and Evolution. 35(11),
2669–2684.
mla: Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for
Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11,
Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.
short: A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018)
2669–2684.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-10-17T11:51:06Z
day: '28'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/molbev/msy163
external_id:
isi:
- '000452567200006'
pmid:
- '30169679'
intvolume: ' 35'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30169679
month: '08'
oa: 1
oa_version: Submitted Version
page: 2669 - 2684
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '8036'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonoptimal gene expression creates latent potential for antibiotic resistance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2018'
...
---
_id: '6'
abstract:
- lang: eng
text: Lesion and electrode location verification are traditionally done via histological
examination of stained brain slices, a time-consuming procedure that requires
manual estimation. Here, we describe a simple, straightforward method for quantifying
lesions and locating electrodes in the brain that is less laborious and yields
more detailed results. Whole brains are stained with osmium tetroxide, embedded
in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes
of the brains with resolutions and virtual section thicknesses dependent on the
sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively).
Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays,
electrolytic lesions, and silicon probes can also be localized. Free and proprietary
software allows experimenters to examine the sample volume from any plane and
segment the volume manually or automatically. Because this method generates whole
brain volume, lesions and electrodes can be quantified to a much higher degree
than in current methods, which will help standardize comparisons within and across
studies.
article_processing_charge: No
author:
- first_name: Javier
full_name: Masís, Javier
last_name: Masís
- first_name: David
full_name: Mankus, David
last_name: Mankus
- first_name: Steffen
full_name: Wolff, Steffen
last_name: Wolff
- first_name: Grigori
full_name: Guitchounts, Grigori
last_name: Guitchounts
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: David
full_name: Cox, David
last_name: Cox
citation:
ama: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based
method for characterising lesions and locating electrodes in small animal brains.
Journal of visualized experiments. 2018;141. doi:10.3791/58585
apa: Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox,
D. (2018). A micro-CT-based method for characterising lesions and locating electrodes
in small animal brains. Journal of Visualized Experiments. MyJove Corporation.
https://doi.org/10.3791/58585
chicago: Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian
A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and
Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments.
MyJove Corporation, 2018. https://doi.org/10.3791/58585.
ieee: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A
micro-CT-based method for characterising lesions and locating electrodes in small
animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation,
2018.
ista: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based
method for characterising lesions and locating electrodes in small animal brains.
Journal of visualized experiments. 141.
mla: Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and
Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments,
vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.
short: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal
of Visualized Experiments 141 (2018).
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-08T00:00:00Z
date_updated: 2023-10-17T11:49:25Z
day: '08'
department:
- _id: MaJö
doi: 10.3791/58585
external_id:
isi:
- '000456469400103'
intvolume: ' 141'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
publication: Journal of visualized experiments
publication_status: published
publisher: MyJove Corporation
publist_id: '8050'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A micro-CT-based method for characterising lesions and locating electrodes
in small animal brains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2018'
...
---
_id: '13055'
abstract:
- lang: eng
text: "Dataset for manuscript 'Social network plasticity decreases disease transmission
in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n
\ - correction of URLs within
README.txt file\r\n"
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect.”
Zenodo, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect, Zenodo,
10.5281/ZENODO.1322669.
mla: Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).
date_created: 2023-05-23T13:24:51Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-10-17T11:50:04Z
day: '23'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.5281/ZENODO.1322669
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.1480665
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '7'
relation: used_in_publication
status: public
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '22'
abstract:
- lang: eng
text: Conventional ultra-high sensitivity detectors in the millimeter-wave range
are usually cooled as their own thermal noise at room temperature would mask the
weak received radiation. The need for cryogenic systems increases the cost and
complexity of the instruments, hindering the development of, among others, airborne
and space applications. In this work, the nonlinear parametric upconversion of
millimeter-wave radiation to the optical domain inside high-quality (Q) lithium
niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise
detection. We experimentally demonstrate coherent upconversion of millimeter-wave
signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing
the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows
that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling
the millimeter-wave WGM, effectively cooling the upconverted mode and allowing
ultra-low noise detection. By theoretically estimating the sensitivity of a correlation
radiometer based on the presented scheme, it is found that room-temperature radiometers
with better sensitivity than state-of-the-art high-electron-mobility transistor
(HEMT)-based radiometers can be designed. This detection paradigm can be used
to develop room-temperature instrumentation for radio astronomy, earth observation,
planetary missions, and imaging systems.
