---
_id: '7000'
abstract:
- lang: eng
text: The main contributions of this paper are the proposition and the convergence
analysis of a class of inertial projection-type algorithm for solving variational
inequality problems in real Hilbert spaces where the underline operator is monotone
and uniformly continuous. We carry out a unified analysis of the proposed method
under very mild assumptions. In particular, weak convergence of the generated
sequence is established and nonasymptotic O(1 / n) rate of convergence is established,
where n denotes the iteration counter. We also present some experimental results
to illustrate the profits gained by introducing the inertial extrapolation steps.
article_number: '161'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Xiao-Huan
full_name: Li, Xiao-Huan
last_name: Li
- first_name: Qiao-Li
full_name: Dong, Qiao-Li
last_name: Dong
citation:
ama: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method
for variational inequalities. Computational and Applied Mathematics. 2019;38(4).
doi:10.1007/s40314-019-0955-9
apa: Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence
analysis of projection method for variational inequalities. Computational and
Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9
chicago: Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence
Analysis of Projection Method for Variational Inequalities.” Computational
and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.
ieee: Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of
projection method for variational inequalities,” Computational and Applied
Mathematics, vol. 38, no. 4. Springer Nature, 2019.
ista: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection
method for variational inequalities. Computational and Applied Mathematics. 38(4),
161.
mla: Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational
Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161,
Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.
short: Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics
38 (2019).
date_created: 2019-11-12T12:41:44Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:20:32Z
day: '01'
ddc:
- '510'
- '515'
- '518'
department:
- _id: VlKo
doi: 10.1007/s40314-019-0955-9
ec_funded: 1
external_id:
arxiv:
- '2101.09081'
isi:
- '000488973100005'
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s40314-019-0955-9
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Computational and Applied Mathematics
publication_identifier:
eissn:
- 1807-0302
issn:
- 2238-3603
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence analysis of projection method for variational inequalities
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '7001'
acknowledged_ssus:
- _id: PreCl
- _id: Bio
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: M
full_name: Balda, M
last_name: Balda
- first_name: M
full_name: Tada, M
last_name: Tada
- first_name: K
full_name: Matter, K
last_name: Matter
- 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: 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.
date_created: 2019-11-12T12:51:06Z
date_published: 2019-10-31T00:00:00Z
date_updated: 2024-03-25T23:30:21Z
day: '31'
ddc:
- '570'
department:
- _id: CaHe
- _id: BjHo
doi: 10.1016/j.cell.2019.10.006
ec_funded: 1
external_id:
isi:
- '000493898000012'
pmid:
- '31675500'
file:
- access_level: open_access
checksum: 33dac4bb77ee630e2666e936b4d57980
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T07:09:45Z
date_updated: 2020-10-21T07:09:45Z
file_id: '8684'
file_name: 2019_Cell_Schwayer_accepted.pdf
file_size: 8805878
relation: main_file
success: 1
file_date_updated: 2020-10-21T07:09:45Z
has_accepted_license: '1'
intvolume: ' 179'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 937-952.e18
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
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News auf IST Website
relation: press_release
url: https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/
record:
- id: '7186'
relation: dissertation_contains
status: public
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 179
year: '2019'
...
---
_id: '7002'
abstract:
- lang: eng
text: Multiple Importance Sampling (MIS) is a key technique for achieving robustness
of Monte Carlo estimators in computer graphics and other fields. We derive optimal
weighting functions for MIS that provably minimize the variance of an MIS estimator,
given a set of sampling techniques. We show that the resulting variance reduction
over the balance heuristic can be higher than predicted by the variance bounds
derived by Veach and Guibas, who assumed only non-negative weights in their proof.
We theoretically analyze the variance of the optimal MIS weights and show the
relation to the variance of the balance heuristic. Furthermore, we establish a
connection between the new weighting functions and control variates as previously
applied to mixture sampling. We apply the new optimal weights to integration problems
in light transport and show that they allow for new design considerations when
choosing the appropriate sampling techniques for a given integration problem.
article_number: '37'
article_processing_charge: No
article_type: original
author:
- first_name: Ivo
full_name: Kondapaneni, Ivo
last_name: Kondapaneni
- first_name: Petr
full_name: Vevoda, Petr
last_name: Vevoda
- first_name: Pascal
full_name: Grittmann, Pascal
last_name: Grittmann
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Philipp
full_name: Slusallek, Philipp
last_name: Slusallek
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
citation:
ama: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal
multiple importance sampling. ACM Transactions on Graphics. 2019;38(4).
doi:10.1145/3306346.3323009
apa: Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., &
Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3306346.3323009
chicago: Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp
Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM
Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.
ieee: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J.
Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics,
vol. 38, no. 4. ACM, 2019.
ista: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J.
2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4),
37.
mla: Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions
on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.
short: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek,
ACM Transactions on Graphics 38 (2019).
date_created: 2019-11-12T13:05:40Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-30T07:21:25Z
day: '01'
department:
- _id: ChWo
doi: 10.1145/3306346.3323009
ec_funded: 1
external_id:
isi:
- '000475740600011'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal multiple importance sampling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '7005'
abstract:
- lang: eng
text: Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during
intense neuronal activity via a two-step process. First, bulk endosomes are formed
direct from the plasma membrane from which SVs are then generated. SV generation
from bulk endosomes requires the efflux of previously accumulated calcium and
activation of the protein phosphatase calcineurin. However, it is still unknown
how calcineurin mediates SV generation. We addressed this question using a series
of acute interventions that decoupled the generation of SVs from bulk endosomes
in rat primary neuronal culture. This was achieved by either disruption of protein–protein
interactions via delivery of competitive peptides, or inhibition of enzyme activity
by known inhibitors. SV generation was monitored using either a morphological
horseradish peroxidase assay or an optical assay that monitors the replenishment
of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides
that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity
and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin
I interaction. Peptides that disrupted syndapin I interactions with eps15 homology
domain-containing proteins had no effect. This revealed that (i) calcineurin must
be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity
is essential for SV fission and (iii) the calcineurin-dependent interaction between
dynamin I and syndapin I is essential for SV generation. We therefore propose
that a calcineurin-dependent dephosphorylation cascade that requires both dynamin
I GTPase and syndapin I lipid-deforming activity is essential for SV generation
from bulk endosomes.
article_processing_charge: No
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Michael A.
full_name: Cousin, Michael A.
last_name: Cousin
citation:
ama: Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk
endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862
apa: Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from
activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin
interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862
chicago: Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation
from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent
Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019.
https://doi.org/10.1111/jnc.14862.
ieee: G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,”
Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.
ista: Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 151(5), 570–583.
mla: Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from
Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin
Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019,
pp. 570–83, doi:10.1111/jnc.14862.
short: G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.
date_created: 2019-11-12T14:37:08Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:21:50Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1111/jnc.14862
external_id:
isi:
- '000490703100001'
pmid:
- '31479508'
file:
- access_level: open_access
checksum: ec1fb2aebb874009bc309adaada6e1d7
content_type: application/pdf
creator: dernst
date_created: 2020-02-05T10:30:02Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7452'
file_name: 2019_JournNeurochemistry_Cheung.pdf
file_size: 4334962
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 570-583
pmid: 1
publication: Journal of Neurochemistry
publication_identifier:
eissn:
- 1471-4159
issn:
- 0022-3042
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptic vesicle generation from activity‐dependent bulk endosomes requires
a dephosphorylation‐dependent dynamin–syndapin interaction
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: 151
year: '2019'
...
---
_id: '7007'
abstract:
- lang: eng
text: 'We consider the primitive relay channel, where the source sends a message
to the relay and to the destination, and the relay helps the communication by
transmitting an additional message to the destination via a separate channel.
Two well-known coding techniques have been introduced for this setting: decode-and-forward
and compress-and-forward. In decode-and-forward, the relay completely decodes
the message and sends some information to the destination; in compress-and-forward,
the relay does not decode, and it sends a compressed version of the received signal
to the destination using Wyner–Ziv coding. In this paper, we present a novel coding
paradigm that provides an improved achievable rate for the primitive relay channel.
