---
_id: '6935'
abstract:
- lang: eng
text: "This paper investigates the power of preprocessing in the CONGEST model.
Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to
study the application of distributed algorithms in Software-Defined Networks (SDNs).
In this paper, we show that a large class of lower bounds in the CONGEST model
still hold in the SUPPORTED model, highlighting the robustness of these bounds.
This also raises the question how much does\r\npreprocessing help in the CONGEST
model."
article_processing_charge: No
author:
- first_name: Klaus-Tycho
full_name: Foerster, Klaus-Tycho
last_name: Foerster
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under
congestion? In: Proceedings of the 2019 ACM Symposium on Principles of Distributed
Computing. ACM; 2019:259-261. doi:10.1145/3293611.3331581'
apa: 'Foerster, K.-T., Korhonen, J., Rybicki, J., & Schmid, S. (2019). Does
preprocessing help under congestion? In Proceedings of the 2019 ACM Symposium
on Principles of Distributed Computing (pp. 259–261). Toronto, ON, Canada:
ACM. https://doi.org/10.1145/3293611.3331581'
chicago: Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid.
“Does Preprocessing Help under Congestion?” In Proceedings of the 2019 ACM
Symposium on Principles of Distributed Computing, 259–61. ACM, 2019. https://doi.org/10.1145/3293611.3331581.
ieee: K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing
help under congestion?,” in Proceedings of the 2019 ACM Symposium on Principles
of Distributed Computing, Toronto, ON, Canada, 2019, pp. 259–261.
ista: 'Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help
under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed
Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.'
mla: Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” Proceedings
of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019,
pp. 259–61, doi:10.1145/3293611.3331581.
short: K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the
2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261.
conference:
end_date: 2019-08-02
location: Toronto, ON, Canada
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2019-07-29
date_created: 2019-10-08T12:57:14Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-09-08T11:37:22Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293611.3331581
ec_funded: 1
external_id:
arxiv:
- '1905.03012'
isi:
- '000570442000037'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.03012
month: '08'
oa: 1
oa_version: Preprint
page: 259-261
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450362177'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Does preprocessing help under congestion?
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '138'
abstract:
- lang: eng
text: Autoregulation is the direct modulation of gene expression by the product
of the corresponding gene. Autoregulation of bacterial gene expression has been
mostly studied at the transcriptional level, when a protein acts as the cognate
transcriptional repressor. A recent study investigating dynamics of the bacterial
toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional
and post-transcriptional levels affects the heterogeneity of Escherichia coli
populations. Toxin–antitoxin systems hold a crucial but still elusive part in
bacterial response to stress. This perspective highlights how these modules can
also serve as a great model system for investigating basic concepts in gene regulation.
However, as the genomic background and environmental conditions substantially
influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin
systems in well-defined setups as well as in conditions that resemble the environmental
niche.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
citation:
ama: 'Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF
toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8'
apa: 'Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from
the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8'
chicago: 'Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from
the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.'
ieee: 'N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the
MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer,
pp. 133–138, 2019.'
ista: 'Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from
the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.'
mla: 'Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from
the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer,
2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.'
short: N. Nikolic, Current Genetics 65 (2019) 133–138.
date_created: 2018-12-11T11:44:50Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-08T13:23:42Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1007/s00294-018-0879-8
ec_funded: 1
external_id:
isi:
- '000456958800017'
file:
- access_level: open_access
checksum: 6779708b0b632a1a6ed28c56f5161142
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:50:58Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5930'
file_name: 2019_CurrentGenetics_Nikolic.pdf
file_size: 776399
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 133-138
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Genetics
publication_status: published
publisher: Springer
publist_id: '7785'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin
system'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2019'
...
---
_id: '151'
abstract:
- lang: eng
text: We construct planar bi-Sobolev mappings whose local volume distortion is bounded
from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2
we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞,
we provide bi-Lipschitz maps. The basic building block of our construction are
bi-Lipschitz maps which stretch a given compact subset of the unit square by a
given factor while preserving the boundary. The construction of these stretching
maps relies on a slight strengthening of the celebrated covering result of Alberti,
Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We
apply our result to a model functional in nonlinear elasticity, the integrand
of which features fast blowup as the Jacobian determinant of the deformation becomes
small. For such functionals, the derivation of the equilibrium equations for minimizers
requires an additional regularization of test functions, which our maps provide.
article_processing_charge: No
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Olivier
full_name: Kneuss, Olivier
last_name: Kneuss
citation:
ama: Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality
in the plane with L p data and applications to nonlinear elasticity. Journal
of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045
apa: Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed
Jacobian inequality in the plane with L p data and applications to nonlinear elasticity.
Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045
chicago: Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed
Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.”
Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.
ieee: J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian
inequality in the plane with L p data and applications to nonlinear elasticity,”
Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311,
2019.
ista: Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian
inequality in the plane with L p data and applications to nonlinear elasticity.
Journal of Differential Equations. 266(1), 257–311.
mla: Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed
Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.”
Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp.
257–311, doi:10.1016/j.jde.2018.07.045.
short: J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.
date_created: 2018-12-11T11:44:54Z
date_published: 2019-01-05T00:00:00Z
date_updated: 2023-09-08T13:25:35Z
day: '05'
department:
- _id: JuFi
doi: 10.1016/j.jde.2018.07.045
external_id:
arxiv:
- '1408.1587'
isi:
- '000449108500010'
intvolume: ' 266'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.1587
month: '01'
oa: 1
oa_version: Preprint
page: 257 - 311
publication: Journal of Differential Equations
publication_status: published
publisher: Elsevier
publist_id: '7770'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with
L p data and applications to nonlinear elasticity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 266
year: '2019'
...
---
_id: '27'
abstract:
- lang: eng
text: The cerebral cortex is composed of a large variety of distinct cell-types
including projection neurons, interneurons and glial cells which emerge from distinct
neural stem cell (NSC) lineages. The vast majority of cortical projection neurons
and certain classes of glial cells are generated by radial glial progenitor cells
(RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis
and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated
in a profound deterministic manner. In this review we focus on recent advances
based mainly on correlative phenotypic data emerging from functional genetic studies
in mice. We establish hypotheses to test in future research and outline a conceptual
framework how epigenetic cues modulate the generation of cell-type diversity during
cortical development. This article is protected by copyright. All rights reserved.
acknowledgement: " This work was supported by IST Austria institutional funds; NÖ
Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from
\ the Human Frontiers Science Program (RGP0053/2014) to SH; the People
\ Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European
\ Research Council (ERC) under the European Union’s Horizon 2020 research
\ and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n"
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation
of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
2019;149(1):12-26. doi:10.1111/jnc.14601
apa: Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating
the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
Wiley. https://doi.org/10.1111/jnc.14601
chicago: Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues
Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal
of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.
ieee: N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the
generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry,
vol. 149, no. 1. Wiley, pp. 12–26, 2019.
ista: Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the
generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry.
149(1), 12–26.
mla: Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type
Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149,
no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.
short: N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019)
12–26.
date_created: 2018-12-11T11:44:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-09-11T13:40:26Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1111/jnc.14601
ec_funded: 1
external_id:
isi:
- '000462680200002'
file:
- access_level: open_access
checksum: db027721a95d36f5de36aadcd0bdf7e6
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:35:52Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7239'
file_name: 2019_Wiley_Amberg.pdf
file_size: 889709
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 149'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 12-26
project:
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Journal of Neurochemistry
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Epigenetic cues modulating the generation of cell type diversity in the cerebral
cortex
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 149
year: '2019'
...
---
_id: '5789'
abstract:
- lang: eng
text: Tissue morphogenesis is driven by mechanical forces that elicit changes in
cell size, shape and motion. The extent by which forces deform tissues critically
depends on the rheological properties of the recipient tissue. Yet, whether and
how dynamic changes in tissue rheology affect tissue morphogenesis and how they
are regulated within the developing organism remain unclear. Here, we show that
blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid,
pronounced and spatially patterned tissue fluidization. Blastoderm fluidization
is temporally controlled by mitotic cell rounding-dependent cell–cell contact
disassembly during the last rounds of cell cleavages. Moreover, fluidization is
spatially restricted to the central blastoderm by local activation of non-canonical
Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby
counteracting the effect of mitotic rounding on contact disassembly. Overall,
our results identify a fluidity transition mediated by loss of cell cohesion as
a critical regulator of embryo morphogenesis.
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
article_type: original
author:
- first_name: Nicoletta
full_name: Petridou, Nicoletta
id: 2A003F6C-F248-11E8-B48F-1D18A9856A87
last_name: Petridou
orcid: 0000-0002-8451-1195
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated
tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature
Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4
apa: Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg,
C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding
and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing
Group. https://doi.org/10.1038/s41556-018-0247-4
chicago: Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo,
and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic
Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature
Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.
ieee: N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg,
“Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical
Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group,
pp. 169–178, 2019.
ista: Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated
tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature
Cell Biology. 21, 169–178.
mla: Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic
Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol.
21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.
short: N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg,
Nature Cell Biology 21 (2019) 169–178.
date_created: 2018-12-30T22:59:15Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-11T14:03:28Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
doi: 10.1038/s41556-018-0247-4
ec_funded: 1
external_id:
isi:
- '000457468300011'
pmid:
- '30559456'
file:
- access_level: open_access
checksum: e38523787b3bc84006f2793de99ad70f
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T07:18:35Z
date_updated: 2020-10-21T07:18:35Z
file_id: '8685'
file_name: 2018_NatureCellBio_Petridou_accepted.pdf
file_size: 71590590
relation: main_file
success: 1
file_date_updated: 2020-10-21T07:18:35Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 169–178
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 253E54C8-B435-11E9-9278-68D0E5697425
grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants (EMBO fellowship)
publication: Nature Cell Biology
publication_identifier:
issn:
- '14657392'
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/when-a-fish-becomes-fluid/
scopus_import: '1'
status: public
title: Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical
Wnt signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2019'
...
---
_id: '196'
abstract:
- lang: eng
text: 'The abelian sandpile serves as a model to study self-organized criticality,
a phenomenon occurring in biological, physical and social processes. The identity
of the abelian group is a fractal composed of self-similar patches, and its limit
is subject of extensive collaborative research. Here, we analyze the evolution
of the sandpile identity under harmonic fields of different orders. We show that
this evolution corresponds to periodic cycles through the abelian group characterized
by the smooth transformation and apparent conservation of the patches constituting
the identity. The dynamics induced by second and third order harmonics resemble
smooth stretchings, respectively translations, of the identity, while the ones
induced by fourth order harmonics resemble magnifications and rotations. Starting
with order three, the dynamics pass through extended regions of seemingly random
configurations which spontaneously reassemble into accentuated patterns. We show
that the space of harmonic functions projects to the extended analogue of the
sandpile group, thus providing a set of universal coordinates identifying configurations
between different domains. Since the original sandpile group is a subgroup of
the extended one, this directly implies that it admits a natural renormalization.
Furthermore, we show that the harmonic fields can be induced by simple Markov
processes, and that the corresponding stochastic dynamics show remarkable robustness
over hundreds of periods. Finally, we encode information into seemingly random
configurations, and decode this information with an algorithm requiring minimal
prior knowledge. Our results suggest that harmonic fields might split the sandpile
group into sub-sets showing different critical coefficients, and that it might
be possible to extend the fractal structure of the identity beyond the boundaries
of its domain. '
acknowledgement: "M.L. is grateful to the members of the C Guet and G Tkacik groups
for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring
communications.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116
apa: Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1812015116
chicago: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian
Sandpile.” Proceedings of the National Academy of Sciences. National Academy
of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
ieee: M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings
of the National Academy of Sciences, vol. 116, no. 8. National Academy of
Sciences, pp. 2821–2830, 2019.
ista: Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 116(8), 2821–2830.
mla: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.”
Proceedings of the National Academy of Sciences, vol. 116, no. 8, National
Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.
short: M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116
(2019) 2821–2830.
date_created: 2018-12-11T11:45:08Z
date_published: 2019-02-19T00:00:00Z
date_updated: 2023-09-11T14:09:34Z
day: '19'
department:
- _id: CaGu
- _id: GaTk
- _id: TaHa
doi: 10.1073/pnas.1812015116
external_id:
arxiv:
- '1806.10823'
isi:
- '000459074400013'
pmid:
- ' 30728300'
intvolume: ' 116'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1812015116
month: '02'
oa: 1
oa_version: Published Version
page: 2821-2830
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/
scopus_import: '1'
status: public
title: Harmonic dynamics of the Abelian sandpile
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2019'
...
---
_id: '14184'
abstract:
- lang: eng
text: "Learning disentangled representations is considered a cornerstone problem
in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated
that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible
and that existing inductive biases and unsupervised methods do not\r\nallow to
consistently learn disentangled representations. However, in many\r\npractical
settings, one might have access to a limited amount of supervision,\r\nfor example
through manual labeling of (some) factors of variation in a few\r\ntraining examples.
In this paper, we investigate the impact of such supervision\r\non state-of-the-art
disentanglement methods and perform a large scale study,\r\ntraining over 52000
models under well-defined and reproducible experimental\r\nconditions. We observe
that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with
potentially imprecise and incomplete labels, is sufficient\r\nto perform model
selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate
the benefit of incorporating supervision into the training process.\r\nOverall,
we empirically validate that with little and imprecise supervision it\r\nis possible
to reliably learn disentangled representations."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling
factors of variation using few labels. In: 8th International Conference on
Learning Representations. ; 2019.'
apa: Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem,
O. (2019). Disentangling factors of variation using few labels. In 8th International
Conference on Learning Representations. Virtual.
chicago: Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard
Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.”
In 8th International Conference on Learning Representations, 2019.
ieee: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem,
“Disentangling factors of variation using few labels,” in 8th International
Conference on Learning Representations, Virtual, 2019.
ista: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019.
Disentangling factors of variation using few labels. 8th International Conference
on Learning Representations. ICLR: International Conference on Learning Representations.'
mla: Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few
Labels.” 8th International Conference on Learning Representations, 2019.
short: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem,
in:, 8th International Conference on Learning Representations, 2019.
conference:
end_date: 2020-05-01
location: Virtual
name: 'ICLR: International Conference on Learning Representations'
start_date: 2020-04-26
date_created: 2023-08-22T14:06:37Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2023-09-12T07:01:34Z
day: '20'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.01258'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.01258
month: '12'
oa: 1
oa_version: Preprint
publication: 8th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disentangling factors of variation using few labels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '14189'
abstract:
- lang: eng
text: "We consider the problem of recovering a common latent source with independent\r\ncomponents
from multiple views. This applies to settings in which a variable is\r\nmeasured
with multiple experimental modalities, and where the goal is to\r\nsynthesize
the disparate measurements into a single unified representation. We\r\nconsider
the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions
of the sources. When the views are considered\r\nseparately, this reduces to nonlinear
Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to
undo the mixing. We present novel\r\nidentifiability proofs that this is possible
when the multiple views are\r\nconsidered jointly, showing that the mixing can
theoretically be undone using\r\nfunction approximators such as deep neural networks.
In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that
independent latent\r\nsources with arbitrary mixing can be recovered as long as
multiple,\r\nsufficiently different noisy views are available."
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Luigi
full_name: Gresele, Luigi
last_name: Gresele
- first_name: Paul K.
full_name: Rubenstein, Paul K.
last_name: Rubenstein
- first_name: Arash
full_name: Mehrjou, Arash
last_name: Mehrjou
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete
Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In:
Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence.
Vol 115. ML Research Press; 2019:217-227.'
apa: 'Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf,
B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial
Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.'
chicago: 'Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello,
and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability
Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference
on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press,
2019.'
ieee: 'L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf,
“The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial
Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.'
ista: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The
incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear
ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence.
UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.'
mla: 'Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability
Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on
Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019,
pp. 217–27.'
short: L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:,
Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence,
ML Research Press, 2019, pp. 217–227.
conference:
end_date: 2019-07-25
location: Tel Aviv, Israel
name: 'UAI: Uncertainty in Artificial Intelligence'
start_date: 2019-07-22
date_created: 2023-08-22T14:08:35Z
date_published: 2019-05-16T00:00:00Z
date_updated: 2023-09-12T08:07:38Z
day: '16'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.06642'
intvolume: ' 115'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.06642
month: '05'
oa: 1
oa_version: Preprint
page: 217-227
publication: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2019'
...
---
_id: '14197'
abstract:
- lang: eng
text: "Recently there has been a significant interest in learning disentangled\r\nrepresentations,
as they promise increased interpretability, generalization to\r\nunseen scenarios
and faster learning on downstream tasks. In this paper, we\r\ninvestigate the
usefulness of different notions of disentanglement for\r\nimproving the fairness
of downstream prediction tasks based on representations.\r\nWe consider the setting
where the goal is to predict a target variable based on\r\nthe learned representation
of high-dimensional observations (such as images)\r\nthat depend on both the target
variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this
setting both the optimal and empirical\r\npredictions can be unfair, even if the
target variable and the sensitive\r\nvariable are independent. Analyzing the representations
of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we
observe that\r\nseveral disentanglement scores are consistently correlated with
increased\r\nfairness, suggesting that disentanglement may be a useful property
to encourage\r\nfairness when sensitive variables are not observed."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gabriele
full_name: Abbati, Gabriele
last_name: Abbati
- first_name: Tom
full_name: Rainforth, Tom
last_name: Rainforth
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the
fairness of disentangled representations. In: Advances in Neural Information
Processing Systems. Vol 32. ; 2019:14611–14624.'
apa: Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem,
O. (2019). On the fairness of disentangled representations. In Advances in
Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver,
Canada.
chicago: Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard
Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.”
In Advances in Neural Information Processing Systems, 32:14611–14624, 2019.
ieee: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem,
“On the fairness of disentangled representations,” in Advances in Neural Information
Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.
ista: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019.
On the fairness of disentangled representations. Advances in Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.'
mla: Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.”
Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.
short: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem,
in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:12:28Z
date_published: 2019-12-08T00:00:00Z
date_updated: 2023-09-12T09:37:22Z
day: '08'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.13662'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.13662
month: '12'
oa: 1
oa_version: Preprint
page: 14611–14624
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the fairness of disentangled representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14191'
abstract:
- lang: eng
text: A broad class of convex optimization problems can be formulated as a semidefinite
program (SDP), minimization of a convex function over the positive-semidefinite
cone subject to some affine constraints. The majority of classical SDP solvers
are designed for the deterministic setting where problem data is readily available.
In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type
methods) provide scalable solutions by leveraging the so-called linear minimization
oracle instead of the projection onto the semidefinite cone. Most problems in
machine learning and modern engineering applications, however, contain some degree
of stochasticity. In this work, we propose the first conditional-gradient-type
method for solving stochastic optimization problems under affine constraints.
Our method guarantees O(k−1/3) convergence rate in expectation on the objective
residual and O(k−5/12) on the feasibility gap.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
- first_name: Olivier
full_name: Fercoq, Olivier
last_name: Fercoq
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite
convex minimization. In: Advances in Neural Information Processing Systems.
Vol 32. ; 2019:14291–14301.'
apa: Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic
Frank-Wolfe for composite convex minimization. In Advances in Neural Information
Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.
chicago: Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher.
“Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in
Neural Information Processing Systems, 32:14291–14301, 2019.
ieee: F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe
for composite convex minimization,” in Advances in Neural Information Processing
Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.
ista: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe
for composite convex minimization. Advances in Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.'
mla: Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.”
Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.
short: F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural
Information Processing Systems, 2019, pp. 14291–14301.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:35Z
date_published: 2019-12-29T00:00:00Z
date_updated: 2023-09-12T08:48:45Z
day: '29'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1901.10348'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.10348
month: '12'
oa: 1
oa_version: Preprint
page: 14291–14301
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic Frank-Wolfe for composite convex minimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14193'
abstract:
- lang: eng
text: "A disentangled representation encodes information about the salient factors\r\nof
variation in the data independently. Although it is often argued that this\r\nrepresentational
format is useful in learning to solve many real-world\r\ndown-stream tasks, there
is little empirical evidence that supports this claim.\r\nIn this paper, we conduct
a large-scale study that investigates whether\r\ndisentangled representations
are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar
to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations
learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based
on these representations, we train 3600 abstract\r\nreasoning models and observe
that disentangled representations do in fact lead\r\nto better down-stream performance.
In particular, they enable quicker learning\r\nusing fewer samples."
article_processing_charge: No
author:
- first_name: Sjoerd van
full_name: Steenkiste, Sjoerd van
last_name: Steenkiste
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Jürgen
full_name: Schmidhuber, Jürgen
last_name: Schmidhuber
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations
helpful for abstract visual reasoning? In: Advances in Neural Information Processing
Systems. Vol 32. ; 2019.'
apa: Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019).
Are disentangled representations helpful for abstract visual reasoning? In Advances
in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.
chicago: Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier
Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?”
In Advances in Neural Information Processing Systems, Vol. 32, 2019.
ieee: S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled
representations helpful for abstract visual reasoning?,” in Advances in Neural
Information Processing Systems, Vancouver, Canada, 2019, vol. 32.
ista: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled
representations helpful for abstract visual reasoning? Advances in Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.'
mla: Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for
Abstract Visual Reasoning?” Advances in Neural Information Processing Systems,
vol. 32, 2019.
short: S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances
in Neural Information Processing Systems, 2019.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:53Z
date_published: 2019-05-29T00:00:00Z
date_updated: 2023-09-12T09:02:43Z
day: '29'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.12506'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.12506
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
status: public
title: Are disentangled representations helpful for abstract visual reasoning?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14200'
abstract:
- lang: eng
text: "The key idea behind the unsupervised learning of disentangled representations\r\nis
that real-world data is generated by a few explanatory factors of variation\r\nwhich
can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide
a sober look at recent progress in the field and challenge some common\r\nassumptions.
We first theoretically show that the unsupervised learning of\r\ndisentangled
representations is fundamentally impossible without inductive\r\nbiases on both
the models and the data. Then, we train more than 12000 models\r\ncovering most
prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental
study on seven different data sets. We observe that\r\nwhile the different methods
successfully enforce properties ``encouraged'' by\r\nthe corresponding losses,
well-disentangled models seemingly cannot be\r\nidentified without supervision.
Furthermore, increased disentanglement does not\r\nseem to lead to a decreased
sample complexity of learning for downstream tasks.\r\nOur results suggest that
future work on disentanglement learning should be\r\nexplicit about the role of
inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits
of enforcing disentanglement of the learned\r\nrepresentations, and consider a
reproducible experimental setup covering\r\nseveral data sets."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Mario
full_name: Lucic, Mario
last_name: Lucic
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the
unsupervised learning of disentangled representations. In: Proceedings of the
36th International Conference on Machine Learning. Vol 97. ML Research Press;
2019:4114-4124.'
apa: 'Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B.,
& Bachem, O. (2019). Challenging common assumptions in the unsupervised learning
of disentangled representations. In Proceedings of the 36th International Conference
on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States:
ML Research Press.'
chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain
Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions
in the Unsupervised Learning of Disentangled Representations.” In Proceedings
of the 36th International Conference on Machine Learning, 97:4114–24. ML Research
Press, 2019.
ieee: F. Locatello et al., “Challenging common assumptions in the unsupervised
learning of disentangled representations,” in Proceedings of the 36th International
Conference on Machine Learning, Long Beach, CA, United States, 2019, vol.
97, pp. 4114–4124.
ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019.
Challenging common assumptions in the unsupervised learning of disentangled representations.
Proceedings of the 36th International Conference on Machine Learning. International
Conference on Machine Learning vol. 97, 4114–4124.
mla: Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised
Learning of Disentangled Representations.” Proceedings of the 36th International
Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.
short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem,
in:, Proceedings of the 36th International Conference on Machine Learning, ML
Research Press, 2019, pp. 4114–4124.
conference:
end_date: 2019-06-15
location: Long Beach, CA, United States
name: International Conference on Machine Learning
start_date: 2019-06-10
date_created: 2023-08-22T14:13:08Z
date_published: 2019-06-09T00:00:00Z
date_updated: 2023-09-13T07:45:30Z
day: '09'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1811.12359'
intvolume: ' 97'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.12359
month: '06'
oa: 1
oa_version: Preprint
page: 4114-4124
publication: Proceedings of the 36th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Challenging common assumptions in the unsupervised learning of disentangled
representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2019'
...
---
_id: '5817'
abstract:
- lang: eng
text: We theoretically study the shapes of lipid vesicles confined to a spherical
cavity, elaborating a framework based on the so-called limiting shapes constructed
from geometrically simple structural elements such as double-membrane walls and
edges. Partly inspired by numerical results, the proposed non-compartmentalized
and compartmentalized limiting shapes are arranged in the bilayer-couple phase
diagram which is then compared to its free-vesicle counterpart. We also compute
the area-difference-elasticity phase diagram of the limiting shapes and we use
it to interpret shape transitions experimentally observed in vesicles confined
within another vesicle. The limiting-shape framework may be generalized to theoretically
investigate the structure of certain cell organelles such as the mitochondrion.
article_processing_charge: No
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: A.
full_name: Sakashita, A.
last_name: Sakashita
- first_name: H.
full_name: Noguchi, H.
last_name: Noguchi
- first_name: P.
full_name: Ziherl, P.
last_name: Ziherl
citation:
ama: Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid
vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h
apa: Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes
of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h
chicago: Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes
of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019.
https://doi.org/10.1039/c8sm01956h.
ieee: B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined
lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry,
pp. 602–614, 2019.
ista: Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined
lipid vesicles. Soft Matter. 15(4), 602–614.
mla: Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter,
vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.
short: B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.
date_created: 2019-01-11T07:37:47Z
date_published: 2019-01-10T00:00:00Z
date_updated: 2023-09-13T08:47:16Z
day: '10'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1039/c8sm01956h
external_id:
isi:
- '000457329700003'
pmid:
- '30629082'
file:
- access_level: open_access
checksum: 614c337d6424ccd3d48d1b1f9513510d
content_type: application/pdf
creator: bkavcic
date_created: 2020-10-09T11:00:05Z
date_updated: 2020-10-09T11:00:05Z
file_id: '8641'
file_name: lmt_sftmtr_V8.pdf
file_size: 5370762
relation: main_file
success: 1
file_date_updated: 2020-10-09T11:00:05Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/3.0/
month: '01'
oa: 1
oa_version: Submitted Version
page: 602-614
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limiting shapes of confined lipid vesicles
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2019'
...
---
_id: '73'
abstract:
- lang: eng
text: We consider the space of probability measures on a discrete set X, endowed
with a dynamical optimal transport metric. Given two probability measures supported
in a subset Y⊆X, it is natural to ask whether they can be connected by a constant
speed geodesic with support in Y at all times. Our main result answers this question
affirmatively, under a suitable geometric condition on Y introduced in this paper.
The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi
equations, which is of independent interest.
article_number: '19'
article_processing_charge: Yes (via OA deal)
article_type: original
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: Melchior
full_name: Wirth, Melchior
last_name: Wirth
citation:
ama: Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal
transport. Calculus of Variations and Partial Differential Equations. 2019;58(1).
doi:10.1007/s00526-018-1456-1
apa: Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in
discrete optimal transport. Calculus of Variations and Partial Differential
Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1
chicago: Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics
in Discrete Optimal Transport.” Calculus of Variations and Partial Differential
Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1.
ieee: M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete
optimal transport,” Calculus of Variations and Partial Differential Equations,
vol. 58, no. 1. Springer, 2019.
ista: Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal
transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.
mla: Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.”