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
full_name: Botello, Gabriel
last_name: Botello
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Kerlos
full_name: Abdalmalak, Kerlos
last_name: Abdalmalak
- first_name: Elliott
full_name: Brown, Elliott
last_name: Brown
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Sascha
full_name: Preu, Sascha
last_name: Preu
- first_name: Daniel
full_name: Segovia Vargas, Daniel
last_name: Segovia Vargas
- first_name: Dmitry
full_name: Strekalov, Dmitry
last_name: Strekalov
- first_name: Luis
full_name: Munoz, Luis
last_name: Munoz
- first_name: Harald
full_name: Schwefel, Harald
last_name: Schwefel
citation:
ama: Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave
photonic radiometers based on efficient electro-optic upconverters. Optica.
2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210
apa: Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E.,
Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic
radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210
chicago: Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak,
Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave
Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica,
2018. https://doi.org/10.1364/OPTICA.5.001210.
ieee: G. Botello et al., “Sensitivity limits of millimeter-wave photonic
radiometers based on efficient electro-optic upconverters,” Optica, vol.
5, no. 10. pp. 1210–1219, 2018.
ista: Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G,
Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity
limits of millimeter-wave photonic radiometers based on efficient electro-optic
upconverters. Optica. 5(10), 1210–1219.
mla: Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers
Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10,
2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.
short: G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G.
Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica
5 (2018) 1210–1219.
date_created: 2018-12-11T11:44:12Z
date_published: 2018-10-20T00:00:00Z
date_updated: 2023-10-17T12:12:40Z
day: '20'
department:
- _id: JoFi
doi: 10.1364/OPTICA.5.001210
external_id:
isi:
- '000447853100007'
intvolume: ' 5'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'www.doi.org/10.1364/OPTICA.5.001210 '
month: '10'
oa: 1
oa_version: Published Version
page: 1210 - 1219
publication: Optica
publication_identifier:
issn:
- '23342536'
publication_status: published
publist_id: '8033'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensitivity limits of millimeter-wave photonic radiometers based on efficient
electro-optic upconverters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...
---
_id: '5677'
abstract:
- lang: eng
text: 'Recently, contract-based design has been proposed as an “orthogonal” approach
that complements system design methodologies proposed so far to cope with the
complexity of system design. Contract-based design provides a rigorous scaffolding
for verification, analysis, abstraction/refinement, and even synthesis. A number
of results have been obtained in this domain but a unified treatment of the topic
that can help put contract-based design in perspective was missing. This monograph
intends to provide such a treatment where contracts are precisely defined and
characterized so that they can be used in design methodologies with no ambiguity.
In particular, this monograph identifies the essence of complex system design
using contracts through a mathematical “meta-theory”, where all the properties
of the methodology are derived from a very abstract and generic notion of contract.
We show that the meta-theory provides deep and illuminating links with existing
contract and interface theories, as well as guidelines for designing new theories.
Our study encompasses contracts for both software and systems, with emphasis on
the latter. We illustrate the use of contracts with two examples: requirement
engineering for a parking garage management, and the development of contracts
for timing and scheduling in the context of the Autosar methodology in use in
the automotive sector.'
article_processing_charge: No
article_type: original
author:
- first_name: Albert
full_name: Benveniste, Albert
last_name: Benveniste
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
- first_name: Benoît
full_name: Caillaud, Benoît
last_name: Caillaud
- first_name: Roberto
full_name: Passerone, Roberto
last_name: Passerone
- first_name: Jean Baptiste
full_name: Raclet, Jean Baptiste
last_name: Raclet
- first_name: Philipp
full_name: Reinkemeier, Philipp
last_name: Reinkemeier
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni-Vincentelli
- first_name: Werner
full_name: Damm, Werner
last_name: Damm
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
citation:
ama: Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations
and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053
apa: Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier,
P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends
in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053
chicago: Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone,
Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner
Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations
and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.
ieee: A. Benveniste et al., “Contracts for system design,” Foundations
and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers,
pp. 124–400, 2018.
ista: Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier
P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts
for system design. Foundations and Trends in Electronic Design Automation. 12(2–3),
124–400.
mla: Benveniste, Albert, et al. “Contracts for System Design.” Foundations and
Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers,
2018, pp. 124–400, doi:10.1561/1000000053.
short: A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier,
A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations
and Trends in Electronic Design Automation 12 (2018) 124–400.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-10-17T11:53:09Z
day: '01'
department:
- _id: ToHe
doi: 10.1561/1000000053
intvolume: ' 12'
issue: 2-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-00757488/
month: '05'
oa: 1
oa_version: Submitted Version
page: 124-400
publication: Foundations and Trends in Electronic Design Automation
publication_identifier:
issn:
- 1551-3939
publication_status: published
publisher: Now Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contracts for system design
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2018'
...