The idea is to combine compress-and-forward and decode-and-forward via a chaining
construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward;
and, in the second block, we use decode-and-forward. More specifically, in the
first block, the relay does not decode, it compresses the received signal via
Wyner–Ziv, and it sends only part of the compression to the destination. In the
second block, the relay completely decodes the message, it sends some information
to the destination, and it also sends the remaining part of the compression coming
from the first block. By doing so, we are able to strictly outperform both compress-and-forward
and decode-and-forward. Note that the proposed coding scheme can be implemented
with polar codes. As such, it has the typical attractive properties of polar coding
schemes, namely, quasi-linear encoding and decoding complexity, and error probability
that decays at super-polynomial speed. As a running example, we take into account
the special case of the erasure relay channel, and we provide a comparison between
the rates achievable by our proposed scheme and the existing upper and lower bounds.'
article_number: '218'
article_type: original
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Rüdiger
full_name: Urbanke, Rüdiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive
relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218
apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm
for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218
chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.
ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the
primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.
ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive
relay channel. Algorithms. 12(10), 218.
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.
short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).
date_created: 2019-11-12T14:46:19Z
date_published: 2019-10-18T00:00:00Z
date_updated: 2023-02-23T12:49:28Z
day: '18'
ddc:
- '510'
department:
- _id: MaMo
doi: 10.3390/a12100218
external_id:
arxiv:
- '1801.03153'
file:
- access_level: open_access
checksum: 267756d8f9db572f496cd1663c89d59a
content_type: application/pdf
creator: dernst
date_created: 2019-11-12T14:48:45Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7008'
file_name: 2019_Algorithms_Mondelli.pdf
file_size: 696791
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Algorithms
publication_identifier:
issn:
- 1999-4893
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '6675'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A new coding paradigm for the primitive relay channel
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: 12
year: '2019'
...
---
_id: '7009'
abstract:
- lang: eng
text: Cell migration is essential for physiological processes as diverse as development,
immune defence and wound healing. It is also a hallmark of cancer malignancy.
Thousands of publications have elucidated detailed molecular and biophysical mechanisms
of cultured cells migrating on flat, 2D substrates of glass and plastic. However,
much less is known about how cells successfully navigate the complex 3D environments
of living tissues. In these more complex, native environments, cells use multiple
modes of migration, including mesenchymal, amoeboid, lobopodial and collective,
and these are governed by the local extracellular microenvironment, specific modalities
of Rho GTPase signalling and non- muscle myosin contractility. Migration through
3D environments is challenging because it requires the cell to squeeze through
complex or dense extracellular structures. Doing so requires specific cellular
adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling.
In addition, besides navigating through diverse ECM environments and overcoming
extracellular barriers, cells often interact with neighbouring cells and tissues
through physical and signalling interactions. Accordingly, cells need to call
on an impressively wide diversity of mechanisms to meet these challenges. This
Review examines how cells use both classical and novel mechanisms of locomotion
as they traverse challenging 3D matrices and cellular environments. It focuses
on principles rather than details of migratory mechanisms and draws comparisons
between 1D, 2D and 3D migration.
article_processing_charge: No
article_type: review
author:
- first_name: KM
full_name: Yamada, KM
last_name: Yamada
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular
Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9
apa: Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature
Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9
chicago: Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature
Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.
ieee: K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews
Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.
ista: Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular
Cell Biology. 20(12), 738–752.
mla: Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature
Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp.
738–752, doi:10.1038/s41580-019-0172-9.
short: K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.
date_created: 2019-11-12T14:54:42Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:22:20Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41580-019-0172-9
external_id:
isi:
- '000497966900007'
pmid:
- '31582855'
intvolume: ' 20'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 738–752
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
eissn:
- 1471-0080
issn:
- 1471-0072
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms of 3D cell migration
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2019'
...