Calculus of Variations and Partial Differential Equations, vol. 58, no.
1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.
short: M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential
Equations 58 (2019).
date_created: 2018-12-11T11:44:29Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-13T09:12:35Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00526-018-1456-1
ec_funded: 1
external_id:
arxiv:
- '1805.06040'
isi:
- '000452849400001'
file:
- access_level: open_access
checksum: ba05ac2d69de4c58d2cd338b63512798
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:37:11Z
date_updated: 2020-07-14T12:47:55Z
file_id: '5895'
file_name: 2018_Calculus_Erbar.pdf
file_size: 645565
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: ' F06504'
name: Taming Complexity in Partial Di erential Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
issn:
- '09442669'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the geometry of geodesics in discrete optimal transport
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 58
year: '2019'
...
---
_id: '14190'
abstract:
- lang: eng
text: "Learning meaningful and compact representations with disentangled semantic\r\naspects
is considered to be of key importance in representation learning. Since\r\nreal-world
data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement
models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose
a novel data-set which consists of over one million images of\r\nphysical 3D objects
with seven factors of variation, such as object color,\r\nshape, size and position.
In order to be able to control all the factors of\r\nvariation precisely, we built
an experimental platform where the objects are\r\nbeing moved by a robotic arm.
In addition, we provide two more datasets which\r\nconsist of simulations of the
experimental setup. These datasets provide for\r\nthe first time the possibility
to systematically investigate how well different\r\ndisentanglement methods perform
on real data in comparison to simulation, and\r\nhow simulated data can be leveraged
to build better representations of the real\r\nworld. We provide a first experimental
study of these questions and our results\r\nindicate that learned models transfer
poorly, but that model and hyperparameter\r\nselection is an effective means of
transferring information to the real world."
article_processing_charge: No
author:
- first_name: Muhammad Waleed
full_name: Gondal, Muhammad Waleed
last_name: Gondal
- first_name: Manuel
full_name: Wüthrich, Manuel
last_name: Wüthrich
- first_name: Đorđe
full_name: Miladinović, Đorđe
last_name: Miladinović
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Martin
full_name: Breidt, Martin
last_name: Breidt
- first_name: Valentin
full_name: Volchkov, Valentin
last_name: Volchkov
- first_name: Joel
full_name: Akpo, Joel
last_name: Akpo
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
citation:
ama: 'Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive
bias from simulation to the real world: a new disentanglement dataset. In: Advances
in Neural Information Processing Systems. Vol 32. ; 2019.'
apa: 'Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov,
V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the
real world: a new disentanglement dataset. In Advances in Neural Information
Processing Systems (Vol. 32). Vancouver, Canada.'
chicago: 'Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco
Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard
Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation
to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information
Processing Systems, Vol. 32, 2019.'
ieee: 'M. W. Gondal et al., “On the transfer of inductive bias from simulation
to the real world: a new disentanglement dataset,” in Advances in Neural Information
Processing Systems, Vancouver, Canada, 2019, vol. 32.'
ista: 'Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V,
Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias
from simulation to the real world: a new disentanglement dataset. Advances in
Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems vol. 32.'
mla: 'Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation
to the Real World: A New Disentanglement Dataset.” Advances in Neural Information
Processing Systems, vol. 32, 2019.'
short: M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov,
J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information
Processing Systems, 2019.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:13Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-13T09:46:38Z
day: '07'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1906.03292'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.03292
month: '06'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
status: public
title: 'On the transfer of inductive bias from simulation to the real world: a new
disentanglement dataset'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2019'
...
---
_id: '6982'
abstract:
- lang: eng
text: "We present an efficient algorithm for a problem in the interface between
clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold
M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint
Jordan arcs between the corresponding vertices. In applications in clustering,
cartography, and visualization, nearby vertices and edges are often bundled to
the same point or overlapping arcs due to data compression or low resolution.
This raises the computational problem of deciding whether a given map ϕ : G →
M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed
into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖
is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings
has recently been found by Fulek and Kynčl. It reduces the problem to solving
a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where
ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices
and edges of G. We improve the running time to O(n log n). Our algorithm is also
conceptually simpler: We perform a sequence of local operations that gradually
“untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak
embedding. It combines local constraints on the orientation of subgraphs directly,
thereby eliminating the need for solving large systems of linear equations.\r\n"
article_number: '50'
article_type: original
author:
- first_name: Hugo
full_name: Akitaya, Hugo
last_name: Akitaya
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba
full_name: Tóth, Csaba
last_name: Tóth
citation:
ama: Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions
on Algorithms. 2019;15(4). doi:10.1145/3344549
apa: Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings
of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549
chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings
of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549.
ieee: H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,”
ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.
ista: Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM
Transactions on Algorithms. 15(4), 50.
mla: Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions
on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.
short: H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).
date_created: 2019-11-04T15:45:17Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-15T12:19:31Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3344549
external_id:
arxiv:
- '1709.09209'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.09209
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: ACM Transactions on Algorithms
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '309'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Recognizing weak embeddings of graphs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...
---
_id: '6894'
abstract:
- lang: eng
text: "Hybrid automata combine finite automata and dynamical systems, and model
the interaction of digital with physical systems. Formal analysis that can guarantee
the safety of all behaviors or rigorously witness failures, while unsolvable in
general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking,
assisted theorem proving.\r\nNevertheless, very few methods have addressed the
time-unbounded reachability analysis of hybrid automata and, for current sound
and automatic tools, scalability remains critical. We develop methods for the
polyhedral abstraction of hybrid automata, which construct coarse overapproximations
and tightens them incrementally, in a CEGAR fashion. We use template polyhedra,
i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile,
previously, directions were given by the user, we introduce (1) the first method\r\nfor
computing template directions from spurious counterexamples, so as to generalize
and\r\neliminate them. The method applies naturally to convex hybrid automata,
i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives
only, while for linear\r\nODE requires further abstraction. Specifically, we introduce
(2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate
(possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight
sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time
interpolation, which, combining interval arithmetic\r\nand template refinement,
computes appropriate (possibly non-uniform) time partitioning\r\nand template
directions along spurious trajectories, so as to eliminate them.\r\nWe obtain
sound and automatic methods for the reachability analysis over dense\r\nand unbounded
time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build
prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art
tools, on several benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
citation:
ama: Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems.
2019. doi:10.15479/AT:ISTA:6894
apa: Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894
chicago: Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.
ieee: M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,”
Institute of Science and Technology Austria, 2019.
ista: Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid
systems. Institute of Science and Technology Austria.
mla: Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid
Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.
short: M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems,
Institute of Science and Technology Austria, 2019.
date_created: 2019-09-22T14:08:44Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:6894
file:
- access_level: open_access
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language:
- iso: eng
month: '09'
oa: 1
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page: '132'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '631'
relation: part_of_dissertation
status: public
- id: '647'
relation: part_of_dissertation
status: public
- id: '140'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Automatic time-unbounded reachability analysis of hybrid systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '9805'
abstract:
- lang: eng
text: The spread of adaptive alleles is fundamental to evolution, and in theory,
this process is well‐understood. However, only rarely can we follow this process—whether
it originates from the spread of a new mutation, or by introgression from another
population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report
on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles
coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP).
The species are usually reproductively isolated from each other, but in 2002 and
2006, bursts of hybridization were observed, when F1 hybrids became abundant.
Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event,
these declined over the following years. In contrast, after 2006, an insecticide
resistance allele that had established in A. gambiae spread into A. coluzzi, and
rose to high frequency there, over 6 years (~75 generations). Whole genome sequences
of 74 individuals showed that A. gambiae SNP from across the genome had become
common in the A. coluzzi population, but that most of these were clustered in
34 genes around the resistance locus. A new set of SNP from 25 of these genes
were assayed over time; over the 4 years since near‐fixation of the resistance
allele; some remained common, whereas others declined. What do these patterns
tell us about this introgression event?
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4'
apa: 'Barton, N. H. (2019). Data from: The consequences of an introgression event.
Dryad. https://doi.org/10.5061/dryad.2kb6fh4'
chicago: 'Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.”
Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.'
ieee: 'N. H. Barton, “Data from: The consequences of an introgression event.” Dryad,
2019.'
ista: 'Barton NH. 2019. Data from: The consequences of an introgression event, Dryad,
10.5061/dryad.2kb6fh4.'
mla: 'Barton, Nicholas H. Data from: The Consequences of an Introgression Event.
Dryad, 2019, doi:10.5061/dryad.2kb6fh4.'
short: N.H. Barton, (2019).
date_created: 2021-08-06T12:03:50Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2023-09-19T10:06:07Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.2kb6fh4
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.2kb6fh4
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '40'
relation: used_in_publication
status: public
status: public
title: 'Data from: The consequences of an introgression event'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '8'
abstract:
- lang: eng
text: Despite their different origins, Drosophila glia and hemocytes are related
cell populations that provide an immune function. Drosophila hemocytes patrol
the body cavity and act as macrophages outside the nervous system whereas glia
originate from the neuroepithelium and provide the scavenger population of the
nervous system. Drosophila glia are hence the functional orthologs of vertebrate
microglia, even though the latter are cells of immune origin that subsequently
move into the brain during development. Interestingly, the Drosophila immune cells
within (glia) and outside the nervous system (hemocytes) require the same transcription
factor Glide/Gcm for their development. This raises the issue of how do glia specifically
differentiate in the nervous system and hemocytes in the procephalic mesoderm.
The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm
is known to ensure glial terminal differentiation. Here we show that Repo also
takes center stage in the process that discriminates between glia and hemocytes.
First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific
factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient
to repress the expression of hemocyte-specific genes. Third, the lack of Repo
triggers the expression of hemocyte markers in glia. Thus, a complex network of
tissue-specific cues biases the potential of Glide/Gcm. These data allow us to
revise the concept of fate determinants and help us understand the bases of cell
specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types
often require the same pioneer transcription factor, raising the issue of how
does one factor trigger different fates. In Drosophila, glia and hemocytes provide
a scavenger activity within and outside the nervous system, respectively. While
they both require the Glide/Gcm transcription factor, glia originate from the
ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors
inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the
expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm.
Repo expression in turn inhibits the expression of hemocyte-specific genes in
the nervous system. These cell-specific networks secure the establishment of the
glial fate only in the nervous system and allow cell diversification.
acknowledgement: This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre
le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC)
and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR
and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques),
and G.T. by governmental and ARC fellowships. This work was also supported by grants
from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut
de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French
state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM.
We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant,
R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC
for reagents and flies. We also thank all of the laboratory members for comments
on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and
antibody facilities for technical assistance; and D. Dembele for help with statistics.
In addition, we thank Alison Brewer for help with Luciferase assays.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Trébuchet, Guillaume
last_name: Trébuchet
- first_name: Pierre B
full_name: Cattenoz, Pierre B
last_name: Cattenoz
- first_name: János
full_name: Zsámboki, János
last_name: Zsámboki
- first_name: David
full_name: Mazaud, David
last_name: Mazaud
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Manolis
full_name: Fanto, Manolis
last_name: Fanto
- first_name: Angela
full_name: Giangrande, Angela
last_name: Giangrande
citation:
ama: Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription
factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal
of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018
apa: Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E.,
Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor
suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal
of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018
chicago: Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud,
Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain
Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the
Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018.
ieee: G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses
hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience,
vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.
ista: Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande
A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in
Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255.
mla: Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses
Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience,
vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018.
short: G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto,
A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.
date_created: 2018-12-11T11:44:07Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2023-09-19T10:10:55Z
day: '09'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1523/JNEUROSCI.1059-18.2018
ec_funded: 1
external_id:
isi:
- '000455189900006'
pmid:
- '30504274'
file:
- access_level: open_access
checksum: 8f6925eb4cd1e8747d8ea25929c68de6
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T09:33:28Z
date_updated: 2020-10-02T09:33:28Z
file_id: '8596'
file_name: 2019_JournNeuroscience_Trebuchet.pdf
file_size: 9455414
relation: main_file
success: 1
file_date_updated: 2020-10-02T09:33:28Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 238-255
pmid: 1
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '8048'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila
and preserves the glial fate
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 39
year: '2019'
...
---
_id: '5'
abstract:
- lang: eng
text: In this paper, we introduce a quantum version of the wonderful compactification
of a group as a certain noncommutative projective scheme. Our approach stems from
the fact that the wonderful compactification encodes the asymptotics of matrix
coefficients, and from its realization as a GIT quotient of the Vinberg semigroup.
In order to define the wonderful compactification for a quantum group, we adopt
a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key
to our construction is a quantum version of the Vinberg semigroup, which we define
as a q-deformation of a certain Rees algebra, compatible with a standard Poisson
structure. Furthermore, we discuss quantum analogues of the stratification of
the wonderful compactification by orbits for a certain group action, and provide
explicit computations in the case of SL2.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Iordan V
full_name: Ganev, Iordan V
id: 447491B8-F248-11E8-B48F-1D18A9856A87
last_name: Ganev
citation:
ama: Ganev IV. The wonderful compactification for quantum groups. Journal of
the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193
apa: Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal
of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193
chicago: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal
of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193.
ieee: I. V. Ganev, “The wonderful compactification for quantum groups,” Journal
of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.
ista: Ganev IV. 2019. The wonderful compactification for quantum groups. Journal
of the London Mathematical Society. 99(3), 778–806.
mla: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal
of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806,
doi:10.1112/jlms.12193.
short: I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.
date_created: 2018-12-11T11:44:06Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-19T10:13:08Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/jlms.12193
external_id:
isi:
- '000470025900008'
file:
- access_level: open_access
checksum: 1be56239b2cd740a0e9a084f773c22f6
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:31:53Z
date_updated: 2020-07-14T12:46:35Z
file_id: '7238'
file_name: 2019_Wiley_Ganev.pdf
file_size: 431754
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 99'
isi: 1
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 778-806
publication: Journal of the London Mathematical Society
publication_status: published
publisher: Wiley
publist_id: '8052'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The wonderful compactification for quantum groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 99
year: '2019'
...
---
_id: '7172'
abstract:
- lang: eng
text: "The development and growth of Arabidopsis thaliana is regulated by a combination
of genetic programing and also by the environmental influences. An important role
in these processes play the phytohormones and among them, auxin is crucial as
it controls many important functions. It is transported through the whole plant
body by creating local and temporal concentration maxima and minima, which have
an impact on the cell status, tissue and organ identity. Auxin has the property
to undergo a directional and finely regulated cell-to-cell transport, which is
enabled by the transport proteins, localized on the plasma membrane. An important
role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar
subcellular localization and determine the directionality of the auxin transport.
During the last years, there were significant advances in understanding how the
trafficking molecular machineries function, including studies on molecular interactions,
function, subcellular localization and intracellular distribution. However, there
is still a lack of detailed characterization on the steps of endocytosis, exocytosis,
endocytic recycling and degradation. Due to this fact, I focused on the identification
of novel trafficking factors and better characterization of the intracellular
trafficking pathways. My PhD thesis consists of an introductory chapter, three
experimental chapters, a chapter containing general discussion, conclusions and
perspectives and also an appendix chapter with published collaborative papers.\r\nThe
first chapter is separated in two different parts: I start by a general introduction
to auxin biology and then I introduce the trafficking pathways in the model plant
Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar
targeting and also the roles of the phytohormone strigolactone.\r\nThe second
chapter includes the characterization of bar1/sacsin mutant, which was identified
in a forward genetic screen for novel trafficking components in Arabidopsis thaliana,
where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and
by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to
study trafficking processes, we identified a novel factor, which is mediating
the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously
uncharacterized gene, encoding a very big protein that we, based on its homologies,
called SACSIN with domains suggesting roles as a molecular chaperon or as a component
of the ubiquitin-proteasome system. Our physiology and imaging studies revealed
that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF
inhibition.\r\nThe third chapter includes six subchapters, where I focus on the
role of the phytohormone strigolactone, which interferes with auxin feedback on
PIN internalization. Strigolactone moderates the polar auxin transport by increasing
the internalization of the PIN auxin efflux carriers, which reduces the canalization
related growth responses. In addition, I also studied the role of phosphorylation
in the strigolactone regulation of auxin feedback on PIN internalization. In this
chapter I also present my results on the MAX2-dependence of strigolactone-mediated
root growth inhibition and I also share my results on the auxin metabolomics profiling
after application of GR24.\r\nIn the fourth chapter I studied the effect of two
small molecules ES-9 and ES9-17, which were identified from a collection of small
molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn
the fifth chapter, I discuss all my observations and experimental findings and
suggest alternative hypothesis to interpret my results.\r\nIn the appendix there
are three collaborative published projects. In the first, I participated in the
characterization of the role of ES9 as a small molecule, which is inhibitor of
clathrin- mediated endocytosis in different model organisms. In the second paper,
I contributed to the characterization of another small molecule ES9-17, which
is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis
not only in plant cells, but also in mammalian HeLa cells. Last but not least,
I also attach another paper, where I tried to establish the grafting method as
a technique in our lab to study canalization related processes."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
citation:
ama: Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis
thaliana. 2019. doi:10.15479/AT:ISTA:7172
apa: Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking
in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172
chicago: Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in
Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7172.
ieee: M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis
thaliana,” Institute of Science and Technology Austria, 2019.
ista: Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis
thaliana. Institute of Science and Technology Austria.
mla: Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis
Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172.
short: M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis
Thaliana, Institute of Science and Technology Austria, 2019.
date_created: 2019-12-11T21:24:39Z
date_published: 2019-12-12T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '12'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:7172
file:
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checksum: ef981c1a3b1d9da0edcbedcff4970d37
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mvasilev
date_created: 2019-12-12T09:32:36Z
date_updated: 2020-07-14T12:47:51Z
file_id: '7175'
file_name: Thesis_Mina_final_upload_7.docx
file_size: 20454014
relation: source_file
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checksum: 3882c4585e46c9cfb486e4225cad54ab
content_type: application/pdf
creator: mvasilev
date_created: 2019-12-12T09:33:10Z
date_updated: 2020-07-14T12:47:51Z
file_id: '7176'
file_name: Thesis_Mina_final_upload_7.pdf
file_size: 11565025
relation: main_file
file_date_updated: 2020-07-14T12:47:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '192'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1346'
relation: part_of_dissertation
status: public
- id: '6377'
relation: part_of_dissertation
status: public
- id: '449'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6093'
abstract:
- lang: eng
text: Blebs are cellular protrusions observed in migrating cells and in cells undergoing
spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm
during bleb formation and the concurrent changes in cell volume using zebrafish
primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation
occurs concomitantly with cytoplasmic inflow into it and that during this process
the total cell volume does not change. We thus show that bleb formation in primordial
germ cells results primarily from redistribution of material within the cell rather
than being driven by flow of water from an external source.
article_number: e0212699
article_processing_charge: No
author:
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Aleix
full_name: Boquet-Pujadas, Aleix
last_name: Boquet-Pujadas
- first_name: Jean Christophe
full_name: Olivo-Marin, Jean Christophe
last_name: Olivo-Marin
- first_name: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during
bleb formation in migrating cells in vivo. PLOS ONE. 2019;14(2). doi:10.1371/journal.pone.0212699
apa: Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., & Raz, E. (2019).
Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE.
Public Library of Science. https://doi.org/10.1371/journal.pone.0212699
chicago: Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin,
and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.”
PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0212699.
ieee: M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics
during bleb formation in migrating cells in vivo,” PLOS ONE, vol. 14, no.
2. Public Library of Science, 2019.
ista: Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics
during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699.
mla: Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating
Cells in Vivo.” PLOS ONE, vol. 14, no. 2, e0212699, Public Library of Science,
2019, doi:10.1371/journal.pone.0212699.
short: M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).
date_created: 2019-03-10T22:59:21Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2023-09-19T14:46:47Z
day: '26'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1371/journal.pone.0212699
external_id:
isi:
- '000459712100022'
file:
- access_level: open_access
checksum: b885de050ed4bb3c86f706487a47197f
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:09:23Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6096'
file_name: 2019_PLoSOne_Goudarzi.pdf
file_size: 2967731
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has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLOS ONE
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluid dynamics during bleb formation in migrating cells in vivo
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2019'
...
---
_id: '6473'
abstract:
- lang: eng
text: "Single cells are constantly interacting with their environment and each other,
more importantly, the accurate perception of environmental cues is crucial for
growth, survival, and reproduction. This communication between cells and their
environment can be formalized in mathematical terms and be quantified as the information
flow between them, as prescribed by information theory. \r\nThe recent availability
of real–time dynamical patterns of signaling molecules in single cells has allowed
us to identify encoding about the identity of the environment in the time–series.
However, efficient estimation of the information transmitted by these signals
has been a data–analysis challenge due to the high dimensionality of the trajectories
and the limited number of samples. In the first part of this thesis, we develop
and evaluate decoding–based estimation methods to lower bound the mutual information
and derive model–based precise information estimates for biological reaction networks
governed by the chemical master equation. This is followed by applying the decoding-based
methods to study the intracellular representation of extracellular changes in
budding yeast, by observing the transient dynamics of nuclear translocation of
10 transcription factors in response to 3 stress conditions. Additionally, we
apply these estimators to previously published data on ERK and Ca2+ signaling
and yeast stress response. We argue that this single cell decoding-based measure
of information provides an unbiased, quantitative and interpretable measure for
the fidelity of biological signaling processes. \r\nFinally, in the last section,
we deal with gene regulation which is primarily controlled by transcription factors
(TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate
TFs activate transcription diminishes the accuracy of regulation with potentially
disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored
source of noise in biochemical networks and puts a strong constraint on their
performance. To mitigate erroneous initiation we propose an out of equilibrium
scheme that implements kinetic proofreading. We show that such architectures are
favored over their equilibrium counterparts for complex organisms despite introducing
noise in gene expression. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
citation:
ama: Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473
apa: Cepeda Humerez, S. A. (2019). Estimating information flow in single cells.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473
chicago: Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.
ieee: S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute
of Science and Technology Austria, 2019.
ista: Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute
of Science and Technology Austria.
mla: Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.
short: S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute
of Science and Technology Austria, 2019.
date_created: 2019-05-21T00:11:23Z
date_published: 2019-05-23T00:00:00Z
date_updated: 2023-09-19T15:13:26Z
day: '23'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:6473
file:
- access_level: closed
checksum: 75f9184c1346e10a5de5f9cc7338309a
content_type: application/zip
creator: scepeda
date_created: 2019-05-23T11:18:16Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6480'
file_name: Thesis_Cepeda.zip
file_size: 23937464
relation: source_file
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checksum: afdc0633ddbd71d5b13550d7fb4f4454
content_type: application/pdf
creator: scepeda
date_created: 2019-05-23T11:18:13Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6481'
file_name: CepedaThesis.pdf
file_size: 16646985
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
keyword:
- Information estimation
- Time-series
- data analysis
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '135'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1576'
relation: dissertation_contains
status: public
- id: '6900'
relation: dissertation_contains
status: public
- id: '281'
relation: dissertation_contains
status: public
- id: '2016'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Estimating information flow in single cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6071'
abstract:
- lang: eng
text: 'Transcription factors, by binding to specific sequences on the DNA, control
the precise spatio-temporal expression of genes inside a cell. However, this specificity
is limited, leading to frequent incorrect binding of transcription factors that
might have deleterious consequences on the cell. By constructing a biophysical
model of TF-DNA binding in the context of gene regulation, I will first explore
how regulatory constraints can strongly shape the distribution of a population
in sequence space. Then, by directly linking this to a picture of multiple types
of transcription factors performing their functions simultaneously inside the
cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
between transcription factors and binding sites that lead to erroneous regulatory
states -- and understand the constraints this places on the design of regulatory
systems. I will then develop a generic theoretical framework to investigate the
coevolution of multiple transcription factors and multiple binding sites, in the
context of a gene regulatory network that performs a certain function. As a particular
tractable version of this problem, I will consider the evolution of two transcription
factors when they transmit upstream signals to downstream target genes. Specifically,
I will describe the evolutionary steady states and the evolutionary pathways involved,
along with their timescales, of a system that initially undergoes a transcription
factor duplication event. To connect this important theoretical model to the prominent
biological event of transcription factor duplication giving rise to paralogous
families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
factors, a major family in humans, and focus on the patterns of evolution that
paralogs have undergone in their various protein domains in the recent past. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
citation:
ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence
space. 2019. doi:10.15479/at:ista:th6071
apa: Prizak, R. (2019). Coevolution of transcription factors and their binding
sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071
chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding
Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in
sequence space,” Institute of Science and Technology Austria, 2019.
ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites
in sequence space. Institute of Science and Technology Austria.
mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites
in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.
short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in
Sequence Space, Institute of Science and Technology Austria, 2019.
date_created: 2019-03-06T16:16:10Z
date_published: 2019-03-11T00:00:00Z
date_updated: 2023-09-22T10:00:48Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GaTk
- _id: NiBa
doi: 10.15479/at:ista:th6071
file:
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checksum: e60a72de35d270b31f1a23d50f224ec0
content_type: application/pdf
creator: rprizak
date_created: 2019-03-06T16:05:07Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6072'
file_name: Thesis_final_PDFA_RoshanPrizak.pdf
file_size: 20995465
relation: main_file
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checksum: 67c2630333d05ebafef5f018863a8465
content_type: application/zip
creator: rprizak
date_created: 2019-03-06T16:09:39Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6073'
file_name: thesis_v2_merge.zip
file_size: 85705272
relation: source_file
title: Latex files
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '189'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1358'
relation: part_of_dissertation
status: public
- id: '955'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Coevolution of transcription factors and their binding sites in sequence space
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7436'
abstract:
- lang: eng
text: 'For an ordinary K3 surface over an algebraically closed field of positive
characteristic we show that every automorphism lifts to characteristic zero. Moreover,
we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one
correspondence with the Fourier-Mukai partners of the geometric generic fiber
of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai
partners of the K3 surfaces with Picard rank two and with discriminant equal to
minus of a prime number, in terms of the class number of the prime, holds over
a field of positive characteristic as well. We show that the image of the derived
autoequivalence group of a K3 surface of finite height in the group of isometries
of its crystalline cohomology has index at least two. Moreover, we provide a conditional
upper bound on the kernel of this natural cohomological descent map. Further,
we give an extended remark in the appendix on the possibility of an F-crystal
structure on the crystalline cohomology of a K3 surface over an algebraically
closed field of positive characteristic and show that the naive F-crystal structure
fails in being compatible with inner product. '
article_processing_charge: No
article_type: original
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177
apa: Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive
characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177
chicago: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive
Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177.
ieee: T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,”
Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.
ista: Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 24, 1135–1177.
mla: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.”
Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.
short: T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.
date_created: 2020-02-02T23:01:06Z
date_published: 2019-05-20T00:00:00Z
date_updated: 2023-10-17T07:42:21Z
day: '20'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.25537/dm.2019v24.1135-1177
external_id:
arxiv:
- '1809.08970'
isi:
- '000517806400019'
file:
- access_level: open_access
checksum: 9a1a64bd49ab03fa4f738fb250fc4f90
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T06:26:12Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7438'
file_name: 2019_DocumMath_Srivastava.pdf
file_size: 469730
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1135-1177
publication: Documenta Mathematica
publication_identifier:
eissn:
- 1431-0643
issn:
- 1431-0635
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On derived equivalences of k3 surfaces in positive characteristic
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: 24
year: '2019'
...
---
_id: '72'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process (TASEP) with non-random
initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle
initially at the origin. For ρ<λ, there is a shock and the second class particle
moves with speed 1−λ−ρ. For large time t, we show that the position of the second
class particle fluctuates on a t1/3 scale and determine its limiting law. We also
obtain the limiting distribution of the number of steps made by the second class
particle until time t.
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Ferrari, Patrick
last_name: Ferrari
- first_name: Promit
full_name: Ghosal, Promit
last_name: Ghosal
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP
with non-random initial condition. Annales de l’institut Henri Poincare (B)
Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916
apa: Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class
particle in TASEP with non-random initial condition. Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics.
https://doi.org/10.1214/18-AIHP916
chicago: Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second
Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics,
2019. https://doi.org/10.1214/18-AIHP916.
ieee: P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle
in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare
(B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical
Statistics, pp. 1203–1225, 2019.
ista: Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle
in TASEP with non-random initial condition. Annales de l’institut Henri Poincare
(B) Probability and Statistics. 55(3), 1203–1225.
mla: Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with
Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability
and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019,
pp. 1203–25, doi:10.1214/18-AIHP916.
short: P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B)
Probability and Statistics 55 (2019) 1203–1225.
date_created: 2018-12-11T11:44:29Z
date_published: 2019-09-25T00:00:00Z
date_updated: 2023-10-17T08:53:45Z
day: '25'
department:
- _id: LaEr
- _id: JaMa
doi: 10.1214/18-AIHP916
ec_funded: 1
external_id:
arxiv:
- '1710.02323'
isi:
- '000487763200001'
intvolume: ' 55'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02323
month: '09'
oa: 1
oa_version: Preprint
page: 1203-1225
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limit law of a second class particle in TASEP with non-random initial condition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '6657'
abstract:
- lang: eng
text: 'In this article a model is described how Open Access definitions can be formed
on the basis of objective criteria. The common Open Access definitions such as
"gold" and "green" are not exactly defined. This becomes a problem as soon as
one begins to measure Open Access, for example if the development of the Open
Access share should be monitored. This was discussed in the working group on Open
Access Monitoring of the AT2OA project and the present model was developed,
which is based on 5 critics with 4 characteristics: location, licence, version,
embargo and conditions of the Open Access publication are taken into account.
In the meantime, the model has also been tested in practice using R scripts, and
the initial results are quite promising.'
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. An Austrian proposal for the classification of Open Access Tuples
(COAT) - distinguish different open access types beyond colors. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65.
doi:10.31263/voebm.v72i1.2276
apa: Danowski, P. (2019). An Austrian proposal for the classification of Open Access
Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276
chicago: Danowski, Patrick. “An Austrian Proposal for the Classification of Open
Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.”
Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare.
Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.
ieee: P. Danowski, “An Austrian proposal for the classification of Open Access Tuples
(COAT) - distinguish different open access types beyond colors,” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol.
72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp.
59–65, 2019.
ista: Danowski P. 2019. An Austrian proposal for the classification of Open Access
Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.
mla: Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access
Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol.
72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019,
pp. 59–65, doi:10.31263/voebm.v72i1.2276.
short: P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 72 (2019) 59–65.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-05-17T00:00:00Z
date_updated: 2023-10-17T11:33:58Z
day: '17'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v72i1.2276
file:
- access_level: open_access
checksum: c0d2695d6d0d34e62ba06fb3f0ebaaed
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-22T08:45:03Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6661'
file_name: 2019_MitteilungenDerVOEB_Danowski.pdf
file_size: 468558
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 72'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 59-65
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
eissn:
- 1022-2588
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
quality_controlled: '1'
related_material:
record:
- id: '5686'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: An Austrian proposal for the classification of Open Access Tuples (COAT) -
distinguish different open access types beyond colors
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: 72
year: '2019'
...
---
_id: '6646'
abstract:
- lang: eng
text: We demonstrate robust retention of valley coherence and its control via polariton
pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity
exciton polaritons at room temperature.
article_number: paper JTu2A.52
article_processing_charge: No
author:
- first_name: Mandeep
full_name: Khatoniar, Mandeep
last_name: Khatoniar
- first_name: Nicholas
full_name: Yama, Nicholas
last_name: Yama
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Sriram
full_name: Guddala, Sriram
last_name: Guddala
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
- first_name: Vinod
full_name: Menon, Vinod
last_name: Menon
citation:
ama: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature
control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications
and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52'
apa: 'Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon,
V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton
polaritons. In CLEO: Applications and Technology. San Jose, CA, United
States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52'
chicago: 'Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan
Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer
WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica
Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.'
ieee: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon,
“Room temperature control of valley coherence in bilayer WS2 exciton polaritons,”
in CLEO: Applications and Technology, San Jose, CA, United States, 2019.'
ista: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room
temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO:
Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper
JTu2A.52.'
mla: 'Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in
Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper
JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.'
short: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:,
CLEO: Applications and Technology, Optica Publishing Group, 2019.'
conference:
end_date: 2019-05-10
location: San Jose, CA, United States
name: 'CLEO: Conference on Lasers and Electro-Optics'
start_date: 2019-05-05
date_created: 2019-07-17T09:40:44Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-10-17T12:14:29Z
day: '01'
department:
- _id: MiLe
doi: 10.1364/cleo_at.2019.jtu2a.52
language:
- iso: eng
month: '05'
oa_version: None
publication: 'CLEO: Applications and Technology'
publication_identifier:
isbn:
- '9781943580576'
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Room temperature control of valley coherence in bilayer WS2 exciton polaritons
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7233'
abstract:
- lang: eng
text: We demonstrate electro-optic frequency comb generation using a doubly resonant
system comprising a whispering gallery mode disk resonator made of lithium niobate
mounted inside a three dimensional copper cavity. We observe 180 sidebands centred
at 1550 nm.
article_number: NM2A.5
article_processing_charge: No
author:
- 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: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic
frequency comb generation in lithium niobate disk resonator inside a microwave
cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing
Group; 2019. doi:10.1364/NLO.2019.NM2A.5'
apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate
disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical
Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group.
https://doi.org/10.1364/NLO.2019.NM2A.5'
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in
Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics,
OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb generation in lithium niobate disk resonator
inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest,
Waikoloa Beach, Hawaii (HI), United States, 2019.
ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant
electro-optic frequency comb generation in lithium niobate disk resonator inside
a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics,
NM2A.5.'
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation
in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics,
OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.
short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:,
Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.
conference:
end_date: 2019-07-19
location: Waikoloa Beach, Hawaii (HI), United States
name: 'NLO: Nonlinear Optics'
start_date: 2019-07-15
date_created: 2020-01-05T23:00:48Z
date_published: 2019-07-15T00:00:00Z
date_updated: 2023-10-17T12:14:46Z
day: '15'
department:
- _id: JoFi
doi: 10.1364/NLO.2019.NM2A.5
language:
- iso: eng
month: '07'
oa_version: None
publication: Nonlinear Optics, OSA Technical Digest
publication_identifier:
isbn:
- '9781557528209'
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb generation in lithium niobate disk resonator
inside a microwave cavity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6240'
abstract:
- lang: eng
text: For a general class of large non-Hermitian random block matrices X we prove
that there are no eigenvalues away from a deterministic set with very high probability.
This set is obtained from the Dyson equation of the Hermitization of X as the
self-consistent approximation of the pseudospectrum. We demonstrate that the analysis
of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers
a unified treatment of many structured matrix ensembles.
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker
random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696.
doi:10.1214/18-AIHP894
apa: Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the
spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare.
Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894
chicago: Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location
of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri
Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.
ieee: J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of
Kronecker random matrices,” Annales de l’institut Henri Poincare, vol.
55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.
ista: Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker
random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.
mla: Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.”
Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré,
2019, pp. 661–96, doi:10.1214/18-AIHP894.
short: J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare
55 (2019) 661–696.
date_created: 2019-04-08T14:05:04Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-10-17T12:20:20Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-AIHP894
ec_funded: 1
external_id:
arxiv:
- '1706.08343'
isi:
- '000467793600003'
intvolume: ' 55'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.08343
month: '05'
oa: 1
oa_version: Preprint
page: 661-696
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annales de l'institut Henri Poincare
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institut Henri Poincaré
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Location of the spectrum of Kronecker random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '7399'
abstract:
- lang: eng
text: Long non-coding (lnc) RNAs are numerous and found throughout the mammalian
genome, and many are thought to be involved in the regulation of gene expression.
However, the majority remain relatively uncharacterised and of uncertain function
making the use of model systems to uncover their mode of action valuable. Imprinted
lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted
genes on the same chromosome, making them one of the best characterized lncRNAs
for silencing distant genes in cis. In this study we examined silencing of the
distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster
in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted
genes by disrupting promoter-enhancer interactions by being transcribed through
the enhancer, which we called the enhancer interference hypothesis. Here we tested
this hypothesis by first using allele-specific chromosome conformation capture
(3C) to detect interactions between the Slc22a3 promoter and the locus of the
Airn lncRNA that silences it on the paternal chromosome. In agreement with the
model, we found interactions enriched on the maternal allele across the entire
Airn gene consistent with multiple enhancer-promoter interactions. Therefore,
to test the enhancer interference hypothesis we devised an approach to delete
the entire Airn gene. However, the deletion showed that there are no essential
enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating
that the Airn RNA rather than its transcription is responsible for silencing distant
imprinted genes. Furthermore, we found that silent imprinted genes were covered
with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose
an alternative hypothesis whereby the chromosome interactions may initially guide
the lncRNA to target imprinted promoters and recruit repressive chromatin, and
that these interactions are lost once silencing is established.
article_number: e1008268
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Andergassen, Daniel
last_name: Andergassen
- first_name: Markus
full_name: Muckenhuber, Markus
last_name: Muckenhuber
- first_name: Philipp C.
full_name: Bammer, Philipp C.
last_name: Bammer
- first_name: Tomasz M.
full_name: Kulinski, Tomasz M.
last_name: Kulinski
- first_name: Hans-Christian
full_name: Theussl, Hans-Christian
last_name: Theussl
- first_name: Takahiko
full_name: Shimizu, Takahiko
last_name: Shimizu
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
citation:
ama: Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require
any DNA elements within its locus to silence distant imprinted genes. PLoS
Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268
apa: Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl,
H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any
DNA elements within its locus to silence distant imprinted genes. PLoS Genetics.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268
chicago: Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski,
Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler,
and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within
Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268.
ieee: D. Andergassen et al., “The Airn lncRNA does not require any DNA elements
within its locus to silence distant imprinted genes,” PLoS Genetics, vol.
15, no. 7. Public Library of Science, 2019.
ista: Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu
T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any
DNA elements within its locus to silence distant imprinted genes. PLoS Genetics.
15(7), e1008268.
mla: Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements
within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol.
15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.
short: D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl,
T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).
date_created: 2020-01-29T16:14:07Z
date_published: 2019-07-22T00:00:00Z
date_updated: 2023-10-17T12:30:27Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pgen.1008268
external_id:
isi:
- '000478689100025'
pmid:
- '31329595'
file:
- access_level: open_access
checksum: 2f51fc91e4a4199827adc51d432ad864
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:11:55Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7446'
file_name: 2019_PlosGenetics_Andergassen.pdf
file_size: 2302307
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Airn lncRNA does not require any DNA elements within its locus to silence
distant imprinted genes
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: 15
year: '2019'
...
---
_id: '7103'
abstract:
- lang: eng
text: Origin and functions of intermittent transitions among sleep stages, including
short awakenings and arousals, constitute a challenge to the current homeostatic
framework for sleep regulation, focusing on factors modulating sleep over large
time scales. Here we propose that the complex micro-architecture characterizing
the sleep-wake cycle results from an underlying non-equilibrium critical dynamics,
bridging collective behaviors across spatio-temporal scales. We investigate θ
and δ wave dynamics in control rats and in rats with lesions of sleep-promoting
neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and
δ rhythms exhibit a complex temporal organization, with long-range power-law correlations
and a robust duality of power law (θ-bursts, active phase) and exponential-like
(δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium
systems self-organizing at criticality. Crucially, such temporal organization
relates to anti-correlated coupling between θ- and δ-bursts, and is independent
of the dominant physiologic state and lesions, a solid indication of a basic principle
in sleep dynamics.
article_number: e1007268
article_processing_charge: No
article_type: original
author:
- first_name: Jilin W. J. L.
full_name: Wang, Jilin W. J. L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Christelle
full_name: Anaclet, Christelle
last_name: Anaclet
- first_name: Plamen Ch.
full_name: Ivanov, Plamen Ch.
last_name: Ivanov
citation:
ama: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical
dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and
wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
apa: Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C.
(2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268
chicago: Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet,
and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ
Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.
ieee: J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15,
no. 11. Public Library of Science, 2019.
ista: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.
mla: Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in
θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.”
PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007268.
short: J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational
Biology 15 (2019).
date_created: 2019-11-25T08:20:47Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-17T12:30:07Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007268
ec_funded: 1
external_id:
isi:
- '000500976100014'
pmid:
- '31725712'
file:
- access_level: open_access
checksum: 2a096a9c6dcc6eaa94077b2603bc6c12
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:24:01Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7104'
file_name: 2019_PLOSComBio_Wang.pdf
file_size: 3982516
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture
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: 15
year: '2019'
...
---
_id: '6569'
abstract:
- lang: eng
text: 'Knowledge distillation, i.e. one classifier being trained on the outputs
of another classifier, is an empirically very successful technique for knowledge
transfer between classifiers. It has even been observed that classifiers learn
much faster and more reliably if trained with the outputs of another classifier
as soft labels, instead of from ground truth data. So far, however, there is no
satisfactory theoretical explanation of this phenomenon. In this work, we provide
the first insights into the working mechanisms of distillation by studying the
special case of linear and deep linear classifiers. Specifically, we prove a
generalization bound that establishes fast convergence of the expected risk of
a distillation-trained linear classifier. From the bound and its proof we extract
three keyfactors that determine the success of distillation: data geometry – geometric
properties of the datadistribution, in particular class separation, has an immediate
influence on the convergence speed of the risk; optimization bias– gradient descentoptimization
finds a very favorable minimum of the distillation objective; and strong monotonicity–
the expected risk of the student classifier always decreases when the size of
the training set grows.'
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings
of the 36th International Conference on Machine Learning. Vol 97. ML Research
Press; 2019:5142-5151.'
apa: 'Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation.
In Proceedings of the 36th International Conference on Machine Learning
(Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.'
chicago: Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.”
In Proceedings of the 36th International Conference on Machine Learning,
97:5142–51. ML Research Press, 2019.
ieee: M. Phuong and C. Lampert, “Towards understanding knowledge distillation,”
in Proceedings of the 36th International Conference on Machine Learning,
Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.
ista: 'Phuong M, Lampert C. 2019. Towards understanding knowledge distillation.
Proceedings of the 36th International Conference on Machine Learning. ICML: International
Conference on Machine Learning vol. 97, 5142–5151.'
mla: Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.”
Proceedings of the 36th International Conference on Machine Learning, vol.
97, ML Research Press, 2019, pp. 5142–51.
short: M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference
on Machine Learning, ML Research Press, 2019, pp. 5142–5151.
conference:
end_date: 2019-06-15
location: Long Beach, CA, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2019-06-10
date_created: 2019-06-20T18:23:03Z
date_published: 2019-06-13T00:00:00Z
date_updated: 2023-10-17T12:31:38Z
day: '13'
ddc:
- '000'
department:
- _id: ChLa
file:
- access_level: open_access
checksum: a66d00e2694d749250f8507f301320ca
content_type: application/pdf
creator: bphuong
date_created: 2019-06-20T18:22:56Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6570'
file_name: paper.pdf
file_size: 686432
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 97'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 5142-5151
publication: Proceedings of the 36th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards understanding knowledge distillation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2019'
...
---
_id: '6590'
abstract:
- lang: eng
text: 'Modern machine learning methods often require more data for training than
a single expert can provide. Therefore, it has become a standard procedure to
collect data from external sources, e.g. via crowdsourcing. Unfortunately, the
quality of these sources is not always guaranteed. As additional complications,
the data might be stored in a distributed way, or might even have to remain private.
In this work, we address the question of how to learn robustly in such scenarios.
Studying the problem through the lens of statistical learning theory, we derive
a procedure that allows for learning from all available sources, yet automatically
suppresses irrelevant or corrupted data. We show by extensive experiments that
our method provides significant improvements over alternative approaches from
robust statistics and distributed optimization. '
article_processing_charge: No
author:
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings
of the 36th International Conference on Machine Learning. Vol 97. ML Research
Press; 2019:3488-3498.'
apa: 'Konstantinov, N. H., & Lampert, C. (2019). Robust learning from untrusted
sources. In Proceedings of the 36th International Conference on Machine Learning
(Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.'
chicago: Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted
Sources.” In Proceedings of the 36th International Conference on Machine Learning,
97:3488–98. ML Research Press, 2019.
ieee: N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,”
in Proceedings of the 36th International Conference on Machine Learning,
Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498.
ista: 'Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources.
Proceedings of the 36th International Conference on Machine Learning. ICML: International
Conference on Machine Learning vol. 97, 3488–3498.'
mla: Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted
Sources.” Proceedings of the 36th International Conference on Machine Learning,
vol. 97, ML Research Press, 2019, pp. 3488–98.
short: N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International
Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.
conference:
end_date: 2919-06-15
location: Long Beach, CA, USA
name: 'ICML: International Conference on Machine Learning'
start_date: 2019-06-10
date_created: 2019-06-27T14:18:23Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-10-17T12:31:55Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1901.10310'
intvolume: ' 97'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.10310
month: '06'
oa: 1
oa_version: Preprint
page: 3488-3498
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 36th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '10799'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Robust learning from untrusted sources
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2019'
...
---
_id: '6999'
abstract:
- lang: eng
text: Plasmodesmata (PD) are plant-specific membrane-lined channels that create
cytoplasmic and membrane continuities between adjacent cells, thereby facilitating
cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms
to regulate PD plasticity in response to numerous environmental stimuli. In particular,
during defense against plant pathogens, the defense hormone, salicylic acid (SA),
plays a crucial role in the regulation of PD permeability in a callose-dependent
manner. Here, we uncover a mechanism by which plants restrict the spreading of
virus and PD cargoes using SA signaling by increasing lipid order and closure
of PD. We showed that exogenous SA application triggered the compartmentalization
of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein,
Remorin (REM). Genetic studies, superresolution imaging, and transmission electron
microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3
are crucial for plasma membrane nanodomain assembly to control PD aperture and
functionality. In addition, we also found that a 14-3-3 epsilon protein modulates
REM clustering and membrane nanodomain compartmentalization through its direct
interaction with REM proteins. This study unveils a molecular mechanism by which
the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization,
thereby regulating PD closure to impede virus spreading.
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: Y
full_name: Sun, Y
last_name: Sun
- first_name: Z
full_name: Ma, Z
last_name: Ma
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: C
full_name: Chen, C
last_name: Chen
- first_name: C
full_name: Ji, C
last_name: Ji
- first_name: TM
full_name: Tran, TM
last_name: Tran
- first_name: L
full_name: Yang, L
last_name: Yang
- first_name: SM
full_name: Lam, SM
last_name: Lam
- first_name: Y
full_name: Han, Y
last_name: Han
- first_name: G
full_name: Shu, G
last_name: Shu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Miao, Y
last_name: Miao
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization. Proceedings of the National Academy of
Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116
apa: Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic
acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116
chicago: Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated
Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.
ieee: D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 42. Proceedings
of the National Academy of Sciences, pp. 21274–21284, 2019.
ista: Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam
S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated
plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of
the National Academy of Sciences of the United States of America. 116(42), 21274–21284.
mla: Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent
Lipid Organization.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 116, no. 42, Proceedings of the National Academy
of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.
short: D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran,
L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings
of the National Academy of Sciences of the United States of America 116 (2019)
21274–21284.
date_created: 2019-11-12T11:42:05Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-10-17T12:32:37Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1911892116
external_id:
isi:
- '000490183000068'
pmid:
- '31575745'
file:
- access_level: open_access
checksum: 258c666bc6253eab81961f61169eefae
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:22:28Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7012'
file_name: 2019_PNAS_Huang.pdf
file_size: 3287466
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 116'
isi: 1
issue: '42'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 21274-21284
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2004738117
scopus_import: '1'
status: public
title: Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '6621'
abstract:
- lang: eng
text: We read with great interest the recent work in PNAS by Bergero et al. (1)
describing differences in male and female recombination patterns on the guppy
(Poecilia reticulata) sex chromosome. We fully agree that recombination in males
is largely confined to the ends of the sex chromosome. Bergero et al. interpret
these results to suggest that our previous findings of population-level variation
in the degree of sex chromosome differentiation in this species (2) are incorrect.
However, we suggest that their results are entirely consistent with our previous
report, and that their interpretation presents a false controversy.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Alison E.
full_name: Wright, Alison E.
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha I.
full_name: Bloch, Natasha I.
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin A.
full_name: Sandkam, Benjamin A.
last_name: Sandkam
- first_name: Séverine D.
full_name: Buechel, Séverine D.
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith E.
full_name: Mank, Judith E.
last_name: Mank
citation:
ama: Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination
events. Proceedings of the National Academy of Sciences of the United States
of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116
apa: Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel,
S. D., … Mank, J. E. (2019). On the power to detect rare recombination events.
Proceedings of the National Academy of Sciences of the United States of America.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116
chicago: Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin
A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and
Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116.
ieee: A. E. Wright et al., “On the power to detect rare recombination events,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608,
2019.
ista: Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N,
Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events.
Proceedings of the National Academy of Sciences of the United States of America.
116(26), 12607–12608.
mla: Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08,
doi:10.1073/pnas.1905555116.
short: A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel,
N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy
of Sciences of the United States of America 116 (2019) 12607–12608.
date_created: 2019-07-07T21:59:25Z
date_published: 2019-06-25T00:00:00Z
date_updated: 2023-10-17T12:44:15Z
day: '25'
department:
- _id: BeVi
doi: 10.1073/pnas.1905555116
external_id:
isi:
- '000472719100010'
pmid:
- '31213531'
intvolume: ' 116'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1905555116
month: '06'
oa: 1
oa_version: Published Version
page: 12607-12608
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the power to detect rare recombination events
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '6856'
abstract:
- lang: eng
text: 'Plant mating systems play a key role in structuring genetic variation both
within and between species. In hybrid zones, the outcomes and dynamics of hybridization
are usually interpreted as the balance between gene flow and selection against
hybrids. Yet, mating systems can introduce selective forces that alter these expectations;
with diverse outcomes for the level and direction of gene flow depending on variation
in outcrossing and whether the mating systems of the species pair are the same
or divergent. We present a survey of hybridization in 133 species pairs from 41
plant families and examine how patterns of hybridization vary with mating system.
We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and
the frequency of reproductive isolating barriers vary in relation to mating system/s
of the species pair. We combine these results with a simulation model and examples
from the literature to address two general themes: (i) the two‐way interaction
between introgression and the evolution of reproductive systems, and (ii) how
mating system can facilitate or restrict interspecific gene flow. We conclude
that examining mating system with hybridization provides unique opportunities
to understand divergence and the processes underlying reproductive isolation.'
article_processing_charge: No
article_type: original
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Yaniv
full_name: Brandvain, Yaniv
last_name: Brandvain
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Sarah
full_name: Yakimowski, Sarah
last_name: Yakimowski
- first_name: Tanmay
full_name: Dixit, Tanmay
last_name: Dixit
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
- first_name: Eva
full_name: Cereghetti, Eva
id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63
last_name: Cereghetti
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid
zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist.
2019;224(3):1035-1047. doi:10.1111/nph.16180'
apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit,
T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180'
chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse,
Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field.
“Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries
to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.'
ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no.
3. Wiley, pp. 1035–1047, 2019.'
ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer
C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.'
mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation,
Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no.
3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.'
short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit,
C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.
date_created: 2019-09-07T14:35:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-18T08:47:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/nph.16180
ec_funded: 1
external_id:
pmid:
- '31505037'
file:
- access_level: open_access
checksum: 21e4c95599bbcaf7c483b89954658672
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:15:05Z
date_updated: 2020-07-14T12:47:42Z
file_id: '7011'
file_name: 2019_NewPhytologist_Pickup.pdf
file_size: 1511958
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1035-1047
pmid: 1
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries
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: 224
year: '2019'
...
---
_id: '14299'
abstract:
- lang: eng
text: DNA origami nano-objects are usually designed around generic single-stranded
“scaffolds”. Many properties of the target object are determined by details of
those generic scaffold sequences. Here, we enable designers to fully specify the
target structure not only in terms of desired 3D shape but also in terms of the
sequences used. To this end, we built design tools to construct scaffold sequences
de novo based on strand diagrams, and we developed scalable production methods
for creating design-specific scaffold strands with fully user-defined sequences.
We used 17 custom scaffolds having different lengths and sequence properties to
study the influence of sequence redundancy and sequence composition on multilayer
DNA origami assembly and to realize efficient one-pot assembly of multiscaffold
DNA origami objects. Furthermore, as examples for functionalized scaffolds, we
created a scaffold that enables direct, covalent cross-linking of DNA origami
via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding
DNA origami domain separation.
article_processing_charge: No
article_type: original
author:
- first_name: Engelhardt
full_name: FAS, Engelhardt
last_name: FAS
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: CH
full_name: Wachauf, CH
last_name: Wachauf
- first_name: G
full_name: Brüggenthies, G
last_name: Brüggenthies
- first_name: F
full_name: Kohler, F
last_name: Kohler
- first_name: B
full_name: Kick, B
last_name: Kick
- first_name: KL
full_name: Kadletz, KL
last_name: Kadletz
- first_name: PN
full_name: Pham, PN
last_name: Pham
- first_name: KL
full_name: Behler, KL
last_name: Behler
- first_name: T
full_name: Gerling, T
last_name: Gerling
- first_name: H
full_name: Dietz, H
last_name: Dietz
citation:
ama: FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable
DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027.
doi:10.1021/acsnano.9b01025
apa: FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick,
B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with
design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025
chicago: FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler,
B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with
Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.
ieee: E. FAS et al., “Custom-size, functional, and durable DNA origami with
design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications,
pp. 5015–5027, 2019.
ista: FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz
K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable
DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027.
mla: FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with
Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications,
2019, pp. 5015–27, doi:10.1021/acsnano.9b01025.
short: E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick,
K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027.
date_created: 2023-09-06T12:48:47Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-11-07T12:17:31Z
day: '16'
doi: 10.1021/acsnano.9b01025
extern: '1'
external_id:
pmid:
- '30990672'
intvolume: ' 13'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.9b01025
month: '04'
oa: 1
oa_version: Published Version
page: 5015-5027
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086x
issn:
- 1936-0851
publication_status: published
publisher: ACS Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Custom-size, functional, and durable DNA origami with design-specific scaffolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2019'
...