---
_id: '435'
abstract:
- lang: eng
text: It is shown that two fundamentally different phenomena, the bound states in
continuum and the spectral singularity (or time-reversed spectral singularity),
can occur simultaneously. This can be achieved in a rectangular core dielectric
waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional
bound state in a continuum is created in the plane of a waveguide cross section,
and it is emitted or absorbed along the waveguide core. The idea can be used for
experimental implementation of a laser or a coherent-perfect-absorber for a photonic
bound state that resides in a continuous spectrum.
acknowledgement: 'Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE)
(291734). B. M. acknowledges the financial support by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013)
under REA.'
article_processing_charge: No
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in
a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607
apa: Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for
bound states in a continuum. Optics Letters. Optica Publishing Group.
https://doi.org/10.1364/OL.43.000607
chicago: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and
Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing
Group, 2018. https://doi.org/10.1364/OL.43.000607.
ieee: B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states
in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group,
pp. 607–610, 2018.
ista: Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states
in a continuum. Optics Letters. 43(3), 607–610.
mla: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser
for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica
Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.
short: B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.
date_created: 2018-12-11T11:46:27Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T12:15:06Z
day: '01'
department:
- _id: MiLe
doi: 10.1364/OL.43.000607
ec_funded: 1
external_id:
arxiv:
- '1711.01986'
isi:
- '000423776600066'
intvolume: ' 43'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.01986
month: '02'
oa: 1
oa_version: Preprint
page: 607 - 610
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Optics Letters
publication_status: published
publisher: Optica Publishing Group
publist_id: '7388'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coherent-perfect-absorber and laser for bound states in a continuum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2018'
...
---
_id: '139'
abstract:
- lang: eng
text: 'Genome-scale diversity data are increasingly available in a variety of biological
systems, and can be used to reconstruct the past evolutionary history of species
divergence. However, extracting the full demographic information from these data
is not trivial, and requires inferential methods that account for the diversity
of coalescent histories throughout the genome. Here, we evaluate the potential
and limitations of one such approach. We reexamine a well-known system of mussel
sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations
computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation
(ABC) framework. We first assess the best sampling strategy (number of: individuals,
loci, and bins in the jSFS), and show that model selection is robust to variation
in the number of individuals and loci. In contrast, different binning choices
when summarizing the jSFS, strongly affect the results: including classes of low
and high frequency shared polymorphisms can more effectively reveal recent migration
events. We then take advantage of the flexibility of ABC to compare more realistic
models of speciation, including variation in migration rates through time (i.e.,
periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration
rates). We show that these models were consistently selected as the most probable,
suggesting that mussels have experienced a complex history of gene flow during
divergence and that the species boundary is semi-permeable. Our work provides
a comprehensive evaluation of ABC demographic inference in mussels based on the
coding jSFS, and supplies guidelines for employing different sequencing techniques
and sampling strategies. We emphasize, perhaps surprisingly, that inferences are
less limited by the volume of data, than by the way in which they are analyzed.'
article_number: '30083438'
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Pierre
full_name: Gagnaire, Pierre
last_name: Gagnaire
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Nicolas
full_name: Faivre, Nicolas
last_name: Faivre
- first_name: John
full_name: Welch, John
last_name: Welch
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: 'Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue
mussel species reconstructed from Approximate Bayesian Computation: The effects
of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7).
doi:10.7717/peerj.5198'
apa: 'Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J.,
& Bierne, N. (2018). The divergence history of European blue mussel species
reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198'
chicago: 'Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier,
Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European
Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects
of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018.
https://doi.org/10.7717/peerj.5198.'
ieee: 'C. Fraisse et al., “The divergence history of European blue mussel
species reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.'
ista: 'Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N.