---
_id: '7010'
abstract:
- lang: eng
text: Numerous biophysical questions require the quantification of short-range interactions
between (functionalized) surfaces and synthetic or biological objects such as
cells. Here, we present an original, custom built setup for reflection interference
contrast microscopy that can assess distances between a substrate and a flowing
object at high speed with nanometric accuracy. We demonstrate its use to decipher
the complex biochemical and mechanical interplay regulating blood cell homing
at the vessel wall in the microcirculation using an in vitro approach. We show
that in the absence of specific biochemical interactions, flowing cells are repelled
from the soft layer lining the vessel wall, contributing to red blood cell repulsion
in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under
flow in the presence of a specific receptor naturally present on activated leucocytes
and a number of cancer cell lines.
article_number: 110760V
article_processing_charge: No
author:
- first_name: Heather S.
full_name: Davies, Heather S.
last_name: Davies
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Nouha
full_name: El Amri, Nouha
last_name: El Amri
- first_name: Liliane
full_name: Coche-Guérente, Liliane
last_name: Coche-Guérente
- first_name: Claude
full_name: Verdier, Claude
last_name: Verdier
- first_name: Lionel
full_name: Bureau, Lionel
last_name: Bureau
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
- first_name: Delphine
full_name: Débarre, Delphine
last_name: Débarre
citation:
ama: 'Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions
probed by reflection interference contrast microscopy. In: Advances in Microscopic
Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058'
apa: 'Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier,
C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed
by reflection interference contrast microscopy. In Advances in Microscopic
Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058'
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel
Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances
in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058.
ieee: H. S. Davies et al., “Blood cell-vessel wall interactions probed by
reflection interference contrast microscopy,” in Advances in Microscopic Imaging
II, Munich, Germany, 2019, vol. 11076.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection
interference contrast microscopy. Advances in Microscopic Imaging II. European
Conferences on Biomedical Optics vol. 11076, 110760V.
mla: Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection
Interference Contrast Microscopy.” Advances in Microscopic Imaging II,
vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE,
2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: European Conferences on Biomedical Optics
start_date: 2019-06-26
date_created: 2019-11-12T15:10:18Z
date_published: 2019-07-22T00:00:00Z
date_updated: 2023-08-29T06:54:38Z
day: '22'
department:
- _id: MaLo
doi: 10.1117/12.2527058
external_id:
isi:
- '000535353000023'
intvolume: ' 11076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf
month: '07'
oa: 1
oa_version: Published Version
publication: Advances in Microscopic Imaging II
publication_identifier:
isbn:
- '9781510628458'
issn:
- 1605-7422
publication_status: published
publisher: SPIE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Blood cell-vessel wall interactions probed by reflection interference contrast
microscopy
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11076
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
arxiv: 1
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: '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
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: 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: 2025-06-02T08:53:47Z
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: '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
arxiv: 1
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: '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:
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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
- access_level: open_access
checksum: 5b227708ff478ca06e3f0448a4efdc2f
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: '7026'
abstract:
- lang: eng
text: Effective design of combination therapies requires understanding the changes
in cell physiology that result from drug interactions. Here, we show that the
genome-wide transcriptional response to combinations of two drugs, measured at
a rigorously controlled growth rate, can predict higher-order antagonism with
a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90%
of the variation in cellular response can be decomposed into three principal components
(PCs) that have clear biological interpretations. We demonstrate that the third
PC captures emergent transcriptional programs that are dependent on both drugs
and can predict antagonism with a third drug targeting the emergent pathway. We
further show that emergent gene expression patterns are most pronounced at a drug
ratio where the drug interaction is strongest, providing a guideline for future
measurements. Our results provide a readily applicable recipe for uncovering emergent
responses in other systems and for higher-order drug combinations. A record of
this paper’s transparent peer review process is included in the Supplemental Information.
acknowledged_ssus:
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations
predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3.
doi:10.1016/j.cels.2019.10.004
apa: Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses
to drug combinations predict higher-order drug interactions. Cell Systems.
Cell Press. https://doi.org/10.1016/j.cels.2019.10.004
chicago: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression
Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell
Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.
ieee: M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to
drug combinations predict higher-order drug interactions,” Cell Systems,
vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.
ista: Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug
combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.
mla: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses
to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems,
vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.
short: M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.
date_created: 2019-11-15T10:51:42Z
date_published: 2019-11-27T00:00:00Z
date_updated: 2023-08-30T07:24:58Z
day: '27'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.cels.2019.10.004
external_id:
isi:
- '000499495400003'
file:
- access_level: open_access
checksum: 7a11d6c2f9523d65b049512d61733178
content_type: application/pdf
creator: dernst
date_created: 2019-11-15T10:57:42Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7027'
file_name: 2019_CellSystems_Lukacisin.pdf
file_size: 4238460
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 423-433.e1-e3
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- 2405-4712
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent gene expression responses to drug combinations predict higher-order
drug interactions
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: 9
year: '2019'
...