---
_id: '6647'
abstract:
- lang: eng
text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states
that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition
X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r,
all share a common point. In this paper, we prove a strengthening of this theorem
that guarantees a partition which, in addition to the above, has the property
that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections.
Possible generalizations and algorithmic aspects are also discussed. As a concrete
application, we show that any n points in the plane in general position span floor[n/3]
vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries
have pairwise nonempty intersections; this number is clearly best possible. A
previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing
triangles. Our result generalizes to a result about simplices in R^d,d >=2.
alternative_title:
- LIPIcs
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Bernd
full_name: Gärtner, Bernd
last_name: Gärtner
- first_name: Andrey
full_name: Kupavskii, Andrey
last_name: Kupavskii
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg
theorem. In: 35th International Symposium on Computational Geometry. Vol
129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38'
apa: 'Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019).
The crossing Tverberg theorem. In 35th International Symposium on Computational
Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38'
chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli
Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on
Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.
ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing
Tverberg theorem,” in 35th International Symposium on Computational Geometry,
Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.
ista: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg
theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium
on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.'
mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International
Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.
short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International
Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019, p. 38:1-38:13.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG 2019: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2019-07-17T10:35:04Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-12-13T12:03:35Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPICS.SOCG.2019.38
external_id:
arxiv:
- '1812.04911'
file:
- access_level: open_access
checksum: d6d017f8b41291b94d102294fa96ae9c
content_type: application/pdf
creator: dernst
date_created: 2019-07-24T06:54:52Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6667'
file_name: 2019_LIPICS_Fulek.pdf
file_size: 559837
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 38:1-38:13
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: 35th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959771047'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '13974'
relation: later_version
status: public
scopus_import: 1
status: public
title: The crossing Tverberg theorem
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '6676'
abstract:
- lang: eng
text: "It is impossible to deterministically solve wait-free consensus in an asynchronous
system. The classic proof uses a valency argument, which constructs an infinite
execution by repeatedly extending a finite execution. We introduce extension-based
proofs, a class of impossibility proofs that are modelled as an interaction between
a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs
based on combinatorial topology, it has been shown that it is impossible to deterministically
solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However,
it was unknown whether proofs based on simpler techniques were possible. We show
that this impossibility result cannot be obtained by an extension-based proof
and, hence, extension-based proofs are limited in power."
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: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
last_name: Zhu
citation:
ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based
proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407'
apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019).
Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT
Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States:
ACM Press. https://doi.org/10.1145/3313276.3316407'
chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM
SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.
ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.
ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based
proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of
Computing. STOC: Symposium on Theory of Computing, 986–996.'
mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press,
2019, pp. 986–96, doi:10.1145/3313276.3316407.
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019,
pp. 986–996.
conference:
end_date: 2019-06-26
location: Phoenix, AZ, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2019-06-23
date_created: 2019-07-24T09:13:05Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-12-13T12:28:28Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3313276.3316407
external_id:
arxiv:
- '1811.01421'
isi:
- '000523199100089'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.01421
month: '06'
oa: 1
oa_version: Preprint
page: 986-996
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- '9781450367059'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
record:
- id: '14364'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Why extension-based proofs fail
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7950'
abstract:
- lang: eng
text: "The input to the token swapping problem is a graph with vertices v1, v2,
. . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The
goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number
of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token
swapping on a tree, also known as “sorting with a transposition tree,” is not
known to be in P nor NP-complete. We present some partial results:\r\n1. An
optimum swap sequence may need to perform a swap on a leaf vertex that has the
correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any
algorithm that fixes happy leaves—as all known approximation algorithms for the
problem do—has approximation factor at least 4/3. Furthermore, the two best-known
2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized
problem—weighted coloured token swapping—is NP-complete on trees, but solvable
in polynomial time on paths and stars. In this version, tokens and vertices
\ have colours, and colours have weights. The goal is to get every
token to a vertex of the same colour, and the cost of a swap is the sum of the
weights of the two tokens involved."
article_number: '1903.06981'
article_processing_charge: No
author:
- first_name: Ahmad
full_name: Biniaz, Ahmad
last_name: Biniaz
- first_name: Kshitij
full_name: Jain, Kshitij
last_name: Jain
- first_name: Anna
full_name: Lubiw, Anna
last_name: Lubiw
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Tillmann
full_name: Miltzow, Tillmann
last_name: Miltzow
- first_name: Debajyoti
full_name: Mondal, Debajyoti
last_name: Mondal
- first_name: Anurag Murty
full_name: Naredla, Anurag Murty
last_name: Naredla
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Alexi
full_name: Turcotte, Alexi
last_name: Turcotte
citation:
ama: Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.
apa: Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte,
A. (n.d.). Token swapping on trees. arXiv.
chicago: Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow,
Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token
Swapping on Trees.” ArXiv, n.d.
ieee: A. Biniaz et al., “Token swapping on trees,” arXiv. .
ista: Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec
J, Turcotte A. Token swapping on trees. arXiv, 1903.06981.
mla: Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.
short: A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla,
J. Tkadlec, A. Turcotte, ArXiv (n.d.).
date_created: 2020-06-08T12:25:25Z
date_published: 2019-03-16T00:00:00Z
date_updated: 2024-01-04T12:42:08Z
day: '16'
department:
- _id: HeEd
- _id: UlWa
- _id: KrCh
external_id:
arxiv:
- '1903.06981'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.06981
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '7944'
relation: dissertation_contains
status: public
- id: '12833'
relation: later_version
status: public
status: public
title: Token swapping on trees
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6418'
abstract:
- lang: eng
text: Males and females of Artemia franciscana, a crustacean commonly used in the
aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes,
but the nature and extent of differentiation of these chromosomes is unknown.
Here, we characterize the Z chromosome by detecting genomic regions that show
lower genomic coverage in female than in male samples, and regions that harbor
an excess of female-specific SNPs. We detect many Z-specific genes, which no longer
have homologs on the W, but also Z-linked genes that appear to have diverged very
recently from their existing W-linked homolog. We assess patterns of male and
female expression in two tissues with extensive morphological dimorphism, gonads,
and heads. In agreement with their morphology, sex-biased expression is common
in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased
genes, and seems to in fact have a mechanism of dosage compensation that leads
to equal expression in males and in females. Both of these patterns are contrary
to most ZW systems studied so far, making A. franciscana an excellent model for
investigating the interplay between the evolution of sexual dimorphism and dosage
compensation, as well as Z chromosome evolution in general.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene
expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome
biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053
apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso,
B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053
chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger,
and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the
Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford
University Press, 2019. https://doi.org/10.1093/gbe/evz053.
ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso,
“Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University
Press, pp. 1033–1044, 2019.
ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased
gene expression and dosage compensation on the Artemia franciscana Z-chromosome.
Genome biology and evolution. 11(4), 1033–1044.
mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation
on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution,
vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.
short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome
Biology and Evolution 11 (2019) 1033–1044.
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2024-02-21T12:45:41Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz053
ec_funded: 1
external_id:
isi:
- '000476569800003'
file:
- access_level: open_access
checksum: 7d0ede297b6741f3dc89cd59017c7642
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:29:38Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6446'
file_name: 2019_GBE_Huylmans.pdf
file_size: 1256303
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1033-1044
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '6060'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...
---
_id: '7016'
abstract:
- lang: eng
text: Organisms cope with change by employing transcriptional regulators. However,
when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. We ask whether the intrinsic instability
of gene duplication and amplification provides a generic alternative to canonical
gene regulation. By real-time monitoring of gene copy number mutations in E. coli,
we show that gene duplications and amplifications enable adaptation to fluctuating
environments by rapidly generating copy number, and hence expression level, polymorphism.
This ‘amplification-mediated gene expression tuning’ occurs on timescales similar
to canonical gene regulation and can deal with rapid environmental changes. Mathematical
modeling shows that amplifications also tune gene expression in stochastic environments
where transcription factor-based schemes are hard to evolve or maintain. The fleeting
nature of gene amplifications gives rise to a generic population-level mechanism
that relies on genetic heterogeneity to rapidly tune expression of any gene, without
leaving any genomic signature.
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016
apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016
chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of
Population-Level Gene Expression Regulation.’” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.
ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation.’” Institute of Science and Technology Austria, 2019.
ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.
mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:7016.
short: I. Tomanek, (2019).
contributor:
- contributor_type: project_leader
first_name: Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
date_created: 2019-11-13T09:07:31Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2024-02-21T12:45:25Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7016
file:
- access_level: open_access
checksum: 72441055043eda4cbf1398a422e2c118
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:21Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified.
file_id: '7017'
file_name: D8_S35_R2_001.fastq
file_size: 2456192500
relation: main_file
title: Locus1_amplified
- access_level: open_access
checksum: a4ac50bf655d9c751f0305ade5c2ee16
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:59Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - ancestral.
file_id: '7018'
file_name: IT028_S11_R2_001.fastq
file_size: 2833452234
relation: main_file
title: Locus1_ancestral
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content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:10Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified, after
DOG-selection.
file_id: '7019'
file_name: D8-DOG1_S47_R2_001.fastq
file_size: 2878017264
relation: main_file
title: Locus1_amplified_DOG
- access_level: open_access
checksum: d9550a4c044116075fa83f8f2ea31d6f
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:27Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified.
file_id: '7020'
file_name: D4_S71_R2_001.fastq
file_size: 2180826995
relation: main_file
title: Locus2_amplified
- access_level: open_access
checksum: 466ceb302c020ac013007a879fcde69d
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:55:58Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - ancestral.
file_id: '7021'
file_name: IT030_S23_R2_001.fastq
file_size: 2108826444
relation: main_file
title: Locus2_ancestral
- access_level: open_access
checksum: 8aeb1da771713c7baa5a847eff889604
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-21T12:31:01Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified, after
DOG-selection.
file_id: '7092'
file_name: D4-DOG1_S83_R2_001.fastq
file_size: 3144330494
relation: main_file
title: Locus2_amplified_DOG
- access_level: open_access
checksum: bf7d4b053f14af4655fb5574209fdb2d
content_type: application/zip
creator: itomanek
date_created: 2020-01-14T11:22:27Z
date_updated: 2020-07-14T12:47:47Z
description: Compressed genbank file format containing the sequence of the chromosomal
reporter gene cassette.
file_id: '7273'
file_name: galK_dual_reporter_cassette.gb.zip
file_size: 4179
relation: main_file
title: DNA sequence of the chromosomal reporter gene cassette
- access_level: open_access
checksum: 5e91cee2eff6f4a7cde456c6fb07c2ff
content_type: text/plain
creator: dernst
date_created: 2020-01-15T14:15:55Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7335'
file_name: Readme_7016.txt
file_size: 435
relation: main_file
title: Read_me_sequence_data
- access_level: open_access
checksum: 5e6745dcfb9c1b11dd935ac3ee45fe33
content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
description: FACS data associated with Fig. 2c - see read_me_FACS
file_id: '7351'
file_name: FACS_data.xlsx.zip
file_size: 3765861
relation: main_file
title: FACS data
- access_level: open_access
checksum: a85caf092ae4b17668f70af2d93fad00
content_type: text/rtf
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7352'
file_name: read_me_FACS.rtf
file_size: 4996
relation: main_file
- access_level: open_access
checksum: fd8ba5d75d24e47ddf7e70bfdadb40d4
content_type: text/rtf
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7353'
file_name: read_me_microfluidics.rtf
file_size: 868
relation: main_file
- access_level: open_access
checksum: 69c5dc5ca5c069a138183c934acc1778
content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:17Z
date_updated: 2020-07-14T12:47:47Z
description: microfluidics time trace data - see read_me_microfluidics
file_id: '7354'
file_name: microfuidics_data.zip
file_size: 8141727
relation: main_file
title: microfluidics data
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- gene amplification
- galactose
- DOG
- experimental evolution
- Illumina sequence data
- FACS data
- microfluidics data
month: '11'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: used_in_publication
status: public
status: public
title: Data for the paper "Gene amplification as a form of population-level gene expression
regulation"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7154'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
citation:
ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated
shells.” 2019. doi:10.15479/AT:ISTA:7154
apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing
of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154
chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing
of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7154.
ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated
shells.’” Institute of Science and Technology Austria, 2019.
ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of
self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.
mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing
of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7154.
short: R. Guseinov, (2019).
contributor:
- first_name: Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Connor
last_name: McMahan
- first_name: Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Chiara
last_name: Daraio
- first_name: Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
date_created: 2019-12-09T07:52:46Z
date_published: 2019-12-06T00:00:00Z
date_updated: 2024-02-21T12:45:03Z
day: '06'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:7154
ec_funded: 1
file:
- access_level: open_access
checksum: 155133e6e188e85b3c0676a5e70b9341
content_type: application/x-zip-compressed
creator: dernst
date_created: 2019-12-09T07:52:17Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7155'
file_name: temporal_morphing_supp_data.zip
file_size: 65307107
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8433'
relation: used_in_publication
status: deleted
- id: '7262'
relation: used_in_publication
status: public
status: public
title: Supplementary data for "Programming temporal morphing of self-actuated shells"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6060'
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019.
doi:10.15479/AT:ISTA:6060
apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al.,
2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060
chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et
Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.
ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). .” Institute of Science and Technology Austria, 2019.
ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.
mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et
Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.
short: B. Vicoso, (2019).
date_created: 2019-02-28T10:55:15Z
date_published: 2019-02-28T00:00:00Z
date_updated: 2024-02-21T12:45:42Z
day: '28'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:6060
file:
- access_level: open_access
checksum: a338a622d728af0e3199cb07e6dd64d3
content_type: application/zip
creator: bvicoso
date_created: 2019-02-28T10:54:27Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6061'
file_name: SupData.zip
file_size: 36646050
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6418'
relation: research_paper
status: public
status: public
title: 'Supplementary data for "Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). '
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6074'
abstract:
- lang: eng
text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary
Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary
Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary
Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential
gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro
(ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene
Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro
(GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro
samples were split into upregulated and downregulated genes (up/down) and the
analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary
Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults
for the differential gene expression analysis for samples from adult mice before
(HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively).
Each sheet shows the results for a different comparison. Sheets 1-3 show results
for comparisons between timepoints for wild type (WT) samples only and sheets
4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results
for comparisons between genotypes at each time point and sheet 10 contains the
results for the analysis of differential expression trajectories between wild
type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults
for k-means clustering of genes by expression. Sheet 1 shows clustering of just
the genes with significantly different expression trajectories between genotypes.
Sheet 2 shows clustering of all genes that are significantly differentially expressed
in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary
Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis and EWCE analysis for enrichment of cell type specific genes for each
cluster identified by clustering genes with different expression trajectories
(see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults
showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet
1 shows protein protein interaction data generated from these results (combined
with data from the STRING database. Sheet 2 shows the results of the statistical
analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults
for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows
results for differential binding of PolII at the transcription start site (TSS)
between genotypes and sheets 2+3 show the corresponding GO enrichment analysis
for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with
increased binding of PolII at the TSS."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.” 2019. doi:10.15479/AT:ISTA:6074
apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research
paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental
gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074
chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research
Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6074.
ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.’” Institute of Science and Technology Austria, 2019.
ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.
mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research
Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:6074.
short: C. Dotter, G. Novarino, (2019).
date_created: 2019-03-07T13:32:35Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2024-02-21T13:41:01Z
day: '09'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:6074
file:
- access_level: open_access
checksum: bc1b285edca9e98a2c63d153c79bb75b
content_type: application/zip
creator: dernst
date_created: 2019-03-07T13:37:19Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6084'
file_name: Setd5_paper.zip
file_size: 33202743
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '3'
relation: research_paper
status: public
status: public
title: Supplementary data for the research paper "Haploinsufficiency of the intellectual
disability gene SETD5 disturbs developmental gene expression and cognition"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6062'
abstract:
- lang: eng
text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section
with Python 3.7).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive
Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062
apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal
Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6062
chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal
Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6062.
ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive
Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.
ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal
Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:6062.
mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal
Cognitive Map Is Attracted to Goals.” Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6062.
short: M. Nardin, (2019).
date_created: 2019-03-04T14:20:58Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2024-02-21T12:46:04Z
day: '29'
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6062
file:
- access_level: open_access
checksum: 48e7b9a02939b763417733239522a236
content_type: application/zip
creator: mnardin
date_created: 2019-03-05T09:29:37Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6068'
file_name: Online_data.zip
file_size: 37002186
relation: main_file
title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals"
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6194'
relation: research_paper
status: public
status: public
title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is
Attracted to Goals"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
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: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6179'
abstract:
- lang: eng
text: "In the first part of this thesis we consider large random matrices with arbitrary
expectation and a general slowly decaying correlation among its entries. We prove
universality of the local eigenvalue statistics and optimal local laws for the
resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic
control of a multivariate cumulant expansion.\r\nIn the second part we consider
Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue
distribution the local eigenvalue statistics are uni- versal and form a Pearcey
process. Since the density of states typically exhibits only square root or cubic
root cusp singularities, our work complements previous results on the bulk and
edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta
universality conjecture for the last remaining universality type. Our analysis
holds not only for exact cusps, but approximate cusps as well, where an ex- tended
Pearcey process emerges. As a main technical ingredient we prove an optimal local
law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow-
nian motion to the cusp regime.\r\nIn the third and final part we explore the
entrywise linear statistics of Wigner ma- trices and identify the fluctuations
for a large class of test functions with little regularity. This enables us to
study the rectangular Young diagram obtained from the interlacing eigenvalues
of the random matrix and its minor, and we find that, despite having the same
limit, the fluctuations differ from those of the algebraic Young tableaux equipped
with the Plancharel measure."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix
theory. 2019. doi:10.15479/AT:ISTA:th6179'
apa: 'Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in
random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179'
chicago: 'Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.'
ieee: 'D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix
theory,” Institute of Science and Technology Austria, 2019.'
ista: 'Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random
matrix theory. Institute of Science and Technology Austria.'
mla: 'Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.'
short: 'D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix
Theory, Institute of Science and Technology Austria, 2019.'
date_created: 2019-03-28T08:58:59Z
date_published: 2019-03-18T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '18'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:th6179
ec_funded: 1
file:
- access_level: closed
checksum: 6926f66f28079a81c4937e3764be00fc
content_type: application/x-gzip
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6180'
file_name: 2019_Schroeder_Thesis.tar.gz
file_size: 7104482
relation: source_file
- access_level: open_access
checksum: 7d0ebb8d1207e89768cdd497a5bf80fb
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6181'
file_name: 2019_Schroeder_Thesis.pdf
file_size: 4228794
relation: main_file
file_date_updated: 2020-07-14T12:47:21Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '375'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1144'
relation: part_of_dissertation
status: public
- id: '6186'
relation: part_of_dissertation
status: public
- id: '6185'
relation: part_of_dissertation
status: public
- id: '6182'
relation: part_of_dissertation
status: public
- id: '1012'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: 'From Dyson to Pearcey: Universal statistics in random matrix theory'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6482'
abstract:
- lang: eng
text: 'Computer vision systems for automatic image categorization have become accurate
and reliable enough that they can run continuously for days or even years as components
of real-world commercial applications. A major open problem in this context, however,
is quality control. Good classification performance can only be expected if systems
run under the specific conditions, in particular data distributions, that they
were trained for. Surprisingly, none of the currently used deep network architectures
have a built-in functionality that could detect if a network operates on data
from a distribution it was not trained for, such that potentially a warning to
the human users could be triggered. In this work, we describe KS(conf), a procedure
for detecting such outside of specifications (out-of-specs) operation, based on
statistical testing of the network outputs. We show by extensive experiments using
the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that
KS(conf) reliably detects out-of-specs situations. It furthermore has a number
of properties that make it a promising candidate for practical deployment: it
is easy to implement, adds almost no overhead to the system, works with all networks,
including pretrained ones, and requires no a priori knowledge of how the data
distribution could change. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Rémy
full_name: Sun, Rémy
last_name: Sun
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside
of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18'
apa: 'Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet
operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at
the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-12939-2_18'
chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-12939-2_18.'
ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition,
Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.'
ista: 'Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS,
vol. 11269, 244–259.'
mla: 'Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet
Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019,
pp. 244–59, doi:10.1007/978-3-030-12939-2_18.'
short: R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.
conference:
end_date: 2018-10-12
location: Stuttgart, Germany
name: 'GCPR: Conference on Pattern Recognition'
start_date: 2018-10-09
date_created: 2019-05-24T09:48:36Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2024-02-22T14:57:29Z
day: '14'
department:
- _id: ChLa
doi: 10.1007/978-3-030-12939-2_18
ec_funded: 1
external_id:
arxiv:
- '1804.04171'
intvolume: ' 11269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04171
month: '02'
oa: 1
oa_version: Preprint
page: 244-259
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030129385'
- '9783030129392'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '6944'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a ConvNet operates outside of Its specifications'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11269
year: '2019'
...
---
_id: '6642'
abstract:
- lang: eng
text: We present a thermodynamically based approach to the design of models for
viscoelastic fluids with stress diffusion effect. In particular, we show how to
add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus,
FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that
the resulting models with the added stress diffusion term are thermodynamically
consistent in the sense that they obey the first and the second law of thermodynamics.
We point out the potential applications of the provided thermodynamical background
in the study of flows of fluids described by the proposed models.
article_number: '020002'
article_processing_charge: No
author:
- first_name: Mark
full_name: Dostalík, Mark
last_name: Dostalík
- first_name: Vít
full_name: Pruša, Vít
last_name: Pruša
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
citation:
ama: 'Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic
rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing;
2019. doi:10.1063/1.5109493'
apa: 'Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of
some classical viscoelastic rate-type models. In AIP Conference Proceedings
(Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493'
chicago: Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of
Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings,
Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.
ieee: M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical
viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech
Republic, 2019, vol. 2107.
ista: Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical
viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference
on Novel Trends in Rheology vol. 2107, 020002.
mla: Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic
Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing,
2019, doi:10.1063/1.5109493.
short: M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing,
2019.
conference:
end_date: 2019-07-31
location: Zlin, Czech Republic
name: 8th International Conference on Novel Trends in Rheology
start_date: 2019-07-30
date_created: 2019-07-15T10:07:09Z
date_published: 2019-05-21T00:00:00Z
date_updated: 2024-02-28T13:01:28Z
day: '21'
department:
- _id: ChWo
doi: 10.1063/1.5109493
external_id:
arxiv:
- '1902.07983'
isi:
- '000479303100002'
intvolume: ' 2107'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07983
month: '05'
oa: 1
oa_version: Preprint
publication: AIP Conference Proceedings
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: On diffusive variants of some classical viscoelastic rate-type models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2107
year: '2019'
...
---
_id: '7226'
article_number: '123504'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Vojkan
full_name: Jaksic, Vojkan
last_name: Jaksic
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Jaksic V, Seiringer R. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
2019;60(12). doi:10.1063/1.5138135'
apa: 'Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical
Physics. AIP Publishing. https://doi.org/10.1063/1.5138135'
chicago: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.'
ieee: 'V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics,
vol. 60, no. 12. AIP Publishing, 2019.'
ista: 'Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
60(12), 123504.'
mla: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.'
short: V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).
date_created: 2020-01-05T23:00:46Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-02-28T13:01:45Z
day: '01'
ddc:
- '500'
department:
- _id: RoSe
doi: 10.1063/1.5138135
external_id:
isi:
- '000505529800002'
file:
- access_level: open_access
checksum: bbd12ad1999a9ad7ba4d3c6f2e579c22
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:59:13Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7244'
file_name: 2019_JournalMathPhysics_Jaksic.pdf
file_size: 1025015
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Introduction to the Special Collection: International Congress on Mathematical
Physics (ICMP) 2018'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2019'
...
---
_id: '7190'
abstract:
- lang: eng
text: We investigate the ground-state energy of a one-dimensional Fermi gas with
two bosonic impurities. We consider spinless fermions with no fermion-fermion
interactions. The fermion-impurity and impurity-impurity interactions are modeled
with Dirac delta functions. First, we study the case where impurity and fermion
have equal masses, and the impurity-impurity two-body interaction is identical
to the fermion-impurity interaction, such that the system is solvable with the
Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity
subsystem is below the energy of the bound state that exists without the Fermi
gas. We interpret this as a manifestation of attractive boson-boson interactions
induced by the fermionic medium, and refer to the impurity-impurity subsystem
as an in-medium bound state. For repulsive interactions, we find no in-medium
bound states. Second, we construct an effective model to describe these interactions,
and compare its predictions to the exact solution. We use this effective model
to study nonintegrable systems with unequal masses and/or potentials. We discuss
parameter regimes for which impurity-impurity attraction induced by the Fermi
gas can lead to the formation of in-medium bound states made of bosons that repel
each other in the absence of the Fermi gas.
article_number: '033177'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Huber, D.
last_name: Huber
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities
in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177
apa: Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states
of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research.
American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177
chicago: Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of
Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research.
American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.
ieee: D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas,” Physical Review Research, vol.
1, no. 3. American Physical Society, 2019.
ista: Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.
mla: Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional
Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical
Society, 2019, doi:10.1103/physrevresearch.1.033177.
short: D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).
date_created: 2019-12-17T13:03:41Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2024-02-28T13:11:40Z
day: '16'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.1.033177
ec_funded: 1
external_id:
arxiv:
- '1908.02483'
file:
- access_level: open_access
checksum: 382eb67e62a77052a23887332d363f96
content_type: application/pdf
creator: dernst
date_created: 2019-12-18T07:13:14Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7193'
file_name: 2019_PhysRevResearch_Huber.pdf
file_size: 1370022
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: In-medium bound states of two bosonic impurities in a one-dimensional Fermi
gas
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: 1
year: '2019'
...
---
_id: '6575'
abstract:
- lang: eng
text: Motivated by recent experimental observations of coherent many-body revivals
in a constrained Rydbergatom chain, we construct a weak quasilocal deformation
of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect.
Our analysis suggests the existence of an underlying nonintegrableHamiltonian
which supports an emergent SU(2)-spin dynamics within a small subspace of the
many-bodyHilbert space. We show that such perfect dynamics necessitates the existence
of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore,
using these insights, we construct a toymodel that hosts exact quantum many-body
scars, providing an intuitive explanation of their origin. Ourresults offer specific
routes to enhancing coherent many-body revivals and provide a step towardestablishing
the stability of quantum many-body scars in the thermodynamic limit.
article_number: '220603'
article_processing_charge: No
article_type: original
author:
- first_name: Soonwon
full_name: Choi, Soonwon
last_name: Choi
- first_name: Christopher J.
full_name: Turner, Christopher J.
last_name: Turner
- first_name: Hannes
full_name: Pichler, Hannes
last_name: Pichler
- first_name: Wen Wei
full_name: Ho, Wen Wei
last_name: Ho
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail D.
full_name: Lukin, Mikhail D.
last_name: Lukin
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum
many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603
apa: Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z.,
… Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body
scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603
chicago: Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios
Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin.
“Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review
Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.
ieee: S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body
scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society,
2019.
ista: Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin
MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars.
