---
_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
checksum: 773beaf4a85dc2acc2c12b578fbe1965
content_type: application/pdf
creator: mgiacobbe
date_created: 2019-09-27T14:15:05Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6916'
file_name: giacobbe_thesis.pdf
file_size: 4100685
relation: main_file
- access_level: closed
checksum: 97f1c3da71feefd27e6e625d32b4c75b
content_type: application/gzip
creator: mgiacobbe
date_created: 2019-09-27T14:22:04Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6917'
file_name: giacobbe_thesis_src.tar.gz
file_size: 7959732
relation: source_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
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
issue: '2'
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:
- access_level: closed
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
- access_level: open_access
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
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
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'
...