---
_id: '7032'
abstract:
- lang: eng
text: Optical frequency combs (OFCs) are light sources whose spectra consists of
equally spaced frequency lines in the optical domain [1]. They have great potential
for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy,
and high-precision measurements [2].
article_number: '8873300'
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: Kuamri, Madhuri
last_name: Kuamri
- first_name: Harald G. L.
full_name: Schwefel, Harald G. L.
last_name: Schwefel
citation:
ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic
frequency comb generation in lithium niobate whispering gallery mode resonators.
In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300'
apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel,
H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering
gallery mode resonators. In 2019 Conference on Lasers and Electro-Optics Europe
& European Quantum Electronics Conference. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300'
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri,
and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium
Niobate Whispering Gallery Mode Resonators.” In 2019 Conference on Lasers and
Electro-Optics Europe & European Quantum Electronics Conference. IEEE,
2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel,
“Electro-optic frequency comb generation in lithium niobate whispering gallery
mode resonators,” in 2019 Conference on Lasers and Electro-Optics Europe &
European Quantum Electronics Conference, Munich, Germany, 2019.
ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic
frequency comb generation in lithium niobate whispering gallery mode resonators.
2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics
Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.'
mla: Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation
in Lithium Niobate Whispering Gallery Mode Resonators.” 2019 Conference on
Lasers and Electro-Optics Europe & European Quantum Electronics Conference,
8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300.
short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:,
2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics
Conference, IEEE, 2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: 'CLEO: Conference on Lasers and Electro-Optics Europe'
start_date: 2019-06-23
date_created: 2019-11-18T13:58:22Z
date_published: 2019-10-17T00:00:00Z
date_updated: 2023-08-30T07:26:01Z
day: '17'
department:
- _id: JoFi
doi: 10.1109/cleoe-eqec.2019.8873300
external_id:
isi:
- '000630002701617'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference
publication_identifier:
isbn:
- '9781728104690'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electro-optic frequency comb generation in lithium niobate whispering gallery
mode resonators
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7034'
abstract:
- lang: eng
text: We find a graph of genus 5 and its drawing on the orientable surface of genus
4 with every pair of independent edges crossing an even number of times. This
shows that the strong Hanani–Tutte theorem cannot be extended to the orientable
surface of genus 4. As a base step in the construction we use a counterexample
to an extension of the unified Hanani–Tutte theorem on the torus.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem
on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7
apa: Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7
chicago: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the
Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer
Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7.
ieee: R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer
Nature, pp. 1267–1279, 2019.
ista: Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.
mla: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte
Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer
Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.
short: R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.
date_created: 2019-11-18T14:29:50Z
date_published: 2019-10-29T00:00:00Z
date_updated: 2023-08-30T07:26:25Z
day: '29'
department:
- _id: UlWa
doi: 10.1007/s00493-019-3905-7
ec_funded: 1
external_id:
arxiv:
- '1709.00508'
isi:
- '000493267200003'
intvolume: ' 39'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.00508
month: '10'
oa: 1
oa_version: Preprint
page: 1267-1279
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Combinatorica
publication_identifier:
eissn:
- 1439-6912
issn:
- 0209-9683
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counterexample to an extension of the Hanani-Tutte theorem on the surface of
genus 4
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2019'
...