Physical Review Letters. 122(22), 220603.
mla: Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body
Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical
Society, 2019, doi:10.1103/PhysRevLett.122.220603.
short: S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn,
M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).
date_created: 2019-06-23T21:59:13Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2024-02-28T13:12:22Z
day: '07'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.122.220603
external_id:
arxiv:
- '1812.05561'
isi:
- '000470885800005'
intvolume: ' 122'
isi: 1
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.05561
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent SU(2) dynamics and perfect quantum many-body scars
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '6092'
abstract:
- lang: eng
text: In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization
of a magnetic material results in mechanical rotation and vice versa. At the microscopic
level, this effect governs the transfer between electron spin and orbital angular
momentum, and lattice degrees of freedom, understanding which is key for molecular
magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now,
the timescales of electron-to-lattice angular momentum transfer remain unclear,
since modeling this process on a microscopic level requires the addition of an
infinite amount of quantum angular momenta. We show that this problem can be solved
by reformulating it in terms of the recently discovered angulon quasiparticles,
which results in a rotationally invariant quantum many-body theory. In particular,
we demonstrate that nonperturbative effects take place even if the electron-phonon
coupling is weak and give rise to angular momentum transfer on femtosecond timescales.
article_number: '064428'
article_processing_charge: No
author:
- first_name: Johann H
full_name: Mentink, Johann H
last_name: Mentink
- first_name: Mikhail
full_name: Katsnelson, Mikhail
last_name: Katsnelson
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de
Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428
apa: Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body
dynamics of the Einstein-de Haas effect. Physical Review B. American Physical
Society. https://doi.org/10.1103/PhysRevB.99.064428
chicago: Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body
Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical
Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428.
ieee: J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics
of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American
Physical Society, 2019.
ista: Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of
the Einstein-de Haas effect. Physical Review B. 99(6), 064428.
mla: Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas
Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society,
2019, doi:10.1103/PhysRevB.99.064428.
short: J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-02-28T13:11:54Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.99.064428
external_id:
arxiv:
- '1802.01638'
isi:
- '000459223400004'
intvolume: ' 99'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.01638
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body dynamics of the Einstein-de Haas effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6786'
abstract:
- lang: eng
text: Dipolar coupling plays a fundamental role in the interaction between electrically
or magnetically polarized species such as magnetic atoms and dipolar molecules
in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike
interactions found in many atomic, molecular, and condensed-matter systems, this
interaction is long-ranged and highly anisotropic, as it changes from repulsive
to attractive depending on the relative positions and orientation of the dipoles.
Because of this unique property, many exotic, symmetry-breaking collective states
have been recently predicted for cold dipolar gases, but only a few have been
experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates.
Here, we report on the first observation of attractive dipolar coupling between
excitonic dipoles using a new design of stacked semiconductor bilayers. We show
that the presence of a dipolar exciton fluid in one bilayer modifies the spatial
distribution and increases the binding energy of excitonic dipoles in a vertically
remote layer. The binding energy changes are explained using a many-body polaron
model describing the deformation of the exciton cloud due to its interaction with
a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud
density indicates the important role of dipolar correlations, which is unique
to dense, strongly interacting dipolar solid-state systems. Our concept provides
a route for the realization of dipolar lattices with strong anisotropic interactions
in semiconductor systems, which open the way for the observation of theoretically
predicted new and exotic collective phases, as well as for engineering and sensing
their collective excitations.
article_number: '021026'
article_processing_charge: No
article_type: original
author:
- first_name: Colin
full_name: Hubert, Colin
last_name: Hubert
- first_name: Yifat
full_name: Baruchi, Yifat
last_name: Baruchi
- first_name: Yotam
full_name: Mazuz-Harpaz, Yotam
last_name: Mazuz-Harpaz
- first_name: Kobi
full_name: Cohen, Kobi
last_name: Cohen
- first_name: Klaus
full_name: Biermann, Klaus
last_name: Biermann
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Ken
full_name: West, Ken
last_name: West
- first_name: Loren
full_name: Pfeiffer, Loren
last_name: Pfeiffer
- first_name: Ronen
full_name: Rapaport, Ronen
last_name: Rapaport
- first_name: Paulo
full_name: Santos, Paulo
last_name: Santos
citation:
ama: Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between
stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026
apa: Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko,
M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids.
Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026
chicago: Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann,
Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos.
“Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review
X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026.
ieee: C. Hubert et al., “Attractive dipolar coupling between stacked exciton
fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.
ista: Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West
K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between
stacked exciton fluids. Physical Review X. 9(2), 021026.
mla: Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton
Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society,
2019, doi:10.1103/PhysRevX.9.021026.
short: C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko,
K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).
date_created: 2019-08-11T21:59:20Z
date_published: 2019-05-08T00:00:00Z
date_updated: 2024-02-28T13:12:48Z
day: '08'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevX.9.021026
external_id:
arxiv:
- '1807.11238'
isi:
- '000467402900001'
file:
- access_level: open_access
checksum: 065ff82ee4a1d2c3773ce4b76ff4213c
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T12:14:18Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6802'
file_name: 2019_PhysReviewX_Hubert.pdf
file_size: 1193550
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attractive dipolar coupling between stacked exciton fluids
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: 9
year: '2019'
...
---
_id: '7013'
abstract:
- lang: eng
text: Chains of superconducting circuit devices provide a natural platform for studies
of synthetic bosonic quantum matter. Motivated by the recent experimental progress
in realizing disordered and interacting chains of superconducting transmon devices,
we study the bosonic many-body localization phase transition using the methods
of exact diagonalization as well as matrix product state dynamics. We estimate
the location of transition separating the ergodic and the many-body localized
phases as a function of the disorder strength and the many-body on-site interaction
strength. The main difference between the bosonic model realized by superconducting
circuits and similar fermionic model is that the effect of the on-site interaction
is stronger due to the possibility of multiple excitations occupying the same
site. The phase transition is found to be robust upon including longer-range hopping
and interaction terms present in the experiments. Furthermore, we calculate experimentally
relevant local observables and show that their temporal fluctuations can be used
to distinguish between the dynamics of Anderson insulator, many-body localization,
and delocalized phases. While we consider unitary dynamics, neglecting the effects
of dissipation, decoherence, and measurement back action, the timescales on which
the dynamics is unitary are sufficient for observation of characteristic dynamics
in the many-body localized phase. Moreover, the experimentally available disorder
strength and interactions allow for tuning the many-body localization phase transition,
thus making the arrays of superconducting circuit devices a promising platform
for exploring localization physics and phase transition.
article_number: '134504'
article_processing_charge: No
article_type: original
author:
- first_name: Tuure
full_name: Orell, Tuure
last_name: Orell
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Matti
full_name: Silveri, Matti
last_name: Silveri
citation:
ama: Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization
phase transition with superconducting circuits. Physical Review B. 2019;100(13).
doi:10.1103/physrevb.100.134504
apa: Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the
many-body localization phase transition with superconducting circuits. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504
chicago: Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing
the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical
Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.
ieee: T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body
localization phase transition with superconducting circuits,” Physical Review
B, vol. 100, no. 13. American Physical Society, 2019.
ista: Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization
phase transition with superconducting circuits. Physical Review B. 100(13), 134504.
mla: Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with
Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504,
American Physical Society, 2019, doi:10.1103/physrevb.100.134504.
short: T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).
date_created: 2019-11-13T08:25:48Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2024-02-28T13:13:13Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/physrevb.100.134504
external_id:
arxiv:
- '1907.04043'
isi:
- '000489036500004'
intvolume: ' 100'
isi: 1
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.04043
month: '10'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing the many-body localization phase transition with superconducting circuits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7200'
abstract:
- lang: eng
text: Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting
films found an emergent inhomogeneity at the scale of tens of nanometers. This
inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity
measured in transport above the superconducting critical temperature Tc. This
behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper
pairs that display a quasiconfinement (i.e., a slowing down of their diffusive
dynamics) on length scales shorter than the inhomogeneity identified by tunneling
experiments. Here, we assume this anomalous diffusive behavior of fluctuating
Cooper pairs and calculate the effect of these fluctuations on the electron density
of states above Tc. We find that the density of states is substantially suppressed
up to temperatures well above Tc. This behavior, which is closely reminiscent
of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper
pairs in the absence of stable preformed pairs, setting the stage for an intermediate
behavior between the two common paradigms in the superconducting-insulator transition,
namely, the localization of Cooper pairs (the so-called bosonic scenario) and
the breaking of Cooper pairs into unpaired electrons due to strong disorder (the
so-called fermionic scenario).
article_number: '174518'
article_processing_charge: No
article_type: original
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Marco
full_name: Grilli, Marco
last_name: Grilli
- first_name: Brigitte
full_name: Leridon, Brigitte
last_name: Leridon
- first_name: Sergio
full_name: Caprara, Sergio
last_name: Caprara
citation:
ama: Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of
fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518
apa: Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous
diffusion of fluctuating Cooper pairs on the density of states of superconducting
NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518
chicago: Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect
of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of
Superconducting NbN Thin Films.” Physical Review B. American Physical Society,
2019. https://doi.org/10.1103/PhysRevB.100.174518.
ieee: P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films,” Physical Review B, vol. 100, no. 17. American Physical Society,
2019.
ista: Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion
of fluctuating Cooper pairs on the density of states of superconducting NbN thin
films. Physical Review B. 100(17), 174518.
mla: Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper
Pairs on the Density of States of Superconducting NbN Thin Films.” Physical
Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.
short: P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).
date_created: 2019-12-22T23:00:41Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2024-02-28T13:14:08Z
day: '25'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.100.174518
external_id:
arxiv:
- '1907.13579'
isi:
- '000498845700006'
intvolume: ' 100'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.13579
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of anomalous diffusion of fluctuating Cooper pairs on the density of
states of superconducting NbN thin films
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '6779'
abstract:
- lang: eng
text: "Recent studies suggest that unstable recurrent solutions of the Navier-Stokes
equation provide new insights\r\ninto dynamics of turbulent flows. In this study,
we compute an extensive network of dynamical connections\r\nbetween such solutions
in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion
symmetric subspace. In particular, we find numerous isolated heteroclinic connections
between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic
orbits—as well as continua of connections forming\r\nhigher-dimensional connecting
manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide
strong evidence that the associated homoclinic tangle forms the chaotic repeller
that underpins transient\r\nturbulence in the symmetric subspace."
article_number: '013112'
article_processing_charge: No
article_type: original
author:
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Ravi Kumar
full_name: Pallantla, Ravi Kumar
last_name: Pallantla
- first_name: Michael F.
full_name: Schatz, Michael F.
last_name: Schatz
- first_name: Roman O.
full_name: Grigoriev, Roman O.
last_name: Grigoriev
citation:
ama: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1).
doi:10.1103/physreve.100.013112
apa: Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic
and homoclinic connections in a Kolmogorov-like flow. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.100.013112
chicago: Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O.
Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.”
Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.
ieee: B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic
and homoclinic connections in a Kolmogorov-like flow,” Physical Review E,
vol. 100, no. 1. American Physical Society, 2019.
ista: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic
connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.
mla: Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like
Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society,
2019, doi:10.1103/physreve.100.013112.
short: B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100
(2019).
date_created: 2019-08-09T09:40:41Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:00Z
day: '25'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/physreve.100.013112
ec_funded: 1
external_id:
arxiv:
- '1907.05860'
isi:
- '000477911800012'
intvolume: ' 100'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.05860
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic and homoclinic connections in a Kolmogorov-like flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7015'
abstract:
- lang: eng
text: We modify the "floating crystal" trial state for the classical homogeneous
electron gas (also known as jellium), in order to suppress the boundary charge
fluctuations that are known to lead to a macroscopic increase of the energy. The
argument is to melt a thin layer of the crystal close to the boundary and consequently
replace it by an incompressible fluid. With the aid of this trial state we show
that three different definitions of the ground-state energy of jellium coincide.
In the first point of view the electrons are placed in a neutralizing uniform
background. In the second definition there is no background but the electrons
are submitted to the constraint that their density is constant, as is appropriate
in density functional theory. Finally, in the third system each electron interacts
with a periodic image of itself; that is, periodic boundary conditions are imposed
on the interaction potential.
article_number: '035127'
article_processing_charge: No
article_type: original
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
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: Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge
fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal
with no boundary charge fluctuations. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.100.035127
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner
Crystal with No Boundary Charge Fluctuations.” Physical Review B. American
Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary
charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical
Society, 2019.
ista: Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary
charge fluctuations. Physical Review B. 100(3), 035127.
mla: Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.”
Physical Review B, vol. 100, no. 3, 035127, American Physical Society,
2019, doi:10.1103/physrevb.100.035127.
short: M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).
date_created: 2019-11-13T08:41:48Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2024-02-28T13:13:23Z
day: '25'
department:
- _id: RoSe
doi: 10.1103/physrevb.100.035127
ec_funded: 1
external_id:
arxiv:
- '1905.09138'
isi:
- '000477888200001'
intvolume: ' 100'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.09138
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal with no boundary charge fluctuations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '7145'
abstract:
- lang: eng
text: End-to-end correlated bound states are investigated in superconductor-semiconductor
hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently
identified from each wire end, and a cross-correlation function is computed that
counts end-to-end coincidences, averaging over thousands of subgap features. Strong
correlations in a short, 300-nm device are reduced by a factor of 4 in a long,
900-nm device. In addition, subgap conductance distributions are investigated,
and correlations between the left and right distributions are identified based
on their mutual information.
article_number: '205412'
article_processing_charge: No
article_type: original
author:
- first_name: G. L. R.
full_name: Anselmetti, G. L. R.
last_name: Anselmetti
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: D.
full_name: Puglia, D.
last_name: Puglia
- first_name: F. K.
full_name: Malinowski, F. K.
last_name: Malinowski
- first_name: J. S.
full_name: Lee, J. S.
last_name: Lee
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M.
full_name: Pendharkar, M.
last_name: Pendharkar
- first_name: C. J.
full_name: Palmstrøm, C. J.
last_name: Palmstrøm
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412
apa: Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski,
F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap
states in hybrid nanowires. Physical Review B. American Physical Society.
https://doi.org/10.1103/physrevb.100.205412
chicago: Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski,
J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.”
Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412.
ieee: G. L. R. Anselmetti et al., “End-to-end correlated subgap states in
hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical
Society, 2019.
ista: Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi
S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end
correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.
mla: Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid
Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical
Society, 2019, doi:10.1103/physrevb.100.205412.
short: G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski,
J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P.
Higginbotham, Physical Review B 100 (2019).
date_created: 2019-12-04T16:02:25Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2024-02-28T13:13:51Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/physrevb.100.205412
external_id:
arxiv:
- '1908.05549'
isi:
- '000495967500006'
intvolume: ' 100'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.05549
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: End-to-end correlated subgap states in hybrid nanowires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2019'
...
---
_id: '5906'
abstract:
- lang: eng
text: We introduce a simple, exactly solvable strong-randomness renormalization
group (RG) model for the many-body localization (MBL) transition in one dimension.
Our approach relies on a family of RG flows parametrized by the asymmetry between
thermal and localized phases. We identify the physical MBL transition in the limit
of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions.
We find a critical point that is localized with power-law distributed thermal
inclusions. The typical size of critical inclusions remains finite at the transition,
while the average size is logarithmically diverging. We propose a two-parameter
scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless
universality class, with the MBL phase corresponding to a stable line of fixed
points with multifractal behavior.
article_number: '040601'
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Goremykina, Anna
last_name: Goremykina
- first_name: Romain
full_name: Vasseur, Romain
last_name: Vasseur
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group
for the many-body localization transition. Physical Review Letters. 2019;122(4).
doi:10.1103/physrevlett.122.040601
apa: Goremykina, A., Vasseur, R., & Serbyn, M. (2019). Analytically solvable
renormalization group for the many-body localization transition. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.040601
chicago: Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable
Renormalization Group for the Many-Body Localization Transition.” Physical
Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.040601.
ieee: A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization
group for the many-body localization transition,” Physical Review Letters,
vol. 122, no. 4. American Physical Society, 2019.
ista: Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization
group for the many-body localization transition. Physical Review Letters. 122(4),
040601.
mla: Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the
Many-Body Localization Transition.” Physical Review Letters, vol. 122,
no. 4, 040601, American Physical Society, 2019, doi:10.1103/physrevlett.122.040601.
short: A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).
date_created: 2019-02-01T08:22:28Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-02-28T13:13:38Z
day: '01'
department:
- _id: MaSe
doi: 10.1103/physrevlett.122.040601
external_id:
arxiv:
- '1807.04285'
isi:
- '000456783700001'
intvolume: ' 122'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.04285
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analytically solvable renormalization group for the many-body localization
transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '6632'
abstract:
- lang: eng
text: We consider a two-component Bose gas in two dimensions at a low temperature
with short-range repulsive interaction. In the coexistence phase where both components
are superfluid, interspecies interactions induce a nondissipative drag between
the two superfluid flows (Andreev-Bashkin effect). We show that this behavior
leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition
in two dimensions. We extend the renormalization of the superfluid densities at
finite temperature using the renormalization-group approach and find that the
vortices of one component have a large influence on the superfluid properties
of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the
vortex unbinding transition in one of the components can induce the breakdown
of superfluidity also in the other, leading to a locking phenomenon for the critical
temperatures of the two gases.
article_number: '063627'
article_processing_charge: No
author:
- first_name: Volker
full_name: Karle, Volker
last_name: Karle
- first_name: Nicolò
full_name: Defenu, Nicolò
last_name: Defenu
- first_name: Tilman
full_name: Enss, Tilman
last_name: Enss
citation:
ama: Karle V, Defenu N, Enss T. Coupled superfluidity of binary Bose mixtures in
two dimensions. Physical Review A. 2019;99(6). doi:10.1103/PhysRevA.99.063627
apa: Karle, V., Defenu, N., & Enss, T. (2019). Coupled superfluidity of binary
Bose mixtures in two dimensions. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.99.063627
chicago: Karle, Volker, Nicolò Defenu, and Tilman Enss. “Coupled Superfluidity of
Binary Bose Mixtures in Two Dimensions.” Physical Review A. American Physical
Society, 2019. https://doi.org/10.1103/PhysRevA.99.063627.
ieee: V. Karle, N. Defenu, and T. Enss, “Coupled superfluidity of binary Bose mixtures
in two dimensions,” Physical Review A, vol. 99, no. 6. American Physical
Society, 2019.
ista: Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures
in two dimensions. Physical Review A. 99(6), 063627.
mla: Karle, Volker, et al. “Coupled Superfluidity of Binary Bose Mixtures in Two
Dimensions.” Physical Review A, vol. 99, no. 6, 063627, American Physical
Society, 2019, doi:10.1103/PhysRevA.99.063627.
short: V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).
date_created: 2019-07-14T21:59:17Z
date_published: 2019-06-28T00:00:00Z
date_updated: 2024-02-28T13:12:34Z
day: '28'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.99.063627
external_id:
arxiv:
- '1903.06759'
isi:
- '000473133600007'
intvolume: ' 99'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.06759
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coupled superfluidity of binary Bose mixtures in two dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '7396'
abstract:
- lang: eng
text: The angular momentum of molecules, or, equivalently, their rotation in three-dimensional
space, is ideally suited for quantum control. Molecular angular momentum is naturally
quantized, time evolution is governed by a well-known Hamiltonian with only a
few accurately known parameters, and transitions between rotational levels can
be driven by external fields from various parts of the electromagnetic spectrum.
Control over the rotational motion can be exerted in one-, two-, and many-body
scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity
of bimolecular reactions, or encode quantum information to name just a few examples.
The corresponding approaches to quantum control are pursued within separate, and
typically disjoint, subfields of physics, including ultrafast science, cold collisions,
ultracold gases, quantum information science, and condensed-matter physics. It
is the purpose of this review to present the various control phenomena, which
all rely on the same underlying physics, within a unified framework. To this end,
recall the Hamiltonian for free rotations, assuming the rigid rotor approximation
to be valid, and summarize the different ways for a rotor to interact with external
electromagnetic fields. These interactions can be exploited for control—from achieving
alignment, orientation, or laser cooling in a one-body framework, steering bimolecular
collisions, or realizing a quantum computer or quantum simulator in the many-body
setting.
article_number: '035005 '
article_processing_charge: No
article_type: original
author:
- first_name: Christiane P.
full_name: Koch, Christiane P.
last_name: Koch
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Dominique
full_name: Sugny, Dominique
last_name: Sugny
citation:
ama: Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews
of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005
apa: Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular
rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005
chicago: Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control
of Molecular Rotation.” Reviews of Modern Physics. American Physical Society,
2019. https://doi.org/10.1103/revmodphys.91.035005.
ieee: C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,”
Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.
ista: Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation.
Reviews of Modern Physics. 91(3), 035005.
mla: Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews
of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019,
doi:10.1103/revmodphys.91.035005.
short: C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).
date_created: 2020-01-29T16:04:19Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2024-02-28T13:15:33Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/revmodphys.91.035005
external_id:
arxiv:
- '1810.11338'
isi:
- '000486661700001'
intvolume: ' 91'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.11338
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Reviews of Modern Physics
publication_identifier:
eissn:
- 1539-0756
issn:
- 0034-6861
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum control of molecular rotation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2019'
...
---
_id: '7606'
abstract:
- lang: eng
text: We derive a tight lower bound on equivocation (conditional entropy), or equivalently
a tight upper bound on mutual information between a signal variable and channel
outputs. The bound is in terms of the joint distribution of the signals and maximum
a posteriori decodes (most probable signals given channel output). As part of
our derivation, we describe the key properties of the distribution of signals,
channel outputs and decodes, that minimizes equivocation and maximizes mutual
information. This work addresses a problem in data analysis, where mutual information
between signals and decodes is sometimes used to lower bound the mutual information
between signals and channel outputs. Our result provides a corresponding upper
bound.
article_number: '8989292'
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information.
In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292'
apa: 'Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound
on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby,
Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292'
chicago: Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper
Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019.
IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.
ieee: M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual
information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden,
2019.
ista: Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information.
IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.
mla: Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE
Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
short: M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop,
ITW 2019, IEEE, 2019.
conference:
end_date: 2019-08-28
location: Visby, Sweden
name: Information Theory Workshop
start_date: 2019-08-25
date_created: 2020-03-22T23:00:47Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '01'
department:
- _id: GaTk
doi: 10.1109/ITW44776.2019.8989292
ec_funded: 1
external_id:
arxiv:
- '1812.01475'
isi:
- '000540384500015'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.01475
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: IEEE Information Theory Workshop, ITW 2019
publication_identifier:
isbn:
- '9781538669006'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A tight upper bound on mutual information
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6933'
abstract:
- lang: eng
text: "We design fast deterministic algorithms for distance computation in the CONGESTED
CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for
all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected
graphs. With a small additional additive factor, this also applies for weighted
graphs. This is the first sub-polynomial constant-factor approximation for APSP
in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem
from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This
is the first sub-polynomial algorithm obtaining this approximation for a set of
sources of polynomial size.\r\n\r\nOur main techniques are new distance tools
that are obtained via improved algorithms for sparse matrix multiplication, which
we leverage to construct efficient hopsets and shortest paths. Furthermore, our
techniques extend to additional distance problems for which we improve upon the
state-of-the-art, including diameter approximation, and an exact single-source
shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."
article_processing_charge: No
author:
- first_name: Keren
full_name: Censor-Hillel, Keren
last_name: Censor-Hillel
- first_name: Michal
full_name: Dory, Michal
last_name: Dory
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Dean
full_name: Leitersdorf, Dean
last_name: Leitersdorf
citation:
ama: 'Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest
paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on
Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633'
apa: 'Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast
approximate shortest paths in the congested clique. In Proceedings of the 2019
ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto,
ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633'
chicago: Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf.
“Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of
the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM,
2019. https://doi.org/10.1145/3293611.3331633.
ieee: K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate
shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium
on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83.
ista: 'Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate
shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium
on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed
Computing, 74–83.'
mla: Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested
Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed
Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633.
short: K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings
of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp.
74–83.
conference:
end_date: 2019-08-02
location: Toronto, ON, Canada
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2019-07-29
date_created: 2019-10-08T12:48:42Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2024-03-07T14:43:38Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293611.3331633
external_id:
arxiv:
- '1903.05956'
isi:
- '000570442000011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.05956
month: '08'
oa: 1
oa_version: Preprint
page: 74-83
publication: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin
publication_identifier:
isbn:
- '9781450362177'
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '7939'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Fast approximate shortest paths in the congested clique
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '15147'
abstract:
- lang: eng
text: Circadian rhythms are generated by a transcription-based feedback loop where
CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind
to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify
a key biochemical and structural difference between CRY1 and CRY2 that underlies
their differential strengths as transcriptional repressors. While both cryptochromes
bind the BMAL1 transactivation domain with similar affinity to sequester it from
coactivators, CRY1 is recruited with much higher affinity to the PAS domain core
of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian
period. We identify a dynamic loop in the secondary pocket that regulates differential
binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels
this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2
forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1
both with and without PER2.
article_processing_charge: No
author:
- first_name: Jennifer L.
full_name: Fribourgh, Jennifer L.
last_name: Fribourgh
- first_name: Ashutosh
full_name: Srivastava, Ashutosh
last_name: Srivastava
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Peter L.
full_name: Hsu, Peter L.
last_name: Hsu
- first_name: Christin
full_name: Rakers, Christin
last_name: Rakers
- first_name: Leslee T.
full_name: Nguyen, Leslee T.
last_name: Nguyen
- first_name: Megan R.
full_name: Torgrimson, Megan R.
last_name: Torgrimson
- first_name: Gian Carlo G.
full_name: Parico, Gian Carlo G.
last_name: Parico
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Ning
full_name: Zheng, Ning
last_name: Zheng
- first_name: Gabriel C.
full_name: Lander, Gabriel C.
last_name: Lander
- first_name: Tsuyoshi
full_name: Hirota, Tsuyoshi
last_name: Hirota
- first_name: Florence
full_name: Tama, Florence
last_name: Tama
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct
biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv.
2019. doi:10.1101/740464
apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L.,
Rakers, C., … Partch, C. L. (2019). Protein dynamics regulate distinct biochemical
properties of cryptochromes in mammalian circadian rhythms. bioRxiv. https://doi.org/10.1101/740464
chicago: Fribourgh, Jennifer L., Ashutosh Srivastava, Colby R. Sandate, Alicia K.
Michael, Peter L. Hsu, Christin Rakers, Leslee T. Nguyen, et al. “Protein Dynamics
Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian
Rhythms.” BioRxiv, 2019. https://doi.org/10.1101/740464.
ieee: J. L. Fribourgh et al., “Protein dynamics regulate distinct biochemical
properties of cryptochromes in mammalian circadian rhythms,” bioRxiv. 2019.
ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen
LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama
F, Partch CL. 2019. Protein dynamics regulate distinct biochemical properties
of cryptochromes in mammalian circadian rhythms. bioRxiv, 10.1101/740464.
mla: Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical
Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019,
doi:10.1101/740464.
short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers,
L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander,
T. Hirota, F. Tama, C.L. Partch, BioRxiv (2019).
date_created: 2024-03-21T07:51:10Z
date_published: 2019-08-20T00:00:00Z
date_updated: 2024-03-25T12:44:44Z
day: '20'
doi: 10.1101/740464
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/740464
month: '08'
oa: 1
oa_version: None
publication: bioRxiv
publication_status: published
status: public
title: Protein dynamics regulate distinct biochemical properties of cryptochromes
in mammalian circadian rhythms
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6392'
abstract:
- lang: eng
text: "The regulation of gene expression is one of the most fundamental processes
in living systems. In recent years, thanks to advances in sequencing technology
and automation, it has become possible to study gene expression quantitatively,
genome-wide and in high-throughput. This leads to the possibility of exploring
changes in gene expression in the context of many external perturbations and their
combinations, and thus of characterising the basic principles governing gene regulation.
In this thesis, I present quantitative experimental approaches to studying transcriptional
and protein level changes in response to combinatorial drug treatment, as well
as a theoretical data-driven approach to analysing thermodynamic principles guiding
transcription of protein coding genes. \r\nIn the first part of this work, I
present a novel methodological framework for quantifying gene expression changes
in drug combinations, termed isogrowth profiling. External perturbations through
small molecule drugs influence the growth rate of the cell, leading to wide-ranging
changes in cellular physiology and gene expression. This confounds the gene expression
changes specifically elicited by the particular drug. Combinatorial perturbations,
owing to the increased stress they exert, influence the growth rate even more
strongly and hence suffer the convolution problem to a greater extent when measuring
gene expression changes. Isogrowth profiling is a way to experimentally abstract
non-specific, growth rate related changes, by performing the measurement using
varying ratios of two drugs at such concentrations that the overall inhibition
rate is constant. Using a robotic setup for automated high-throughput re-dilution
culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise
interactions of four small molecule drugs through sequencing RNA along a growth
isobole. Through principal component analysis, I demonstrate here that isogrowth
profiling can uncover drug-specific as well as drug-interaction-specific gene
expression changes. I show that drug-interaction-specific gene expression changes
can be used for prediction of higher-order drug interactions. I propose a simplified
generalised framework of isogrowth profiling, with few measurements needed for
each drug pair, enabling the broad application of isogrowth profiling to high-throughput
screening of inhibitors of cellular growth and beyond. Such high-throughput screenings
of gene expression changes specific to pairwise drug interactions will be instrumental
for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second
part of this work, I extend isogrowth profiling to single-cell measurements of
gene expression, characterising population heterogeneity in the budding yeast
in response to combinatorial drug perturbation while controlling for non-specific
growth rate effects. Through flow cytometry of strains with protein products fused
to green fluorescent protein, I discover multiple proteins with bi-modally distributed
expression levels in the population in response to drug treatment. I characterize
more closely the effect of an ionic stressor, lithium chloride, and find that
it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts
and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B.
Time-lapse microscopy of a microfluidic culture system revealed that the induced
Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after
long starvation, but to preferential proliferation of Rps22B-high cells after
short starvation. Overall, this suggests that yeast cells might use splicing of
ribosomal genes for bet-hedging in fluctuating environments. I give specific examples
of how further exploration of cellular heterogeneity in yeast in response to external
perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn
the last part of this thesis, a re-analysis of a published sequencing dataset
of nascent elongating transcripts is used to characterise the thermodynamic constraints
for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position
throughout the transcribed genome with single nucleotide resolution are used to
infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking.
This analysis reveals that the basepairing strength of the eight nucleotide-long
RNA:DNA duplex relative to the basepairing strength of the same sequence when
in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement,
is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating,
but also of RNAP pausing while backtracking and of the backtracking length. The
quantitative dependence of RNAP pausing on basepairing energetics is used to infer
the increase in pausing due to transcriptional mismatches, leading to a hypothesis
that pervasive RNA polymerase II pausing is due to basepairing energetics, as
an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work
advances our understanding of the general principles governing gene expression,
with the goal of making computational predictions of single-cell gene expression
responses to combinatorial perturbations based on the individual perturbations
possible. This ability would substantially facilitate the design of drug combination
treatments and, in the long term, lead to our increased ability to more generally
design targeted manipulations to any biological system. "
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
citation:
ama: Lukacisin M. Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392
apa: Lukacisin, M. (2019). Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392
chicago: Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.
ieee: M. Lukacisin, “Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory,” IST Austria, 2019.
ista: Lukacisin M. 2019. Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria.
mla: Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.
short: M. Lukacisin, Quantitative Investigation of Gene Expression Principles through
Combinatorial Drug Perturbation and Theory, IST Austria, 2019.
date_created: 2019-05-09T19:53:00Z
date_published: 2019-05-09T00:00:00Z
date_updated: 2023-09-22T09:19:41Z
day: '09'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:6392
extern: '1'
file:
- access_level: closed
checksum: 829bda074444857c7935171237bb7c0c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mlukacisin
date_created: 2019-05-10T13:51:49Z
date_updated: 2020-07-14T12:47:29Z
embargo_to: open_access
file_id: '6409'
file_name: Thesis_Draft_v3.4Final.docx
file_size: 43740796
relation: hidden
- access_level: open_access
checksum: 56cb5e97f5f8fc41692401b53832d8e0
content_type: application/pdf
creator: mlukacisin
date_created: 2019-05-10T14:13:42Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2020-04-17
file_id: '6410'
file_name: Thesis_Draft_v3.4FinalA.pdf
file_size: 35228388
relation: main_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '103'
publication_identifier:
isbn:
- 978-3-99078-001-5
issn:
- 2663-337X
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '1029'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Quantitative investigation of gene expression principles through combinatorial
drug perturbation and theory
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6435'
abstract:
- lang: eng
text: "Social insect colonies tend to have numerous members which function together
like a single organism in such harmony that the term ``super-organism'' is often
used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells
of a metazoan, while the sterile worker caste corresponds to somatic cells. The
worker castes, like tissues, are\r\nin charge of all functions of a living being,
besides reproduction. The establishment of new super-organismal units\r\n(i.e.
new colonies) is accomplished by the co-dependent castes. The term oftentimes
goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation,
nutrient regulation and gas exchange of a social insect colony. Furthermore, we
assert that the super-organism has an immune system, and benefits from ``social
immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists
to resolve the apparent discrepancy between the expected high frequency of disease
outbreak amongst numerous, closely related tightly-interacting hosts, living in
stable and microbially-rich environments, against the exceptionally scarce epidemic
accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly
of behaviours which have evolved to effectively keep the pathogenic enemies of
a colony at bay. The field of social immunity has drawn interest, as it becomes
increasingly urgent to stop\r\nthe collapse of pollinator species and curb the
growth of invasive pests. In the past decade, several mechanisms of\r\nsocial
immune responses have been dissected, but many more questions remain open.\r\n\r\nI
present my work in two experimental chapters. In the first, I use invasive garden
ants (*Lasius neglectus*) to study how pathogen load and its distribution among
nestmates affect the grooming response of the group. Any given group of ants will
carry out the same total grooming work, but will direct their grooming effort
towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation,
the highest risk of transmission does not stem from grooming highly contaminated
ants, but instead, we suggest that the grooming response likely minimizes spore
loss to the environment, reducing contamination from inadvertent pickup from the
substrate.\r\n\r\nThe second is a comparative developmental approach. I follow
black garden ant queens (*Lasius niger*) and their colonies from mating flight,
through hibernation for a year. Colonies which grow fast from the start, have
a lower chance of survival through hibernation, and those which survive grow at
a lower pace later. This is true for colonies of naive\r\nand challenged queens.
Early pathogen exposure of the queens changes colony dynamics in an unexpected
way: colonies from exposed queens are more likely to grow slowly and recover in
numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental
chapters, this thesis includes a co-authored published review on organisational\r\nimmunity,
where we enlist the experimental evidence and theoretical framework on which this
hypothesis is built,\r\nidentify the caveats and underline how the field is ripe
to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative
efforts, one to develop an image-based tracker, and the second to develop a classifier
for ant\r\nbehaviour."
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
citation:
ama: Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen.
2019. doi:10.15479/AT:ISTA:6435
apa: Casillas Perez, B. E. (2019). Collective defenses of garden ants against
a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435
chicago: Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against
a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.
ieee: B. E. Casillas Perez, “Collective defenses of garden ants against a fungal
pathogen,” Institute of Science and Technology Austria, 2019.
ista: Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal
pathogen. Institute of Science and Technology Austria.
mla: Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a
Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.
short: B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal
Pathogen, Institute of Science and Technology Austria, 2019.
date_created: 2019-05-13T08:58:35Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2023-09-07T12:57:04Z
day: '07'
ddc:
- '570'
- '006'
- '578'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:6435
ec_funded: 1
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file_size: 7365118
relation: source_file
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has_accepted_license: '1'
keyword:
- Social Immunity
- Sanitary care
- Social Insects
- Organisational Immunity
- Colony development
- Multi-target tracking
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '183'
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1999'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Collective defenses of garden ants against a fungal pathogen
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6269'
abstract:
- lang: eng
text: 'Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking
that is constantly regulated for mediating developmental and physiological responses.
The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic
trafficking in the whole multicellular organ systems of Arabidopsis. The first
chapter of my thesis describes the search for new components involved in CME.
Tandem affinity purification was conducted using CLC and its interacting partners
were identified. Amongst the identified proteins were the Auxilin-likes1 and 2
(Axl1/2), putative uncoating factors, for which we made a full functional analysis.
Over-expression of Axl1/2 causes extreme modifications in the dynamics of the
machinery proteins and inhibition of endocytosis altogether. However the loss
of function of the axl1/2 did not present any cellular or physiological phenotype,
meaning Auxilin-likes do not form the major uncoating machinery. The second chapter
of my thesis describes the establishment/utilisation of techniques to capture
the dynamicity and the complexity of CME and post-endocytic trafficking. We have
studied the development of endocytic pits at the PM – specifically, the mode of
membrane remodeling during pit development and the role of actin in it, given
plant cells possess high turgor pressure. Utilizing the improved z-resolution
of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events
at the plasma membrane; and using particle detection software, we quantitatively
analysed all the endocytic trajectories in an unbiased way to obtain the endocytic
rate of the system. This together with the direct analysis of cargo internalisation
from the PM provided an estimate on the endocytic potential of the cell. We also
developed a methodology for ultrastructural analysis of different populations
of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed
protoplasts. Structural analysis, together with the intensity profile of CCSs
at the PM show that the mode of CCP development at the PM follows ‘Constant curvature
model’; meaning that clathrin polymerisation energy is a major contributing factor
of membrane remodeling. In addition, other analyses clearly show that actin is
not required for membrane remodeling during invagination or any other step of
CCP development, despite the prevalent high turgor pressure. However, actin is
essential in orchestrating the post-endocytic trafficking of CCVs facilitating
the EE formation. We also observed that the uncoating process post-endocytosis
is not immediate; an alternative mechanism of uncoating – Sequential multi-step
process – functions in the cell. Finally we also looked at one of the important
physiological stimuli modulating the process – hormone, auxin. auxin has been
known to influence CME before. We have made a detailed study on the concentration-time
based effect of auxin on the machinery proteins, CCP development, and the specificity
of cargoes endocytosed. To this end, we saw no general effect of auxin on CME
at earlier time points. However, very low concentration of IAA, such as 50nM,
accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory
control with high specificity to PIN2 could be essential in modulating its polarity. '
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
citation:
ama: Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and
their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075
apa: Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:th1075
chicago: Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic
Trafficking and Their Regulatory Controls in Plants .” Institute of Science and
Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.
ieee: M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants ,” Institute of Science and Technology
Austria, 2019.
ista: Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria.
mla: Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants . Institute of Science and Technology
Austria, 2019, doi:10.15479/at:ista:th1075.
short: M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants , Institute of Science and Technology
Austria, 2019.
date_created: 2019-04-09T14:37:06Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2023-09-08T11:43:03Z
day: '04'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/at:ista:th1075
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has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '412'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory
controls in plants '
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '11222'
acknowledgement: This work was supported by the ERC and EU Horizon 2020 (ERC 692692;
MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).
article_number: A3.27
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle
pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic
Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27'
apa: 'Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis
of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy.
In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological
Society. https://doi.org/10.25006/ia.7.s1-a3.27'
chicago: Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis
of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.”
In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019.
https://doi.org/10.25006/ia.7.s1-a3.27.
ieee: O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked
vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in
Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.
ista: 'Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked
vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic
Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological
Society vol. 7, A3.27.'
mla: Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal
Mossy Fiber Terminals by Electron Microscopy.” Intrinsic Activity, vol.
7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27.
short: O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian
Pharmacological Society, 2019.
conference:
end_date: 2019-09-27
location: Innsbruck, Austria
name: 'ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological
Society'
start_date: 2019-09-25
date_created: 2022-04-20T15:06:05Z
date_published: 2019-09-11T00:00:00Z
date_updated: 2024-03-28T23:30:07Z
day: '11'
department:
- _id: PeJo
doi: 10.25006/ia.7.s1-a3.27
ec_funded: 1
intvolume: ' 7'
issue: Suppl. 1
keyword:
- hippocampus
- mossy fibers
- readily releasable pool
- electron microscopy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.intrinsicactivity.org/2019/7/S1/A3.27/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Intrinsic Activity
publication_identifier:
issn:
- 2309-8503
publication_status: published
publisher: Austrian Pharmacological Society
quality_controlled: '1'
related_material:
record:
- id: '11196'
relation: dissertation_contains
status: public
status: public
title: Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals
by electron microscopy
type: conference_abstract
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 7
year: '2019'
...
---
_id: '6947'
abstract:
- lang: eng
text: Lymph nodes are es s ential organs of the immune s ys tem where adaptive
immune responses originate, and consist of various leukocyte populations and a
stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells
and form a sponge-like extracellular matrix network, called conduits , which they thems
elves enwrap and contract. Lymph, containing s oluble antigens , arrive
in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps
ular s inus and conduit network. According to the current paradigm, the conduit network dis
tributes afferent lymph through lymph nodes and thus provides acces
s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the
immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the
size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s
ize remains remarkedly s table under homeostatic conditions. It is only
partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is
able to swell in inflammation. The role of the FRC network in lymph node s
welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s
tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal
metastases.We examined the role of a mechanical feedback in regulation of lymph node
swelling. Using parallel plate compression and UV-las er cutting experiments we dis
s ected the mechanical force dynamics of the whole lymph node, and individually
for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens
ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis
s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells
∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps
ule, and how are lymphocytes able to enter in conditions that resist
swelling remain open ques tions . We s how that tens ion on the FRC network is important
to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion.
This is illustrated by interfering with FRC contractility, which leads to faster
swelling rates and a dis organized FRC network in the inflamed lymph node.
Growth of the FRC network in turn is expected to releas e tens ion on thes
e s tructures and lowers the res is tance to swelling, thereby allowing
more lymphocytes to enter the organ and drive more swelling. Halt of swelling
coincides with a thickening of the caps ule, which forms a thick res
is tant band around the organ and lowers tens ion on the FRC network to form
a new force equilibrium.The FRC and conduit network are further believed to be a privileged s
ite of s oluble information within the lymph node, although many details remain uns
olved. We s how by 3D ultra-recons truction that FRCs and antigen pres
enting cells cover the s urface of conduit s ys tem for more than 99%
and we dis cus s the implications for s oluble information exchangeat the conduit
level.Finally, there is an ongoing debate in the cancer field whether and how
cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus
ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels.
Once in the blood circulation, these cells are able to form metastases in
distal tissues.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
citation:
ama: 'Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947'
apa: 'Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between
stroma contractility, morphology and lymphocyte trafficking. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947'
chicago: 'Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.'
ieee: 'F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking,” Institute of Science and
Technology Austria, 2019.'
ista: 'Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking. Institute of Science and
Technology Austria.'
mla: 'Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of
Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.'
short: 'F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma
Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and
Technology Austria, 2019.'
date_created: 2019-10-14T16:54:52Z
date_published: 2019-10-09T00:00:00Z
date_updated: 2023-09-13T08:50:57Z
day: '9'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6947
file:
- access_level: closed
checksum: 53a739752a500f84d0f8ec953cbbd0b6
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: fassen
date_created: 2019-11-06T12:30:02Z
date_updated: 2020-11-07T23:30:03Z
embargo_to: open_access
file_id: '6990'
file_name: PhDthesis_FrankAssen_revised2.docx
file_size: 214172667
relation: source_file
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checksum: 8c156b65d9347bb599623a4b09f15d15
content_type: application/pdf
creator: fassen
date_created: 2019-11-06T12:30:57Z
date_updated: 2020-11-07T23:30:03Z
embargo: 2020-11-06
file_id: '6991'
file_name: PhDthesis_FrankAssen_revised2.pdf
file_size: 83637532
relation: main_file
file_date_updated: 2020-11-07T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '142'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '664'
relation: part_of_dissertation
status: public
- id: '402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6849'
abstract:
- lang: eng
text: 'Brain function is mediated by complex dynamical interactions between excitatory
and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons)
are one of the least studied types, despite being suspected to play important
roles in cognitive processes. We studied the network effects of optogenetic silencing
of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states.
The cell firing pattern in response to light pulses allowed us to classify the
recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal
cell and interneurons, and the inhibited interneurons corresponding to the CCK
group. The light application, which inhibited the activity of CCK interneurons
triggered wider changes in the firing dynamics of cells. We observed rate changes
(i.e. remapping) of pyramidal cells during the exploration session in which the
light was applied relative to the previous control session that was not restricted
neither in time nor space to the light delivery. Also, the disinhibited pyramidal
cells had higher increase in bursting than in single spike firing rate as a result
of CCK silencing. In addition, the firing activity patterns during exploratory
periods were more weakly reactivated in sleep for those periods in which CCK-interneuron
were silenced than in the unaffected periods. Furthermore, light pulses during
sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK
neurons during exploration suppressed the reactivation of waking firing patterns
in sleep and CCK interneuron activity was also required during sleep for the normal
reactivation of waking patterns. These findings demonstrate the involvement of
CCK cells in reactivation-related memory consolidation. An important part of our
analysis was to test the relationship of the identified CCKinterneurons to brain
oscillations. Our findings showed that these cells exhibited different oscillatory
behaviour during anaesthesia and natural waking and sleep conditions. We showed
that: 1) Contrary to the past studies performed under anaesthesia, the identified
CCKinterneurons fired on the descending portion of the theta phase in waking exploration.
2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3)
Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons
increased around the peak activity of the sharp-wave ripple (SWR) events in natural
sleep, which is congruent with new reports about their functional connectivity.
We also found that light driven CCK-interneuron silencing altered the dynamics
on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted
their preferred theta phases when the light was applied, while interneurons responses
were less consistent. 2) As a population, pyramidal cells negatively shifted their
preferred activity during gamma oscillations, albeit we did not find gamma modulation
differences related to the light application when pyramidal cells were subdivided
into the disinhibited and unaffected groups. 3) During the peak of SWR events,
all but the CCK-interneurons had a reduction in their relative firing rate change
during the light application as compared to the change observed at SWR initiation.
Finally, regarding to the place field activity of the recorded pyramidal neurons,
we showed that the disinhibited pyramidal cells had reduced place field similarity,
coherence and spatial information, but only during the light application. The
mechanisms behind such observed behaviours might involve eCB signalling and plastic
changes in CCK-interneuron synapses. In conclusion, the observed changes related
to the light-mediated silencing of CCKinterneurons have unravelled characteristics
of this interneuron subpopulation that might change the understanding not only
of their particular network interactions, but also of the current theories about
the emergence of certain cognitive processes such as place coding needed for navigation
or hippocampus-dependent memory consolidation. '
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
citation:
ama: Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal
network dynamics. 2019. doi:10.15479/AT:ISTA:6849
apa: Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating
hippocampal network dynamics. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6849
chicago: Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating
Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:6849.
ieee: D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal
network dynamics,” Institute of Science and Technology Austria, 2019.
ista: Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal
network dynamics. Institute of Science and Technology Austria.
mla: Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.
short: D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics, Institute of Science and Technology Austria, 2019.
date_created: 2019-09-06T06:54:16Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2023-09-19T10:01:12Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6849
file:
- access_level: closed
checksum: 244dc4f74dbfc94f414156092298831f
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: drangel
date_created: 2019-09-09T13:09:45Z
date_updated: 2021-02-10T23:30:09Z
embargo_to: open_access
file_id: '6865'
file_name: Thesis_Damaris_Rangel_source.docx
file_size: 18253100
relation: source_file
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checksum: 59c73be40eeaa1c4db24067270151555
content_type: application/pdf
creator: drangel
date_created: 2019-09-09T13:09:52Z
date_updated: 2020-09-11T22:30:04Z
embargo: 2020-09-10
file_id: '6866'
file_name: Thesis_Damaris_Rangel_pdfa.pdf
file_size: 2160109
relation: main_file
request_a_copy: 0
file_date_updated: 2021-02-10T23:30:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '97'
publication_identifier:
isbn:
- '9783990780039'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5914'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The role of CCK-interneurons in regulating hippocampal network dynamics
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6351'
abstract:
- lang: eng
text: "A process of restorative patterning in plant roots correctly replaces eliminated
cells to heal local injuries despite the absence of cell migration, which underpins
wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell
divisions and acquisition of specific cell identities. Plants regularly endure
wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary
abilities to restore their tissues after injuries. Here, we provide insight into
a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted
elimination of different cells in Arabidopsis root combined with live-imaging
tracking during vertical growth allowed analysis of the regeneration processes
in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated
their stem cell transcriptional programs. They accelerated their progression through
cell cycle, coordinately changed the cell division orientation, and ultimately
acquired de novo the correct cell fates to replace missing cells. These observations
highlight existence of unknown intercellular positional signaling and demonstrate
the capability of specified cells to re-acquire stem cell programs as a crucial
part of the plant-specific mechanism of wound healing."
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell.
2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015
apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml,
J. (2019). Re-activation of stem cell pathways for pattern restoration in plant
wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015
chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková,
and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in
Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.
ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml,
“Re-activation of stem cell pathways for pattern restoration in plant wound healing,”
Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.
ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4),
957–969.e13.
mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration
in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13,
doi:10.1016/j.cell.2019.04.015.
short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell
177 (2019) 957–969.e13.
date_created: 2019-04-28T21:59:14Z
date_published: 2019-05-02T00:00:00Z
date_updated: 2024-03-28T23:30:10Z
day: '02'
ddc:
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cell.2019.04.015
ec_funded: 1
external_id:
isi:
- '000466843000015'
pmid:
- '31051107'
file:
- access_level: open_access
checksum: 4ceba04a96a74f5092ec3ce2c579a0c7
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T06:12:45Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6411'
file_name: 2019_Cell_Marhava.pdf
file_size: 10272032
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 177'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 957-969.e13
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: Cell
publication_identifier:
eissn:
- '10974172'
issn:
- '00928674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Re-activation of stem cell pathways for pattern restoration in plant wound
healing
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 177
year: '2019'
...
---
_id: '6943'
abstract:
- lang: eng
text: Plants as sessile organisms are constantly under attack by herbivores, rough
environmental situations, or mechanical pressure. These challenges often lead
to the induction of wounds or destruction of already specified and developed tissues.
Additionally, wounding makes plants vulnerable to invasion by pathogens, which
is why wound signalling often triggers specific defence responses. To stay competitive
or, eventually, survive under these circumstances, plants need to regenerate efficiently,
which in rigid, tissue migration-incompatible plant tissues requires post-embryonic
patterning and organogenesis. Now, several studies used laser-assisted single
cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we
discuss their findings and put them into context of a broader spectrum of wound
signalling, pathogen responses and tissue as well as organ regeneration.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing
and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130.
doi:10.1016/j.pbi.2019.08.006
apa: Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights
into wound healing and restorative patterning. Current Opinion in Plant Biology.
Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006
chicago: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights
into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology.
Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006.
ieee: L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound
healing and restorative patterning,” Current Opinion in Plant Biology,
vol. 52. Elsevier, pp. 124–130, 2019.
ista: Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound
healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.
mla: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into
Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology,
vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006.
short: L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.
date_created: 2019-10-14T07:00:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-03-28T23:30:10Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2019.08.006
ec_funded: 1
external_id:
isi:
- '000502890600017'
pmid:
- '31585333'
file:
- access_level: open_access
checksum: d6fd68a6e965f1efe3f0bf2d2070a616
content_type: application/pdf
creator: dernst
date_created: 2019-10-14T14:48:21Z
date_updated: 2020-07-14T12:47:45Z
file_id: '6946'
file_name: 2019_CurrentOpinionPlant_Hoermayer.pdf
file_size: 1659288
relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 124-130
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: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Targeted cell ablation-based insights into wound healing and restorative patterning
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2019'
...
---
_id: '7391'
abstract:
- lang: eng
text: Electron microscopy (EM) is a technology that enables visualization of single
proteins at a nanometer resolution. However, current protein analysis by EM mainly
relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised
by large size of antibody, precluding precise detection of protein location in
biological samples. Here, we develop a specific chemical labeling method for EM
detection of proteins at single-molecular level. Rational design of α-helical
peptide tag and probe structure provided a complementary reaction pair that enabled
specific cysteine conjugation of the tag. The developed chemical labeling with
gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency
and detectability of high-density clusters of tag-fused G protein-coupled receptors
in freeze-fracture replicas compared with immunogold labeling. Furthermore, in
ultrathin sections, the spatial resolution of the chemical labeling was significantly
higher than that of antibody-mediated labeling. These results demonstrate substantial
advantages of the chemical labeling approach for single protein visualization
by EM.
article_processing_charge: No
article_type: original
author:
- first_name: Shigekazu
full_name: Tabata, Shigekazu
id: 4427179E-F248-11E8-B48F-1D18A9856A87
last_name: Tabata
- first_name: Marijo
full_name: Jevtic, Marijo
id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87
last_name: Jevtic
- first_name: Nobutaka
full_name: Kurashige, Nobutaka
last_name: Kurashige
- first_name: Hirokazu
full_name: Fuchida, Hirokazu
last_name: Fuchida
- first_name: Munetsugu
full_name: Kido, Munetsugu
last_name: Kido
- first_name: Kazushi
full_name: Tani, Kazushi
last_name: Tani
- first_name: Naoki
full_name: Zenmyo, Naoki
last_name: Zenmyo
- first_name: Shohei
full_name: Uchinomiya, Shohei
last_name: Uchinomiya
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Itaru
full_name: Hamachi, Itaru
last_name: Hamachi
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Akio
full_name: Ojida, Akio
last_name: Ojida
citation:
ama: Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single
membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268.
doi:10.1016/j.isci.2019.11.025
apa: Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida,
A. (2019). Electron microscopic detection of single membrane proteins by a specific
chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025
chicago: Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida,
Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection
of Single Membrane Proteins by a Specific Chemical Labeling.” IScience.
Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.
ieee: S. Tabata et al., “Electron microscopic detection of single membrane
proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier,
pp. 256–268, 2019.
ista: Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya
S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic
detection of single membrane proteins by a specific chemical labeling. iScience.