2018. The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies. PeerJ. 2018(7), 30083438.'
mla: 'Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel
Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing
Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438,
PeerJ, 2018, doi:10.7717/peerj.5198.'
short: C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne,
PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-10-17T12:25:28Z
day: '30'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.7717/peerj.5198
external_id:
isi:
- '000440484800002'
file:
- access_level: open_access
checksum: 7d55ae22598a1c70759cd671600cff53
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:42:11Z
date_updated: 2020-07-14T12:44:48Z
file_id: '5739'
file_name: 2018_PeerJ_Fraisse.pdf
file_size: 1480792
relation: main_file
file_date_updated: 2020-07-14T12:44:48Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '7784'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '33'
abstract:
- lang: eng
text: Secondary contact is the reestablishment of gene flow between sister populations
that have diverged. For instance, at the end of the Quaternary glaciations in
Europe, secondary contact occurred during the northward expansion of the populations
which had found refugia in the southern peninsulas. With the advent of multi-locus
markers, secondary contact can be investigated using various molecular signatures
including gradients of allele frequency, admixture clines, and local increase
of genetic differentiation. We use coalescent simulations to investigate if molecular
data provide enough information to distinguish between secondary contact following
range expansion and an alternative evolutionary scenario consisting of a barrier
to gene flow in an isolation-by-distance model. We find that an excess of linkage
disequilibrium and of genetic diversity at the suture zone is a unique signature
of secondary contact. We also find that the directionality index ψ, which was
proposed to study range expansion, is informative to distinguish between the two
hypotheses. However, although evidence for secondary contact is usually conveyed
by statistics related to admixture coefficients, we find that they can be confounded
by isolation-by-distance. We recommend to account for the spatial repartition
of individuals when investigating secondary contact in order to better reflect
the complex spatio-temporal evolution of populations and species.
acknowledgement: 'Johanna Bertl was supported by the Vienna Graduate School of Population
Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while
employed at the Department of Statistics and Operations Research, University of
Vienna, Austria. This article was developed in the framework of the Grenoble Alpes
Data Institute, which is supported by the French National Research Agency under
the “Investissments d’avenir” program (ANR-15-IDEX-02).'
article_number: e5325
article_processing_charge: No
author:
- first_name: Johanna
full_name: Bertl, Johanna
last_name: Bertl
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Michaël
full_name: Blum, Michaël
last_name: Blum
citation:
ama: Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion
be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325
apa: Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following
range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ.
https://doi.org/10.7717/peerj.5325
chicago: Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact
Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ.
PeerJ, 2018. https://doi.org/10.7717/peerj.5325.
ieee: J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range
expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018,
no. 10. PeerJ, 2018.
ista: Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range
expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.
mla: Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be
Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325,
PeerJ, 2018, doi:10.7717/peerj.5325.
short: J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-10-17T12:24:43Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7717/peerj.5325
external_id:
isi:
- '000447204400001'
pmid:
- '30294507'
file:
- access_level: open_access
checksum: 3334886c4b39678db4c4b74299ca14ba
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:46:06Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5692'
file_name: 2018_PeerJ_Bertl.pdf
file_size: 1328344
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '8022'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can secondary contact following range expansion be distinguished from barriers
to gene flow?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '5673'
abstract:
- lang: eng
text: Cell polarity, manifested by the localization of proteins to distinct polar
plasma membrane domains, is a key prerequisite of multicellular life. In plants,
PIN auxin transporters are prominent polarity markers crucial for a plethora of
developmental processes. Cell polarity mechanisms in plants are distinct from
other eukaryotes and still largely elusive. In particular, how the cell polarities
are propagated and maintained following cell division remains unknown. Plant cytokinesis
is orchestrated by the cell plate—a transient centrifugally growing endomembrane
compartment ultimately forming the cross wall1. Trafficking of polar membrane
proteins is typically redirected to the cell plate, and these will consequently
have opposite polarity in at least one of the daughter cells2–5. Here, we provide
mechanistic insights into post-cytokinetic re-establishment of cell polarity as
manifested by the apical, polar localization of PIN2. We show that the apical
domain is defined in a cell-intrinsic manner and that re-establishment of PIN2
localization to this domain requires de novo protein secretion and endocytosis,
but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related
kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated
specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2
polarity re-establishment.
article_processing_charge: No
author:
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment
of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088.
doi:10.1038/s41477-018-0318-3
apa: Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for
cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature
Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3
chicago: Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework
for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature
Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.
ieee: M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division,” Nature Plants,
vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.
ista: Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.
mla: Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment
of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature
Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.