---
_id: '7035'
abstract:
- lang: eng
text: 'The aim of this short note is to expound one particular issue that was discussed
during the talk [10] given at the symposium ”Researches on isometries as preserver
problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses
by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new
results.From an isometric point of view, in some cases, metric spaces of measures
are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations
of the underlying space. Of course, it depends on the particular choice of the metric how nice these
transformations should be. Sometimes, as we will see, being a homeomorphism is
enough to generate an isometry. But sometimes we need more: the transformation
must preserve the underlying distance as well. Statements claiming that isometries
in questions are necessarily induced by homeomorphisms are called Banach-Stone-type
results, while results asserting that the underlying transformation is necessarily
an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural
question arises:Is it enough to understand how an isometry acts on the set of
Dirac masses? Does this action extend uniquely to all measures?In what follows,
we will thoroughly investigate this question.'
article_processing_charge: No
author:
- first_name: Gyorgy Pal
full_name: Geher, Gyorgy Pal
last_name: Geher
- first_name: Tamas
full_name: Titkos, Tamas
last_name: Titkos
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: 'Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In:
Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences,
Kyoto University; 2019:34-41.'
apa: 'Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric
rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan:
Research Institute for Mathematical Sciences, Kyoto University.'
chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and
Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute
for Mathematical Sciences, Kyoto University, 2019.
ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,”
in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.
ista: Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity.
Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related
topics vol. 2125, 34–41.
mla: Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS
Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto
University, 2019, pp. 34–41.
short: G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research
Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.
conference:
end_date: 2019-01-30
location: Kyoto, Japan
name: Research on isometries as preserver problems and related topics
start_date: 2019-01-28
date_created: 2019-11-18T15:39:53Z
date_published: 2019-01-30T00:00:00Z
date_updated: 2021-01-12T08:11:33Z
day: '30'
department:
- _id: LaEr
intvolume: ' 2125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html
month: '01'
oa: 1
oa_version: Submitted Version
page: 34-41
publication: Kyoto RIMS Kôkyûroku
publication_status: published
publisher: Research Institute for Mathematical Sciences, Kyoto University
quality_controlled: '1'
status: public
title: Dirac masses and isometric rigidity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2125
year: '2019'
...
---
_id: '7093'
abstract:
- lang: eng
text: "In graph theory, as well as in 3-manifold topology, there exist several width-type
parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold
is. These parameters, such as pathwidth or treewidth for graphs, or the concept
of thin position for 3-manifolds, play an important role when studying algorithmic
problems; in particular, there is a variety of problems in computational 3-manifold
topology - some of them known to be computationally hard in general - that become
solvable in polynomial time as soon as the dual graph of the input triangulation
has bounded treewidth.\r\nIn view of these algorithmic results, it is natural
to ask whether every 3-manifold admits a triangulation of bounded treewidth. We
show that this is not the case, i.e., that there exists an infinite family of
closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth
(the latter implies the former, but we present two separate proofs).\r\nWe derive
these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann,
Schultens and Saito by exhibiting explicit connections between the topology of
a 3-manifold M on the one hand and width-type parameters of the dual graphs of
triangulations of M on the other hand, answering a question that had been raised
repeatedly by researchers in computational 3-manifold topology. In particular,
we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has
a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M
is at most 18(k+1) (resp. 4(3k+1))."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Jonathan
full_name: Spreer, Jonathan
last_name: Spreer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds.
Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5
apa: Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated
3-manifolds. Journal of Computational Geometry. Computational Geometry
Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5
chicago: Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of
Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational
Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5.
ieee: K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,”
Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry
Laborartoy, pp. 70–98, 2019.
ista: Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds.
Journal of Computational Geometry. 10(2), 70–98.
mla: Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal
of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy,
2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5.
short: K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019)
70–98.
date_created: 2019-11-23T12:14:09Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-07T13:18:26Z
day: '01'
ddc:
- '514'
department:
- _id: UlWa
doi: 10.20382/JOGC.V10I2A5
external_id:
arxiv:
- '1712.00434'
file:
- access_level: open_access
checksum: c872d590d38d538404782bca20c4c3f5
content_type: application/pdf
creator: khuszar
date_created: 2019-11-23T12:35:16Z
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intvolume: ' 10'
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language:
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month: '11'
oa: 1
oa_version: Published Version
page: 70–98
publication: Journal of Computational Geometry
publication_identifier:
issn:
- 1920-180X
publication_status: published
publisher: Computational Geometry Laborartoy
quality_controlled: '1'
related_material:
record:
- id: '285'
relation: earlier_version
status: public
- id: '8032'
relation: part_of_dissertation
status: public
status: public
title: On the treewidth of triangulated 3-manifolds
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: 10
year: '2019'
...