22(12), 256–268.
mla: Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane
Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier,
2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.
short: S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo,
S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience
22 (2019) 256–268.
date_created: 2020-01-29T15:56:56Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2024-03-28T23:30:12Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.isci.2019.11.025
ec_funded: 1
external_id:
isi:
- :000504652000020
pmid:
- '31786521'
file:
- access_level: open_access
checksum: f3e90056a49f09b205b1c4f8c739ffd1
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:48:36Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7448'
file_name: 2019_iScience_Tabata.pdf
file_size: 7197776
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 256-268
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: iScience
publication_identifier:
issn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Electron microscopic detection of single membrane proteins by a specific chemical
labeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
year: '2019'
...
---
_id: '6848'
abstract:
- lang: eng
text: Proton-translocating transhydrogenase (also known as nicotinamide nucleotide
transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner
mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride
between NADH and NADP+, coupled to the translocation of one proton across the
membrane. Its main physiological function is the generation of NADPH, which is
a substrate in anabolic reactions and a regulator of oxidative status; however,
NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid
deficiency in humans and metabolic abnormalities in mice, similar to those observed
in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve
a rotation of around 180° of the entire NADP(H)-binding domain that alternately
participates in hydride transfer and proton-channel gating. However, owing to
the lack of high-resolution structures of intact NNT, the details of this process
remain unclear5,6. Here we present the cryo-electron microscopy structure of intact
mammalian NNT in different conformational states. We show how the NADP(H)-binding
domain opens the proton channel to the opposite sides of the membrane, and we
provide structures of these two states. We also describe the catalytically important
interfaces and linkers between the membrane and the soluble domains and their
roles in nucleotide exchange. These structures enable us to propose a revised
mechanism for a coupling process in NNT that is consistent with a large body of
previous biochemical work. Our results are relevant to the development of currently
unavailable NNT inhibitors, which may have therapeutic potential in ischaemia
reperfusion injury, metabolic syndrome and some cancers7,8,9.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: " We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their
assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing
was performed at the IST high-performance computing cluster.\r\nThis project has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement no. 665385."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2
apa: Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial
proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019.
https://doi.org/10.1038/s41586-019-1519-2.
ieee: D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating
transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295,
2019.
ista: Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 573(7773), 291–295.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer
Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.
short: D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.
date_created: 2019-09-04T06:21:41Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2024-03-28T23:30:15Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
file:
- access_level: open_access
checksum: 52728cda5210a3e9b74cc204e8aed3d5
content_type: application/pdf
creator: lsazanov
date_created: 2020-11-26T16:33:44Z
date_updated: 2020-11-26T16:33:44Z
file_id: '8821'
file_name: Manuscript_final_acc_withFigs_SI_opt_red.pdf
file_size: 3066206
relation: main_file
success: 1
file_date_updated: 2020-11-26T16:33:44Z
has_accepted_license: '1'
intvolume: ' 573'
isi: 1
issue: '7773'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 291–295
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/
record:
- id: '8340'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of mitochondrial proton-translocating transhydrogenase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 573
year: '2019'
...
---
_id: '6194'
abstract:
- lang: eng
text: Grid cells with their rigid hexagonal firing fields are thought to provide
an invariant metric to the hippocampal cognitive map, yet environmental geometrical
features have recently been shown to distort the grid structure. Given that the
hippocampal role goes beyond space, we tested the influence of nonspatial information
on the grid organization. We trained rats to daily learn three new reward locations
on a cheeseboard maze while recording from the medial entorhinal cortex and the
hippocampal CA1 region. Many grid fields moved toward goal location, leading to
long-lasting deformations of the entorhinal map. Therefore, distortions in the
grid structure contribute to goal representation during both learning and recall,
which demonstrates that grid cells participate in mnemonic coding and do not merely
provide a simple metric of space.
article_processing_charge: No
article_type: original
author:
- first_name: Charlotte N.
full_name: Boccara, Charlotte N.
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive
map is attracted to goals. Science. 2019;363(6434):1443-1447. doi:10.1126/science.aav4837
apa: Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., & Csicsvari, J. L.
(2019). The entorhinal cognitive map is attracted to goals. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.aav4837
chicago: Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill,
and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.”
Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aav4837.
ieee: C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The
entorhinal cognitive map is attracted to goals,” Science, vol. 363, no.
6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.
ista: Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal
cognitive map is attracted to goals. Science. 363(6434), 1443–1447.
mla: Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to
Goals.” Science, vol. 363, no. 6434, American Association for the Advancement
of Science, 2019, pp. 1443–47, doi:10.1126/science.aav4837.
short: C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363
(2019) 1443–1447.
date_created: 2019-04-04T08:39:30Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2024-03-28T23:30:16Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1126/science.aav4837
ec_funded: 1
external_id:
isi:
- '000462738000034'
file:
- access_level: open_access
checksum: 5e6b16742cde10a560cfaf2130764da1
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:11:10Z
date_updated: 2020-07-14T12:47:23Z
file_id: '7826'
file_name: 2019_Science_Boccara.pdf
file_size: 9045923
relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: ' 363'
isi: 1
issue: '6434'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1443-1447
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/
record:
- id: '6062'
relation: popular_science
status: public
- id: '11932'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The entorhinal cognitive map is attracted to goals
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 363
year: '2019'
...
---
_id: '7132'
abstract:
- lang: eng
text: "A major challenge in neuroscience research is to dissect the circuits that
orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian
species, such as microbial opsins, have been successfully transplanted to specific
neuronal targets to override their natural communication patterns. The goal of
our work is to manipulate synaptic communication in a manner that closely incorporates
the functional intricacies of synapses by preserving temporal encoding (i.e. the
firing pattern of the presynaptic neuron) and connectivity (i.e. target specific
synapses rather than specific neurons). Our strategy to achieve this goal builds
on the use of non-mammalian transplants to create a synthetic synapse. The mode
of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN)
into synaptic vesicles by means of a genetically targeted transporter selective
for the SN. Upon natural vesicular release, exposure of the SN to the synaptic
cleft will modify the post-synaptic potential through an orthogonal ligand gated
ion channel. To achieve this goal we have functionally characterized a mixed cationic
methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally
characterize a synthetic transporter in isolated synaptic vesicles without the
need for transgenic animals, identified and extracted multiple prokaryotic uptake
systems that are substrate specific for methionine (Met), and established a primary/cell
line co-culture system that would allow future combinatorial testing of this orthogonal
transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a
unique opportunity to manipulate synaptic communication while maintaining the
electrophysiological integrity of the pre-synaptic cell. In this way, information
may be preserved that was generated in upstream circuits and that could be essential
for concerted function and information processing."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
citation:
ama: Mckenzie C. Design and characterization of methods and biological components
to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132
apa: Mckenzie, C. (2019). Design and characterization of methods and biological
components to realize synthetic neurotransmission. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:7132
chicago: Mckenzie, Catherine. “Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/at:ista:7132.
ieee: C. Mckenzie, “Design and characterization of methods and biological components
to realize synthetic neurotransmission,” Institute of Science and Technology Austria,
2019.
ista: Mckenzie C. 2019. Design and characterization of methods and biological components
to realize synthetic neurotransmission. Institute of Science and Technology Austria.
mla: Mckenzie, Catherine. Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission. Institute of Science and
Technology Austria, 2019, doi:10.15479/at:ista:7132.
short: C. Mckenzie, Design and Characterization of Methods and Biological Components
to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria,
2019.
date_created: 2019-11-27T09:07:14Z
date_published: 2019-06-27T00:00:00Z
date_updated: 2024-03-28T23:30:21Z
day: '27'
ddc:
- '571'
- '573'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/at:ista:7132
file:
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checksum: 34d0fe0f6e0af97b5937205a3e350423
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-11-27T09:06:10Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7133'
file_name: McKenzie PhD Thesis August 2018 - Corrected Final.docx
file_size: 5054633
relation: source_file
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checksum: 140dfb5e3df7edca34f4b6fcc55d876f
content_type: application/pdf
creator: dernst
date_created: 2019-11-27T09:06:10Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7134'
file_name: McKenzie PhD Thesis August 2018 - Corrected Final.pdf
file_size: 3231837
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '95'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6266'
relation: old_edition
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Design and characterization of methods and biological components to realize
synthetic neurotransmission
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '5949'
abstract:
- lang: eng
text: Aberrant proteostasis of protein aggregation may lead to behavior disorders
including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations
that underlie CMI are not well understood. We recorded the local field potential
and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically
overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling
sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein
aggregation, disturbances in the dopaminergic system and attention-related deficits.
Recordings were performed during exploration of familiar and novel open field
environments and during sleep, allowing investigation of neuronal abnormalities
in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited
smaller place fields and decreased speed-modulation of their firing rates, demonstrating
altered spatial coding and deficits in encoding location-independent sensory inputs.
Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase
locking strength during novelty, limiting their phase coding ability. However,
their mean theta phases were more variable at the population level, reducing oscillatory
network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced
shift in their preferred theta and gamma firing phases, indicating deficits in
coding of novel environments with oscillatory firing. By combining single cell
and neuronal population analyses, we link DISC1 protein pathology with abnormal
hippocampal neural coding and network synchrony, and thereby gain a more comprehensive
understanding of CMI mechanisms.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Hugo
full_name: Malagon-Vina, Hugo
last_name: Malagon-Vina
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: Joseph
full_name: O'Neill, Joseph
last_name: O'Neill
- first_name: Svenja V.
full_name: Trossbach, Svenja V.
last_name: Trossbach
- first_name: Carsten
full_name: Korth, Carsten
last_name: Korth
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression
disrupts hippocampal coding and oscillatory synchronization. Hippocampus.
2019;29(9):802-816. doi:10.1002/hipo.23076
apa: Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V.,
Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression
disrupts hippocampal coding and oscillatory synchronization. Hippocampus.
Wiley. https://doi.org/10.1002/hipo.23076
chicago: Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja
V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia
1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.”
Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076.
ieee: K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts
hippocampal coding and oscillatory synchronization,” Hippocampus, vol.
29, no. 9. Wiley, pp. 802–816, 2019.
ista: Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari
JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding
and oscillatory synchronization. Hippocampus. 29(9), 802–816.
mla: Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts
Hippocampal Coding and Oscillatory Synchronization.” Hippocampus, vol.
29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076.
short: K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth,
J.L. Csicsvari, Hippocampus 29 (2019) 802–816.
date_created: 2019-02-10T22:59:18Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2024-03-28T23:30:22Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1002/hipo.23076
ec_funded: 1
external_id:
isi:
- '000480635400003'
file:
- access_level: open_access
checksum: 5e8de271ca04aef92a5de42d6aac4404
content_type: application/pdf
creator: dernst
date_created: 2019-02-11T10:42:51Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5950'
file_name: 2019_Hippocampus_Kaefer.pdf
file_size: 2132893
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 802-816
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: Inter-and intracellular signalling in schizophrenia
publication: Hippocampus
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '6825'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and
oscillatory synchronization
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6825'
abstract:
- lang: eng
text: "The solving of complex tasks requires the functions of more than one brain
area and their interaction. Whilst spatial navigation and memory is dependent
on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC).
To further examine the roles of the hippocampus and mPFC, we recorded their neural
activity during a task that depends on both of these brain regions.\r\nWith tetrodes,
we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC
neurons in Long-Evans rats performing a rule-switching task on the plus-maze.
The plus-maze task had a spatial component since it required navigation along
one of the two start arms and at the maze center a choice between one of the two
goal arms. Which goal contained a reward depended on the rule currently in place.
After an uncued rule change the animal had to abandon the old strategy and switch
to the new rule, testing cognitive flexibility. Investigating the coordination
of activity between the HPC and mPFC allows determination during which task stages
their interaction is required. Additionally, comparing neural activity patterns
in these two brain regions allows delineation of the specialized functions of
the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC
in terms of oscillatory interactions, rule coding and replay.\r\nWe found that
theta coherence between the HPC and mPFC is increased at the center and goals
of the maze, both when the rule was stable or has changed. Similar results were
found for locking of HPC and mPFC neurons to HPC theta oscillations. However,
no differences in HPC-mPFC theta coordination were observed between the spatially-
and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations
was not modulated by\r\nmaze position or rule type. We found that the HPC coded
for the two different rules with cofiring relationships between\r\ncell pairs.
However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective
firing in the mPFC generalized between the two start and two goal arms. With Bayesian
positional decoding, we found that the mPFC reactivated non-local positions during
awake immobility periods. Replay of these non-local positions could represent
entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore,
mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching
performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently
of each other. These results show that the mPFC can replay ordered patterns of
activity during awake immobility, possibly underlying its role in flexible behavior. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
citation:
ama: Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior.
2019. doi:10.15479/AT:ISTA:6825
apa: Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible
behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825
chicago: Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible
Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.
ieee: K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,”
Institute of Science and Technology Austria, 2019.
ista: Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible
behavior. Institute of Science and Technology Austria.
mla: Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible
Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.
short: K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior,
Institute of Science and Technology Austria, 2019.
date_created: 2019-08-21T15:00:57Z
date_published: 2019-08-24T00:00:00Z
date_updated: 2023-09-07T13:01:42Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6825
file:
- access_level: open_access
checksum: 2664420e332a33338568f4f3bfc59287
content_type: application/pdf
creator: kkaefer
date_created: 2019-09-03T08:07:13Z
date_updated: 2020-09-06T22:30:03Z
embargo: 2020-09-05
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file_size: 3205202
relation: main_file
request_a_copy: 0
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5949'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The hippocampus and medial prefrontal cortex during flexible behavior
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6713'
abstract:
- lang: eng
text: Evolutionary studies are often limited by missing data that are critical to
understanding the history of selection. Selection experiments, which reproduce
rapid evolution under controlled conditions, are excellent tools to study how
genomes evolve under selection. Here we present a genomic dissection of the Longshanks
selection experiment, in which mice were selectively bred over 20 generations
for longer tibiae relative to body mass, resulting in 13% longer tibiae in two
replicates. We synthesized evolutionary theory, genome sequences and molecular
genetics to understand the selection response and found that it involved both
polygenic adaptation and discrete loci of major effect, with the strongest loci
tending to be selected in parallel between replicates. We show that selection
may favor de-repression of bone growth through inactivating two limb enhancers
of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is
possible to connect individual base-pair changes to the overall selection response.
article_number: e42014
article_processing_charge: No
author:
- first_name: João Pl
full_name: Castro, João Pl
last_name: Castro
- first_name: Michelle N.
full_name: Yancoskie, Michelle N.
last_name: Yancoskie
- first_name: Marta
full_name: Marchini, Marta
last_name: Marchini
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
- first_name: Layla
full_name: Hiramatsu, Layla
last_name: Hiramatsu
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: William H.
full_name: Beluch, William H.
last_name: Beluch
- first_name: Ronald
full_name: Naumann, Ronald
last_name: Naumann
- first_name: Isabella
full_name: Skuplik, Isabella
last_name: Skuplik
- first_name: John
full_name: Cobb, John
last_name: Cobb
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis
of the Longshanks selection experiment for longer limbs in mice. eLife.
2019;8. doi:10.7554/eLife.42014
apa: Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L.,
Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.42014
chicago: Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy,
Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic
Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife.
eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.
ieee: J. P. Castro et al., “An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences
Publications, 2019.
ista: Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch
WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative
genomic analysis of the Longshanks selection experiment for longer limbs in mice.
eLife. 8, e42014.
mla: Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks
Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014,
eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.
short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M.
Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F.
Chan, ELife 8 (2019).
date_created: 2019-07-28T21:59:17Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2024-03-28T23:30:23Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7554/eLife.42014
external_id:
isi:
- '000473588700001'
pmid:
- '31169497'
file:
- access_level: open_access
checksum: fa0936fe58f0d9e3f8e75038570e5a17
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-29T07:41:18Z
date_updated: 2020-07-14T12:47:38Z
file_id: '6721'
file_name: 2019_eLife_Castro.pdf
file_size: 6748249
relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '9804'
relation: research_data
status: public
- id: '11388'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An integrative genomic analysis of the Longshanks selection experiment for
longer limbs in mice
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '10065'
abstract:
- lang: eng
text: We study double quantum dots in a Ge/SiGe heterostructure and test their maturity
towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability,
from two single quantum dots to a double quantum dot. We measure Pauli spin blockade
and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for
sensing charge transitions in the double quantum dot at interest. In conclusion,
Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We thank Matthias Brauns for helpful discussions and careful proofreading
of the manuscript. This project has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie grant agreement
No 844511 and from the FWF project P30207. The research was supported by the Scientific
Service Units of IST Austria through resources provided by the MIBA machine shop
and the nanofabrication\r\nfacility."
article_number: '1910.05841'
article_processing_charge: No
author:
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Maxim
full_name: Borovkov, Maxim
last_name: Borovkov
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Jacopo
full_name: Frigerio, Jacopo
last_name: Frigerio
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe
quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841
apa: Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A.,
Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum
dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841
chicago: Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez,
Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios
Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet
Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841.
ieee: A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots
as hosts for singlet-triplet qubits,” arXiv. .
ista: Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio
J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum
dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.
mla: Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots
as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841.
short: A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J.
Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).
date_created: 2021-10-01T12:14:51Z
date_published: 2019-10-13T00:00:00Z
date_updated: 2024-03-28T23:30:27Z
day: '13'
department:
- _id: GeKa
doi: 10.48550/arXiv.1910.05841
ec_funded: 1
external_id:
arxiv:
- '1910.05841'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.05841
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10058'
relation: dissertation_contains
status: public
status: public
title: Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet
qubits
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6187'
abstract:
- lang: eng
text: Aberrant display of the truncated core1 O-glycan T-antigen is a common feature
of human cancer cells that correlates with metastasis. Here we show that T-antigen
in Drosophila melanogaster macrophages is involved in their developmentally programmed
tissue invasion. Higher macrophage T-antigen levels require an atypical major
facilitator superfamily (MFS) member that we named Minerva which enables macrophage
dissemination and invasion. We characterize for the first time the T and Tn glycoform
O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva
increases the presence of T-antigen on proteins in pathways previously linked
to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required
for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the
minerva mutant’s migration and T-antigen glycosylation defects. We thus identify
a key conserved regulator that orchestrates O-glycosylation on a protein subset
to activate a program governing migration steps important for both development
and cancer metastasis.
acknowledged_ssus:
- _id: LifeSc
article_number: e41801
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
- first_name: Julia
full_name: Biebl, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Biebl
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Michaela
full_name: Misova, Michaela
id: 495A3C32-F248-11E8-B48F-1D18A9856A87
last_name: Misova
orcid: 0000-0003-2427-6856
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Patricia
full_name: Rodrigues, Patricia
id: 2CE4065A-F248-11E8-B48F-1D18A9856A87
last_name: Rodrigues
- first_name: Katerina
full_name: Shkarina, Katerina
last_name: Shkarina
- first_name: Ida Signe Bohse
full_name: Larsen, Ida Signe Bohse
last_name: Larsen
- first_name: Sergey Y
full_name: Vakhrushev, Sergey Y
last_name: Vakhrushev
- first_name: Henrik
full_name: Clausen, Henrik
last_name: Clausen
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily
member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion.
eLife. 2019;8. doi:10.7554/elife.41801
apa: Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M.,
… Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates
a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.41801
chicago: Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila
György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator
Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage
Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.
ieee: K. Valosková et al., “A conserved major facilitator superfamily member
orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife,
vol. 8. eLife Sciences Publications, 2019.
ista: Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh
A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE.
2019. A conserved major facilitator superfamily member orchestrates a subset of
O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.
mla: Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member
Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife,
vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801.
short: K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A.
Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen,
D.E. Siekhaus, ELife 8 (2019).
date_created: 2019-03-28T13:37:45Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2024-03-28T23:30:30Z
day: '26'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/elife.41801
ec_funded: 1
external_id:
isi:
- '000462530200001'
file:
- access_level: open_access
checksum: cc0d1a512559d52e7e7cb0e9b9854b40
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T14:00:41Z
date_updated: 2020-07-14T12:47:23Z
file_id: '6188'
file_name: 2019_eLife_Valoskova.pdf
file_size: 4496017
relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 253CDE40-B435-11E9-9278-68D0E5697425
grant_number: '24283'
name: Examination of the role of a MFS transporter in the migration of Drosophila
immune cells
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 25388084-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329540'
name: 'Breaking barriers: Investigating the junctional and mechanobiological changes
underlying the ability of Drosophila immune cells to invade an epithelium'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/
record:
- id: '6530'
relation: dissertation_contains
- id: '8983'
relation: dissertation_contains
status: public
- id: '6546'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation
to aid macrophage tissue invasion
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6546'
abstract:
- lang: eng
text: "Invasive migration plays a crucial role not only during development and homeostasis
but also in pathological states, such as tumor metastasis. Drosophila macrophage
migration into the extended germband is an interesting system to study invasive
migration. It carries similarities to immune cell transmigration and cancer cell
invasion, therefore studying this process could also bring new understanding of
invasion in higher organisms. In our work, we uncover a highly conserved member
of the major facilitator family that plays a role in tissue invasion through regulation
of glycosylation on a subgroup of proteins and/or by aiding the precise timing
of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1
O-glycan T-antigen is a common feature of human cancer cells that correlates with
metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages
is involved in their developmentally programmed tissue invasion. Higher macrophage
T-antigen levels require an atypical major facilitator superfamily (MFS) member
that we named Minerva which enables macrophage dissemination and invasion. We
characterize for the first time the T and Tn glycoform O-glycoproteome of the
Drosophila melanogaster embryo, and determine that Minerva increases the presence
of T-antigen on proteins in pathways previously linked to cancer, most strongly
on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue
entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration
and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator
that orchestrates O-glycosylation on a protein subset to activate \r\na program
governing migration steps important for both development and cancer metastasis.
\r\n"
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
citation:
ama: Valosková K. The role of a highly conserved major facilitator superfamily member
in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546
apa: Valosková, K. (2019). The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546
chicago: Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator
Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of
Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.
ieee: K. Valosková, “The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration,” Institute of Science and
Technology Austria, 2019.
ista: Valosková K. 2019. The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science and
Technology Austria.
mla: Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.
short: K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration, Institute of Science and
Technology Austria, 2019.
date_created: 2019-06-07T12:49:19Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-19T10:15:54Z
day: '07'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:6546
file:
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checksum: 68949c2d96210b45b981a23e9c9cd93c
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date_created: 2019-06-07T13:00:04Z
date_updated: 2020-07-14T12:47:33Z
embargo_to: open_access
file_id: '6549'
file_name: Katarina Valoskova_PhD thesis_final version.docx
file_size: 14110626
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creator: khribikova
date_created: 2019-06-07T13:00:08Z
date_updated: 2021-02-11T11:17:14Z
embargo: 2020-06-07
file_id: '6550'
file_name: Katarina Valoskova_PhD thesis_final version.pdf
file_size: 10054156
relation: main_file
file_date_updated: 2021-02-11T11:17:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '141'
project:
- _id: 253CDE40-B435-11E9-9278-68D0E5697425
grant_number: '24283'
name: Examination of the role of a MFS transporter in the migration of Drosophila
immune cells
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6187'
relation: part_of_dissertation
status: public
- id: '544'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: The role of a highly conserved major facilitator superfamily member in Drosophila
embryonic macrophage migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6363'
abstract:
- lang: eng
text: "Distinguishing between similar experiences is achieved by the brain
\ in a process called pattern separation. In the hippocampus, pattern
\ separation reduces the interference of memories and increases the storage
capacity by decorrelating similar inputs patterns of neuronal activity into
\ non-overlapping output firing patterns. Winners-take-all (WTA) mechanism
\ is a theoretical model for pattern separation in which a \"winner\"
\ cell suppresses the activity of the neighboring neurons through feedback
inhibition. However, if the network properties of the dentate gyrus support WTA
as a biologically conceivable model remains unknown. Here, we showed that the
connectivity rules of PV+interneurons and their synaptic properties are optimizedfor
efficient pattern separation. We found using multiple whole-cell in vitrorecordings
that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition,
a form of feedback inhibition in which a GC inhibits other GCs but not
\ itself through the activation of PV+interneurons. Thus, lateral inhibition
between GC–PV+interneurons was ~10 times more abundant than recurrent connections.
Furthermore, the GC–PV+interneuron connectivity was more spatially confined
\ but less abundant than PV+interneurons–GC connectivity, leading to an
\ asymmetrical distribution of excitatory and inhibitory connectivity. Our
network model of the dentate gyrus with incorporated real connectivity rules efficiently
decorrelates neuronal activity patterns using WTA as the primary mechanism.
\ This process relied on lateral inhibition, fast-signaling properties of
\ PV+interneurons and the asymmetrical distribution of excitatory and inhibitory
connectivity. Finally, we found that silencing the activity of PV+interneurons
in vivoleads to acute deficits in discrimination between similar environments,
suggesting that PV+interneuron networks are necessary for behavioral relevant
computations. Our results demonstrate that PV+interneurons possess unique
connectivity and fast signaling properties that confer to the dentate
\ gyrus network properties that allow the emergence of pattern separation. Thus,
our results contribute to the knowledge of how specific forms of network organization
underlie sophisticated types of information processing. \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
citation:
ama: Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation
in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363
apa: Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient
pattern separation in hippocampal microcircuits. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:6363
chicago: Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient
Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.
ieee: C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits,” Institute of Science and Technology
Austria, 2019.
ista: Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits. Institute of Science and Technology Austria.
mla: Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits. Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6363.
short: C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria,
2019.
date_created: 2019-04-30T11:56:10Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-09-15T12:03:48Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
doi: 10.15479/AT:ISTA:6363
file:
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checksum: 77c6c05cfe8b58c8abcf1b854375d084
content_type: application/pdf
creator: cespinoza
date_created: 2019-05-07T16:00:39Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-09
file_id: '6389'
file_name: Espinozathesis_all2.pdf
file_size: 13966891
relation: main_file
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checksum: f6aa819f127691a2b0fc21c76eb09746
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cespinoza
date_created: 2019-05-07T16:00:48Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6390'
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file_size: 11159900
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '140'
publication_identifier:
isbn:
- 978-3-99078-000-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Parvalbumin+ interneurons enable efficient pattern separation in hippocampal
microcircuits
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6780'
abstract:
- lang: eng
text: "In this work, we consider the almost-sure termination problem for probabilistic
programs that asks whether a\r\ngiven probabilistic program terminates with probability
1. Scalable approaches for program analysis often\r\nrely on modularity as their
theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof
Floyd-Hoare logic provides the foundation for modular analysis. Extension of this
rule to almost-sure\r\ntermination of probabilistic programs is quite tricky,
and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic
variant cautiously addresses the key issue of integrability, we show that the
proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic
programs.\r\nBesides establishing unsoundness of the previous rule, our contributions
are as follows: First, we present a\r\nsound modular rule for almost-sure termination
of probabilistic programs. Our approach is based on a novel\r\nnotion of descent
supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat
are linear and show that they can be synthesized in polynomial time. Finally,
we present experimental\r\nresults on a variety of benchmarks and several natural
examples that model various types of nested while\r\nloops in probabilistic programs
and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination
property"
article_number: '129'
article_processing_charge: No
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure
termination of probabilistic programs. In: Proceedings of the 34th ACM International
Conference on Object-Oriented Programming, Systems, Languages, and Applications
. Vol 3. ACM; 2019. doi:10.1145/3360555'
apa: 'Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular
verification for almost-sure termination of probabilistic programs. In Proceedings
of the 34th ACM International Conference on Object-Oriented Programming, Systems,
Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555'
chicago: Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic
Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555.
ieee: M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification
for almost-sure termination of probabilistic programs,” in Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , Athens, Greece, 2019, vol. 3.
ista: 'Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for
almost-sure termination of probabilistic programs. Proceedings of the 34th ACM
International Conference on Object-Oriented Programming, Systems, Languages, and
Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications
vol. 3, 129.'
mla: Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination
of Probabilistic Programs.” Proceedings of the 34th ACM International Conference
on Object-Oriented Programming, Systems, Languages, and Applications , vol.