short: M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-12-03T00:00:00Z
date_updated: 2023-10-17T12:19:28Z
day: '03'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0318-3
ec_funded: 1
external_id:
isi:
- '000454576600017'
pmid:
- '30518833'
intvolume: ' 4'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30518833
month: '12'
oa: 1
oa_version: Submitted Version
page: 1082-1088
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity
after cell division
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '198'
abstract:
- lang: eng
text: We consider a class of students learning a language from a teacher. The situation
can be interpreted as a group of child learners receiving input from the linguistic
environment. The teacher provides sample sentences. The students try to learn
the grammar from the teacher. In addition to just listening to the teacher, the
students can also communicate with each other. The students hold hypotheses about
the grammar and change them if they receive counter evidence. The process stops
when all students have converged to the correct grammar. We study how the time
to convergence depends on the structure of the classroom by introducing and evaluating
various complexity measures. We find that structured communication between students,
although potentially introducing confusion, can greatly reduce some of the complexity
measures. Our theory can also be interpreted as applying to the scientific process,
where nature is the teacher and the scientists are the students.
article_number: '20180073'
article_processing_charge: No
article_type: original
author:
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with
communication between learners. Journal of the Royal Society Interface.
2018;15(140). doi:10.1098/rsif.2018.0073
apa: Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language
acquisition with communication between learners. Journal of the Royal Society
Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073
chicago: Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Language Acquisition with Communication between Learners.” Journal
of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.
ieee: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition
with communication between learners,” Journal of the Royal Society Interface,
vol. 15, no. 140. The Royal Society, 2018.
ista: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition
with communication between learners. Journal of the Royal Society Interface. 15(140),
20180073.
mla: Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between
Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073,
The Royal Society, 2018, doi:10.1098/rsif.2018.0073.
short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal
Society Interface 15 (2018).
date_created: 2018-12-11T11:45:09Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-10-18T06:36:00Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rsif.2018.0073
ec_funded: 1
external_id:
isi:
- '000428576200023'
pmid:
- '29593089'
file:
- access_level: open_access
checksum: 444e1a9d98eb0e780671be82b13025f3
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T07:54:37Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5955'
file_name: 2018_RS_IbsenJensen.pdf
file_size: 219837
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '140'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: The Royal Society
publist_id: '7715'
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4028971
record:
- id: '9814'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Language acquisition with communication between learners
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '5859'
abstract:
- lang: eng
text: The emergence of syntax during childhood is a remarkable example of how complex
correlations unfold in nonlinear ways through development. In particular, rapid
transitions seem to occur as children reach the age of two, which seems to separate
a two-word, tree-like network of syntactic relations among words from the scale-free
graphs associated with the adult, complex grammar. Here, we explore the evolution
of syntax networks through language acquisition using the chromatic number, which
captures the transition and provides a natural link to standard theories on syntactic
structures. The data analysis is compared to a null model of network growth dynamics
which is shown to display non-trivial and sensible differences. At a more general
level, we observe that the chromatic classes define independent regions of the
graph, and thus, can be interpreted as the footprints of incompatibility relations,
somewhat as opposed to modularity considerations.
acknowledgement: This work was supported by the James McDonnell Foundation (B.C-M.,
S.V. and R.S.)
article_number: '181286'
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Martí Sànchez
full_name: Fibla, Martí Sànchez
last_name: Fibla
- first_name: Sergi
full_name: Valverde, Sergi
last_name: Valverde
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in
the emergence of syntax networks. Royal Society Open Science. 2018;5(12).
doi:10.1098/rsos.181286
apa: Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic
transitions in the emergence of syntax networks. Royal Society Open Science.
The Royal Society. https://doi.org/10.1098/rsos.181286
chicago: Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard
Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society
Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.
ieee: B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions
in the emergence of syntax networks,” Royal Society Open Science, vol.
5, no. 12. The Royal Society, 2018.
ista: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions
in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.
mla: Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of
Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The
Royal Society, 2018, doi:10.1098/rsos.181286.
short: B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open
Science 5 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-10-18T06:41:12Z
day: '12'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1098/rsos.181286
external_id:
isi:
- '000456566500027'
pmid:
- '30662738'
file:
- access_level: open_access
checksum: 9664d4417f6b792242e31eea77ce9501
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:38:09Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5924'
file_name: 2018_RoyalSocOS_Corominas.pdf
file_size: 646732
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Royal Society Open Science
publication_identifier:
issn:
- 2054-5703
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatic transitions in the emergence of syntax networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2018'
...