---
_id: '7095'
abstract:
- lang: eng
text: BAX, a member of the BCL2 gene family, controls the committed step of the
intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed
feature of apoptosis, which occurs through the process of mitochondrial fission.
BAX has consistently been associated with mitochondrial fission, yet how BAX participates
in the process of mitochondrial fragmentation during apoptosis remains to be tested.
Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates
that rapid mitochondrial fragmentation during apoptosis occurs after the complete
recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement
of a fully functioning BAX protein for the fission process was demonstrated further
in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant
performed fusion to restore the mitochondrial network. but was not demonstrably
recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial
fragmentation was blocked. Additionally, we show that loss of the fission protein,
dynamin-like protein 1 (DRP1), does not temporally affect the initiation time
or rate of BAX recruitment, but does reduce the final level of BAX recruited to
the MOM during the late phase of BAX recruitment. These correlative observations
suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial
fragmentation machinery in apoptotic cells.
article_number: '16565'
article_processing_charge: No
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: J. A.
full_name: Grosser, J. A.
last_name: Grosser
- first_name: R. L.
full_name: Fehrman, R. L.
last_name: Fehrman
- first_name: C. L.
full_name: Schlamp, C. L.
last_name: Schlamp
- first_name: R. W.
full_name: Nickells, R. W.
last_name: Nickells
citation:
ama: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX
recruitment correlates with mitochondrial fission during apoptosis. Scientific
Reports. 2019;9. doi:10.1038/s41598-019-53049-w
apa: Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells,
R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission
during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w
chicago: Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W.
Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission
during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w.
ieee: M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells,
“Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,”
Scientific Reports, vol. 9. Springer Nature, 2019.
ista: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion
of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific
Reports. 9, 16565.
mla: Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial
Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer
Nature, 2019, doi:10.1038/s41598-019-53049-w.
short: M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific
Reports 9 (2019).
date_created: 2019-11-25T07:45:17Z
date_published: 2019-11-12T00:00:00Z
date_updated: 2023-08-30T07:26:54Z
day: '12'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41598-019-53049-w
external_id:
isi:
- '000495857600019'
pmid:
- '31719602'
file:
- access_level: open_access
checksum: 9ab397ed9c1c454b34bffb8cc863d734
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T07:49:52Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7096'
file_name: 2019_ScientificReports_Maes.pdf
file_size: 6467393
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has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Completion of BAX recruitment correlates with mitochondrial fission during
apoptosis
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: 9
year: '2019'
...
---
_id: '7097'
abstract:
- lang: eng
text: Early endosomes, also called sorting endosomes, are known to mature into late
endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early
endosome existence isthought to be maintained by the continual fusion of transport
vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show
instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial
for the formation of endosomes andthe subsequent endolysosomal traffic regulated
by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide
exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p
and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components
is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and
the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation
and identify the TGN as a critical location forregulating progress through the
endolysosomal trafficking pathway.
article_number: '419'
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- 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: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation
is regulated at the trans-Golgi network. Communications Biology. 2019;2(1).
doi:10.1038/s42003-019-0670-5
apa: Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated
endosome formation is regulated at the trans-Golgi network. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5
chicago: Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated
Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications
Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.
ieee: M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome
formation is regulated at the trans-Golgi network,” Communications Biology,
vol. 2, no. 1. Springer Nature, 2019.
ista: Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome
formation is regulated at the trans-Golgi network. Communications Biology. 2(1),
419.
mla: Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the
Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer
Nature, 2019, doi:10.1038/s42003-019-0670-5.
short: M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology
2 (2019).
date_created: 2019-11-25T07:55:01Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2023-08-30T07:27:55Z
day: '15'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1038/s42003-019-0670-5
external_id:
isi:
- '000496767800005'
file:
- access_level: open_access
checksum: c63c69a264fc8a0e52f2b0d482f3bdae
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T07:58:05Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7098'
file_name: 2019_CommunicBiology_Nagano.pdf
file_size: 2626069
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rab5-mediated endosome formation is regulated at the trans-Golgi network
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: 2
year: '2019'
...