3, 129, ACM, 2019, doi:10.1145/3360555.
short: M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , ACM, 2019.
conference:
end_date: 2019-10-25
location: Athens, Greece
name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications'
start_date: 2019-10-23
date_created: 2019-08-09T09:54:20Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3360555
ec_funded: 1
external_id:
arxiv:
- '1901.06087'
file:
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checksum: 3482d8ace6fb4991eb7810e3b70f1b9f
content_type: application/pdf
creator: akafshda
date_created: 2019-08-12T15:40:57Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6807'
file_name: oopsla-2019.pdf
file_size: 1024643
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checksum: 4e5a6fb2b59a75222a4e8335a5a60eac
content_type: application/pdf
creator: dernst
date_created: 2020-05-12T15:15:14Z
date_updated: 2020-07-14T12:47:40Z
file_id: '7821'
file_name: 2019_ACM_Huang.pdf
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file_date_updated: 2020-07-14T12:47:40Z
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intvolume: ' 3'
language:
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license: https://creativecommons.org/licenses/by-nc/4.0/
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: 'Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications '
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Modular verification for almost-sure termination of probabilistic programs
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2019'
...
---
_id: '6380'
abstract:
- lang: eng
text: 'There is a huge gap between the speeds of modern caches and main memories,
and therefore cache misses account for a considerable loss of efficiency in programs.
The predominant technique to address this issue has been Data Packing: data elements
that are frequently accessed within time proximity are packed into the same cache
block, thereby minimizing accesses to the main memory. We consider the algorithmic
problem of Data Packing on a two-level memory system. Given a reference sequence
R of accesses to data elements, the task is to partition the elements into cache
blocks such that the number of cache misses on R is minimized. The problem is
notoriously difficult: it is NP-hard even when the cache has size 1, and is hard
to approximate for any cache size larger than 4. Therefore, all existing techniques
for Data Packing are based on heuristics and lack theoretical guarantees. In this
work, we present the first positive theoretical results for Data Packing, along
with new and stronger negative results. We consider the problem under the lens
of the underlying access hypergraphs, which are hypergraphs of affinities between
the data elements, where the order of an access hypergraph corresponds to the
size of the affinity group. We study the problem parameterized by the treewidth
of access hypergraphs, which is a standard notion in graph theory to measure the
closeness of a graph to a tree. Our main results are as follows: We show there
is a number q* depending on the cache parameters such that (a) if the access hypergraph
of order q* has constant treewidth, then there is a linear-time algorithm for
Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph
of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy
depending on a single parameter, namely, the highest order among access hypegraphs
that have constant treewidth; and establish the optimal value q* of this parameter.
Finally, we present an experimental evaluation of a prototype implementation of
our algorithm. Our results demonstrate that, in practice, access hypergraphs of
many commonly-used algorithms have small treewidth. We compare our approach with
several state-of-the-art heuristic-based algorithms and show that our algorithm
leads to significantly fewer cache-misses. '
article_number: '53'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
2019;3(POPL). doi:10.1145/3290366
apa: Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019).
Efficient parameterized algorithms for data packing. Proceedings of the ACM
on Programming Languages. ACM. https://doi.org/10.1145/3290366
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas
Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings
of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.
ieee: K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient
parameterized algorithms for data packing,” Proceedings of the ACM on Programming
Languages, vol. 3, no. POPL. ACM, 2019.
ista: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
3(POPL), 53.
mla: Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data
Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no.
POPL, 53, ACM, 2019, doi:10.1145/3290366.
short: K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of
the ACM on Programming Languages 3 (2019).
date_created: 2019-05-06T12:18:17Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2024-03-28T23:30:33Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3290366
ec_funded: 1
file:
- access_level: open_access
checksum: c157752f96877b36685ad7063ada4524
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:23:11Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6381'
file_name: 2019_ACM_POPL_Chatterjee.pdf
file_size: 1294962
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 3'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
issn:
- 2475-1421
publication_status: published
publisher: ACM
pubrep_id: '1056'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Efficient parameterized algorithms for data packing
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: '2019'
...
---
_id: '6056'
abstract:
- lang: eng
text: In today's programmable blockchains, smart contracts are limited to being
deterministic and non-probabilistic. This lack of randomness is a consequential
limitation, given that a wide variety of real-world financial contracts, such
as casino games and lotteries, depend entirely on randomness. As a result, several
ad-hoc random number generation approaches have been developed to be used in smart
contracts. These include ideas such as using an oracle or relying on the block
hash. However, these approaches are manipulatable, i.e. their output can be tampered
with by parties who might not be neutral, such as the owner of the oracle or the
miners.We propose a novel game-theoretic approach for generating provably unmanipulatable
pseudorandom numbers on the blockchain. Our approach allows smart contracts to
access a trustworthy source of randomness that does not rely on potentially compromised
miners or oracles, hence enabling the creation of a new generation of smart contracts
that are not limited to being non-probabilistic and can be drawn from the much
more general class of probabilistic programs.
article_number: '8751326'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts:
Secure randomness on the blockchain. In: IEEE International Conference on Blockchain
and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic
smart contracts: Secure randomness on the blockchain. In IEEE International
Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE
International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart
contracts: Secure randomness on the blockchain,” in IEEE International Conference
on Blockchain and Cryptocurrency, Seoul, Korea, 2019.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts:
Secure randomness on the blockchain. IEEE International Conference on Blockchain
and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency,
8751326.'
mla: 'Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness
on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency,
8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International
Conference on Blockchain and Cryptocurrency, IEEE, 2019.
conference:
end_date: 2019-05-17
location: Seoul, Korea
name: IEEE International Conference on Blockchain and Cryptocurrency
start_date: 2019-05-14
date_created: 2019-02-26T09:03:15Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2024-03-28T23:30:33Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/BLOC.2019.8751326
ec_funded: 1
external_id:
arxiv:
- '1902.07986'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07986
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: IEEE International Conference on Blockchain and Cryptocurrency
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: 'Probabilistic smart contracts: Secure randomness on the blockchain'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6378'
abstract:
- lang: eng
text: 'In today''s cryptocurrencies, Hashcash proof of work is the most commonly-adopted
approach to mining. In Hashcash, when a miner decides to add a block to the chain,
she has to solve the difficult computational puzzle of inverting a hash function.
While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it
has attracted significant and harsh criticism due to its massive waste of electricity,
its carbon footprint and environmental effects, and the inherent lack of usefulness
in inverting a hash function. Various other mining protocols have been suggested,
including proof of stake, in which a miner''s chance of adding the next block
is proportional to her current balance. However, such protocols lead to a higher
entry cost for new miners who might not still have any stake in the cryptocurrency,
and can in the worst case lead to an oligopoly, where the rich have complete control
over mining. In this paper, we propose Hybrid Mining: a new mining protocol that
combines solving real-world useful problems with Hashcash. Our protocol allows
new miners to join the network by taking part in Hashcash mining without having
to own an initial stake. It also allows nodes of the network to submit hard computational
problems whose solutions are of interest in the real world, e.g.~protein folding
problems. Then, miners can choose to compete in solving these problems, in lieu
of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners
to solve useful problems, such as hard computational problems arising in biology,
in a distributed manner. It also gives researchers in other areas an easy-to-use
tool to outsource their hard computations to the blockchain network, which has
enormous computational power, by paying a reward to the miner who solves the problem
for them. Moreover, our protocol provides strong security guarantees and is at
least as resilient to double spending as Bitcoin.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s
computational power for distributed problem solving. In: Proceedings of the
34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381.
doi:10.1145/3297280.3297319'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining:
Exploiting blockchain’s computational power for distributed problem solving. In
Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772,
pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem
Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing,
Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving,” in Proceedings
of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol.
Part F147772, pp. 374–381.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving. Proceedings
of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing
vol. Part F147772, 374–381.'
mla: 'Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational
Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium
on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: ACM Symposium on Applied Computing
start_date: 2019-04-08
date_created: 2019-05-06T12:11:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3297280.3297319
ec_funded: 1
external_id:
isi:
- '000474685800049'
file:
- access_level: open_access
checksum: fbfbcd5a0c7a743862bfc3045539a614
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:09:27Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6379'
file_name: 2019_ACM_Chatterjee.pdf
file_size: 1023934
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 374-381
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
- '9781450359337'
publication_status: published
publisher: ACM
pubrep_id: '1069'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Hybrid Mining: Exploiting blockchain’s computational power for distributed
problem solving'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: Part F147772
year: '2019'
...
---
_id: '6175'
abstract:
- lang: eng
text: "We consider the problem of expected cost analysis over nondeterministic probabilistic
programs,\r\nwhich aims at automated methods for analyzing the resource-usage
of such programs.\r\nPrevious approaches for this problem could only handle nonnegative
bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis
of cryptocurrency protocols,\r\nboth positive and negative costs are necessary
and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and
efficient approach to obtain polynomial bounds on the\r\nexpected accumulated
cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a)
general positive and negative costs with bounded updates in\r\nvariables; and
(b) nonnegative costs with general updates to variables.\r\nWe show that several
natural examples which could not be\r\nhandled by previous approaches are captured
in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time
algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs
could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our
approach using experimental results on a variety of programs for which we efficiently
synthesize tight resource-usage bounds."
article_processing_charge: No
author:
- first_name: Peixin
full_name: Wang, Peixin
last_name: Wang
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Xudong
full_name: Qin, Xudong
last_name: Qin
- first_name: Wenjun
full_name: Shi, Wenjun
last_name: Shi
citation:
ama: 'Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of
nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the
40th ACM SIGPLAN Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581'
apa: 'Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W.
(2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019:
Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design
and Implementation (pp. 204–220). Phoenix, AZ, United States: Association
for Computing Machinery. https://doi.org/10.1145/3314221.3314581'
chicago: 'Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee,
Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.”
In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming
Language Design and Implementation, 204–20. Association for Computing Machinery,
2019. https://doi.org/10.1145/3314221.3314581.'
ieee: 'P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost
analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings
of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation,
Phoenix, AZ, United States, 2019, pp. 204–220.'
ista: 'Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis
of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th
ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI:
Conference on Programming Language Design and Implementation, 204–220.'
mla: 'Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.”
PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language
Design and Implementation, Association for Computing Machinery, 2019, pp.
204–20, doi:10.1145/3314221.3314581.'
short: 'P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI
2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2019, pp. 204–220.'
conference:
end_date: 2019-06-26
location: Phoenix, AZ, United States
name: 'PLDI: Conference on Programming Language Design and Implementation'
start_date: 2019-06-22
date_created: 2019-03-25T10:13:25Z
date_published: 2019-06-08T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '08'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3314221.3314581
ec_funded: 1
external_id:
arxiv:
- '1902.04659'
isi:
- '000523190300014'
file:
- access_level: open_access
checksum: 703a5e9b8c8587f2a44085ffd9a4db64
content_type: application/pdf
creator: akafshda
date_created: 2019-03-25T10:11:22Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6176'
file_name: paper.pdf
file_size: 4051066
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
isi: 1
keyword:
- Program Cost Analysis
- Program Termination
- Probabilistic Programs
- Martingales
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 204-220
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: 'PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming
Language Design and Implementation'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5457'
relation: earlier_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cost analysis of nondeterministic probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6490'
abstract:
- lang: eng
text: "Smart contracts are programs that are stored and executed on the Blockchain
and can receive, manage and transfer money (cryptocurrency units). Two important
problems regarding smart contracts are formal analysis and compiler optimization.
Formal analysis is extremely important, because smart contracts hold funds worth
billions of dollars and their code is immutable after deployment. Hence, an undetected
bug can cause significant financial losses. Compiler optimization is also crucial,
because every action of a smart contract has to be executed by every node in the
Blockchain network. Therefore, optimizations in compiling smart contracts can
lead to significant savings in computation, time and energy.\r\n\r\nTwo classical
approaches in program analysis and compiler optimization are intraprocedural and
interprocedural analysis. In intraprocedural analysis, each function is analyzed
separately, while interprocedural analysis considers the entire program. In both
cases, the analyses are usually reduced to graph problems over the control flow
graph (CFG) of the program. These graph problems are often computationally expensive.
Hence, there has been ample research on exploiting structural properties of CFGs
for efficient algorithms. One such well-studied property is the treewidth, which
is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs
of structured programs have treewidth at most 6, whereas the interprocedural treewidth
cannot be bounded. This result has been used as a basis for many efficient intraprocedural
analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth
of smart contracts for formal analysis and compiler optimization. First, similar
to classical programs, we show that the intraprocedural treewidth of structured
Solidity and Vyper smart contracts is at most 9. Second, for global analysis,
we prove that the interprocedural treewidth of structured smart contracts is bounded
by 10 and, in sharp contrast with classical programs, treewidth-based algorithms
can be easily applied for interprocedural analysis. Finally, we supplement our
theoretical results with experiments using a tool we implemented for computing
treewidth of smart contracts and show that the treewidth is much lower in practice.
We use 36,764 real-world Ethereum smart contracts as benchmarks and find that
they have an average treewidth of at most 3.35 for the intraprocedural case and
3.65 for the interprocedural case.\r\n"
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
citation:
ama: 'Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts.
In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part
F147772. ACM; :400-408. doi:10.1145/3297280.3297322'
apa: 'Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (n.d.). The treewidth
of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing
(Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady.
“The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium
on Applied Computing, Part F147772:400–408. ACM, n.d. https://doi.org/10.1145/3297280.3297322.
ieee: K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart
contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing,
Limassol, Cyprus, vol. Part F147772, pp. 400–408.
ista: 'Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts.
Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on
Applied Computing vol. Part F147772, 400–408.'
mla: Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings
of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, pp.
400–08, doi:10.1145/3297280.3297322.
short: K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, n.d., pp. 400–408.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: 'SAC: Symposium on Applied Computing'
start_date: 2019-04-08
date_created: 2019-05-26T21:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3297280.3297322
external_id:
isi:
- '000474685800052'
file:
- access_level: open_access
checksum: dddc20f6d9881f23b8755eb720ec9d6f
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:50:11Z
date_updated: 2020-07-14T12:47:32Z
file_id: '7827'
file_name: 2019_ACM_Chatterjee.pdf
file_size: 6937138
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 400-408
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
- '9781450359337'
publication_status: submitted
publisher: ACM
pubrep_id: '1070'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The treewidth of smart contracts
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: Part F147772
year: '2019'
...
---
_id: '7158'
abstract:
- lang: eng
text: "Interprocedural analysis is at the heart of numerous applications in programming
languages, such as alias analysis, constant propagation, and so on. Recursive
state machines (RSMs) are standard models for interprocedural analysis. We consider
a general framework with RSMs where the transitions are labeled from a semiring
and path properties are algebraic with semiring operations. RSMs with algebraic
path properties can model interprocedural dataflow analysis problems, the shortest
path problem, the most probable path problem, and so on. The traditional algorithms
for interprocedural analysis focus on path properties where the starting point
is fixed as the entry point of a specific method. In this work, we consider possible
multiple queries as required in many applications such as in alias analysis. The
study of multiple queries allows us to bring in an important algorithmic distinction
between the resource usage of the one-time preprocessing vs for each individual
query. The second aspect we consider is that the control flow graphs for most
programs have constant treewidth.\r\n\r\nOur main contributions are simple and
implementable algorithms that support multiple queries for algebraic path properties
for RSMs that have constant treewidth. Our theoretical results show that our algorithms
have small additional one-time preprocessing but can answer subsequent queries
significantly faster as compared to the current algorithmic solutions for interprocedural
dataflow analysis. We have also implemented our algorithms and evaluated their
performance for performing on-demand interprocedural dataflow analysis on various
domains, such as for live variable analysis and reaching definitions, on a standard
benchmark set. Our experimental results align with our theoretical statements
and show that after a lightweight preprocessing, on-demand queries are answered
much faster than the standard existing algorithmic approaches.\r\n"
article_number: '23'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Prateesh
full_name: Goyal, Prateesh
last_name: Goyal
- 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: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster
algorithms for dynamic algebraic queries in basic RSMs with constant treewidth.
ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525
apa: Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis,
A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with
constant treewidth. ACM Transactions on Programming Languages and Systems.
ACM. https://doi.org/10.1145/3363525
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus
Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic
Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming
Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525.
ieee: K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis,
“Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,”
ACM Transactions on Programming Languages and Systems, vol. 41, no. 4.
ACM, 2019.
ista: Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019.
Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth.
ACM Transactions on Programming Languages and Systems. 41(4), 23.
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries
in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages
and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.
short: K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis,
ACM Transactions on Programming Languages and Systems 41 (2019).
date_created: 2019-12-09T08:33:33Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3363525
ec_funded: 1
external_id:
isi:
- '000564108400004'
file:
- access_level: open_access
checksum: 291cc86a07bd010d4815e177dac57b70
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T12:58:10Z
date_updated: 2020-10-08T12:58:10Z
file_id: '8632'
file_name: 2019_ACMTransactions_Chatterjee.pdf
file_size: 667357
relation: main_file
success: 1
file_date_updated: 2020-10-08T12:58:10Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted 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: 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'
publication: ACM Transactions on Programming Languages and Systems
publication_identifier:
issn:
- 0164-0925
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Faster algorithms for dynamic algebraic queries in basic RSMs with constant
treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2019'
...
---
_id: '7014'
abstract:
- lang: eng
text: "We study the problem of developing efficient approaches for proving\r\nworst-case
bounds of non-deterministic recursive programs. Ranking functions\r\nare sound
and complete for proving termination and worst-case bounds of\r\nnonrecursive
programs. First, we apply ranking functions to recursion,\r\nresulting in measure
functions. We show that measure functions provide a sound\r\nand complete approach
to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second
contribution is the synthesis of measure functions in\r\nnonpolynomial forms.
We show that non-polynomial measure functions with\r\nlogarithm and exponentiation
can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms,
Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous
methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds
of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$
is not an integer. We present\r\nexperimental results to demonstrate that our
approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms
such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair
problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii)
Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm
for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that
$r$ is not an integer and\r\nclose to the best-known bounds for the respective
algorithms."
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive
programs. ACM Transactions on Programming Languages and Systems. 2019;41(4).
doi:10.1145/3339984
apa: Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case
analysis of recursive programs. ACM Transactions on Programming Languages and
Systems. ACM. https://doi.org/10.1145/3339984
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial
Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming
Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.
ieee: K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis
of recursive programs,” ACM Transactions on Programming Languages and Systems,
vol. 41, no. 4. ACM, 2019.
ista: Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis
of recursive programs. ACM Transactions on Programming Languages and Systems.
41(4), 20.
mla: Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive
Programs.” ACM Transactions on Programming Languages and Systems, vol.
41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.
short: K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages
and Systems 41 (2019).
date_created: 2019-11-13T08:33:43Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3339984
ec_funded: 1
external_id:
arxiv:
- '1705.00317'
isi:
- '000564108400001'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.00317
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: ACM Transactions on Programming Languages and Systems
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '639'
relation: earlier_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-polynomial worst-case analysis of recursive programs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2019'
...
---
_id: '6486'
abstract:
- lang: eng
text: Based on a novel control scheme, where a steady modification of the streamwise
velocity profile leads to complete relaminarization of initially fully turbulent
pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs
for such control. The custom-shaped honeycombs are used as stationary flow management
devices which generate specific modifications of the streamwise velocity profile.
Stereoscopic particle image velocimetry and pressure drop measurements are used
to investigate and capture the development of the relaminarizing flow downstream
these devices. We compare the performance of straight (constant length across
the radius of the pipe) honeycombs with custom-shaped ones (variable length across
the radius) and try to determine the optimal shape for maximal relaminarization
at minimal pressure loss. The optimally modified streamwise velocity profile is
found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization
is found to be of the order of 10,000. Consequently, the respective reduction
in skin friction downstream of the device is almost by a factor of 5. The break-even
point, where the additional pressure drop caused by the device is balanced by
the savings due to relaminarization and a net gain is obtained, corresponds to
a downstream stretch of distances as low as approximately 100 pipe diameters of
laminar flow.
acknowledged_ssus:
- _id: M-Shop
article_number: '111105'
article_processing_charge: No
article_type: original
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed
shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494
apa: Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow
by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering.
ASME. https://doi.org/10.1115/1.4043494
chicago: Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe
Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering.
ASME, 2019. https://doi.org/10.1115/1.4043494.
ieee: J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means
of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141,
no. 11. ASME, 2019.
ista: Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means
of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.
mla: Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed
Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105,
ASME, 2019, doi:10.1115/1.4043494.
short: J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).
date_created: 2019-05-26T21:59:13Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2024-03-28T23:30:36Z
day: '01'
department:
- _id: BjHo
doi: 10.1115/1.4043494
ec_funded: 1
external_id:
arxiv:
- '1809.07625'
isi:
- '000487748600005'
intvolume: ' 141'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.07625
month: '11'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluids Engineering
publication_identifier:
eissn:
- 1528901X
issn:
- '00982202'
publication_status: published
publisher: ASME
quality_controlled: '1'
related_material:
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarization of pipe flow by means of 3D-printed shaped honeycombs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 141
year: '2019'
...
---
_id: '6228'
abstract:
- lang: eng
text: Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.
article_processing_charge: No
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal
of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191
apa: Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by
wall movement. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2019.191
chicago: Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow
by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press,
2019. https://doi.org/10.1017/jfm.2019.191.
ieee: D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,”
Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948,
2019.
ista: Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement.
Journal of Fluid Mechanics. 867, 934–948.
mla: Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal
of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48,
doi:10.1017/jfm.2019.191.
short: D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.
date_created: 2019-04-07T21:59:14Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2024-03-28T23:30:36Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2019.191
ec_funded: 1
external_id:
arxiv:
- '1807.05357'
isi:
- '000462606100001'
intvolume: ' 867'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05357
month: '05'
oa: 1
oa_version: Preprint
page: 934-948
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 25104D44-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '737549'
name: Eliminating turbulence in oil pipelines
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- '14697645'
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.1017/jfm.2019.191
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarising pipe flow by wall movement
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 867
year: '2019'
...
---
_id: '6260'
abstract:
- lang: eng
text: Polar auxin transport plays a pivotal role in plant growth and development.
PIN auxin efflux carriers regulate directional auxin movement by establishing
local auxin maxima, minima, and gradients that drive multiple developmental processes
and responses to environmental signals. Auxin has been proposed to modulate its
own transport by regulating subcellular PIN trafficking via processes such as
clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further
investigated the mechanisms by which auxin affects PIN trafficking by screening
auxin analogs and identified pinstatic acid (PISA) as a positive modulator of
polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on
hypocotyl elongation and adventitious root formation via positive regulation of
auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN
accumulation at the cell surface by inhibiting PIN internalization from the plasma
membrane. This work demonstrates PISA to be a promising chemical tool to dissect
the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.
acknowledgement: "We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden
University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University
of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis
work was supported by the Ministry of Education, Culture, Sports, Science, and Technology
(Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology
and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.),
and the European Union’s Horizon2020 program (European Research Council grant agreement
no. 742985 to J.F.)."
article_processing_charge: No
article_type: original
author:
- first_name: A
full_name: Oochi, A
last_name: Oochi
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: K
full_name: Fukui, K
last_name: Fukui
- first_name: Y
full_name: Nakao, Y
last_name: Nakao
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: M
full_name: Quareshy, M
last_name: Quareshy
- first_name: K
full_name: Takahashi, K
last_name: Takahashi
- first_name: T
full_name: Kinoshita, T
last_name: Kinoshita
- first_name: SR
full_name: Harborough, SR
last_name: Harborough
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
- first_name: H
full_name: Kasahara, H
last_name: Kasahara
- first_name: RM
full_name: Napier, RM
last_name: Napier
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: KI
full_name: Hayashi, KI
last_name: Hayashi
citation:
ama: Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by
inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165.
doi:10.1104/pp.19.00201
apa: Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., …
Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN
internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201
chicago: Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy,
K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.
ieee: A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting
PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165,
2019.
ista: Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita
T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic
acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology.
180(2), 1152–1165.
mla: Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65,
doi:10.1104/pp.19.00201.
short: A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi,
T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K.
Hayashi, Plant Physiology 180 (2019) 1152–1165.
date_created: 2019-04-09T08:38:20Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2024-03-28T23:30:38Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.19.00201
ec_funded: 1
external_id:
isi:
- '000470086100045'
pmid:
- '30936248'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.19.00201
month: '06'
oa: 1
oa_version: Published Version
page: 1152-1165
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: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Pinstatic acid promotes auxin transport by inhibiting PIN internalization
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
_id: '6508'
abstract:
- lang: eng
text: Segregation of maternal determinants within the oocyte constitutes the first
step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming
leads to the segregation of ooplasm from yolk granules along the animal-vegetal
axis of the oocyte. Here, we show that this process does not rely on cortical
actin reorganization, as previously thought, but instead on a cell-cycle-dependent
bulk actin polymerization wave traveling from the animal to the vegetal pole of
the oocyte. This wave functions in segregation by both pulling ooplasm animally
and pushing yolk granules vegetally. Using biophysical experimentation and theory,
we show that ooplasm pulling is mediated by bulk actin network flows exerting
friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism
closely resembling actin comet formation on yolk granules. Our study defines a
novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte
polarization via ooplasmic segregation.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia
Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with
zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful
discussions, and the Bioimaging and zebrafish facilities at IST Austria for their
continuous support. This project has received funding from the European Union (European
Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science
Fund (FWF) (P 31639 to E.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin
dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18.
doi:10.1016/j.cell.2019.04.030
apa: Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg,
C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030
chicago: Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo,
and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in
Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.
ieee: S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg,
“Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell,
vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.
ista: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk
actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.
mla: Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.
short: S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg,
Cell 177 (2019) 1463–1479.e18.
date_created: 2019-06-02T21:59:12Z
date_published: 2019-05-30T00:00:00Z
date_updated: 2024-03-28T23:30:39Z
day: '30'
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id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
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- first_name: Shayan
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id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
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id: 39427864-F248-11E8-B48F-1D18A9856A87
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citation:
ama: Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight
junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18.
doi:10.1016/j.cell.2019.10.006
apa: Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada,
M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends
on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006
chicago: Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra
Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation
of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell
Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.
ieee: C. Schwayer et al., “Mechanosensation of tight junctions depends on
ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p.
937–952.e18, 2019.
ista: Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter
K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1
phase separation and flow. Cell. 179(4), 937–952.e18.
mla: Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on
ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019,
p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.
short: C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada,
K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.
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