---
_id: '7099'
acknowledgement: "The authors thank Gabi Schmid for excellent technical support. We
also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the
specificity\r\nof some of the antibodies used in this study on replicas. Funding
was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung)
Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.),
and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National
Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous
version of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Kasugai, Yu
last_name: Kasugai
- first_name: Elisabeth
full_name: Vogel, Elisabeth
last_name: Vogel
- first_name: Heide
full_name: Hörtnagl, Heide
last_name: Hörtnagl
- first_name: Sabine
full_name: Schönherr, Sabine
last_name: Schönherr
- first_name: Enrica
full_name: Paradiso, Enrica
last_name: Paradiso
- first_name: Markus
full_name: Hauschild, Markus
last_name: Hauschild
- first_name: Georg
full_name: Göbel, Georg
last_name: Göbel
- first_name: Ivan
full_name: Milenkovic, Ivan
last_name: Milenkovic
- first_name: Yvan
full_name: Peterschmitt, Yvan
last_name: Peterschmitt
- first_name: Ramon
full_name: Tasan, Ramon
last_name: Tasan
- first_name: Günther
full_name: Sperk, Günther
last_name: Sperk
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Werner
full_name: Sieghart, Werner
last_name: Sieghart
- first_name: Nicolas
full_name: Singewald, Nicolas
last_name: Singewald
- first_name: Andreas
full_name: Lüthi, Andreas
last_name: Lüthi
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
citation:
ama: Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling
of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4.
doi:10.1016/j.neuron.2019.08.013
apa: Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild,
M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic
synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013
chicago: Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica
Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling
of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier,
2019. https://doi.org/10.1016/j.neuron.2019.08.013.
ieee: Y. Kasugai et al., “Structural and functional remodeling of amygdala
GABAergic synapses in associative fear learning,” Neuron, vol. 104, no.
4. Elsevier, p. 781–794.e4, 2019.
ista: Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel
G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald
N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala
GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.
mla: Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic
Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier,
2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013.
short: Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild,
G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W.
Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.
date_created: 2019-11-25T08:02:39Z
date_published: 2019-11-20T00:00:00Z
date_updated: 2023-08-30T07:28:22Z
day: '20'
ddc:
- '571'
- '599'
department:
- _id: RySh
doi: 10.1016/j.neuron.2019.08.013
external_id:
isi:
- '000497963500017'
pmid:
- '31543297'
has_accepted_license: '1'
intvolume: ' 104'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.08.013
month: '11'
oa: 1
oa_version: Published Version
page: 781-794.e4
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural and functional remodeling of amygdala GABAergic synapses in associative
fear learning
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2019'
...
---
_id: '7100'
abstract:
- lang: eng
text: We present microscopic derivations of the defocusing two-dimensional cubic
nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman
interacting N-particle system of bosons. We consider the interaction potential
to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx),
for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R).
In both cases we prove the convergence of the reduced density corresponding to
the exact time evolution to the projector onto the solution of the corresponding
nonlinear Schrödinger equation in trace norm. For the latter potential VN we show
that it is crucial to take the microscopic structure of the condensate into account
in order to obtain the correct dynamics.
acknowledgement: OA fund by IST Austria
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maximilian
full_name: Jeblick, Maximilian
last_name: Jeblick
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69.
doi:10.1007/s00220-019-03599-x
apa: Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time
dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x
chicago: Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of
the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications
in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.
ieee: M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent
Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical
Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.
ista: Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.
mla: Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii
Equation in Two Dimensions.” Communications in Mathematical Physics, vol.
372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.
short: M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics
372 (2019) 1–69.
date_created: 2019-11-25T08:08:02Z
date_published: 2019-11-08T00:00:00Z
date_updated: 2023-09-06T10:47:43Z
day: '08'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03599-x
ec_funded: 1
external_id:
isi:
- '000495193700002'
file:
- access_level: open_access
checksum: cd283b475dd739e04655315abd46f528
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:11:11Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7101'
file_name: 2019_CommMathPhys_Jeblick.pdf
file_size: 884469
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 372'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1-69
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the time dependent Gross–Pitaevskii equation in two dimensions
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: 372
year: '2019'
...