---
_id: '6890'
abstract:
- lang: eng
text: Describing the protein interactions that form pleomorphic and asymmetric viruses
represents a considerable challenge to most structural biology techniques, including
X-ray crystallography and single particle cryo-electron microscopy. Obtaining
a detailed understanding of these interactions is nevertheless important, considering
the number of relevant human pathogens that do not follow strict icosahedral or
helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide
structural insights into complex biological environments and are well suited to
go beyond structures of perfectly symmetric viruses. This chapter discusses recent
developments showing that cryo-ET and subtomogram averaging can provide high-resolution
insights into hitherto unknown structural features of pleomorphic and asymmetric
virus particles. It also describes how these methods have significantly added
to our understanding of retrovirus capsid assemblies in immature and mature viruses.
Additional examples of irregular viruses and their associated proteins, whose
structures have been studied via cryo-ET and subtomogram averaging, further support
the versatility of these methods.
article_processing_charge: No
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary
Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus
Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008'
apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and
asymmetric viruses using cryo-electron tomography and subtomogram averaging. In
F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function
(Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008
chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic
and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
In Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.
ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric
viruses using cryo-electron tomography and subtomogram averaging,” in Complementary
Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed.
Elsevier, 2019, pp. 117–159.
ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies
to Study Virus Structure and Function. vol. 105, 117–159.'
mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and
Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.
short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study
Virus Structure and Function, Elsevier, 2019, pp. 117–159.
date_created: 2019-09-18T08:15:37Z
date_published: 2019-08-27T00:00:00Z
date_updated: 2023-08-30T06:56:00Z
day: '27'
department:
- _id: FlSc
doi: 10.1016/bs.aivir.2019.07.008
editor:
- first_name: Félix A.
full_name: Rey, Félix A.
last_name: Rey
external_id:
isi:
- '000501594500006'
pmid:
- ' 31522703'
intvolume: ' 105'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 117-159
pmid: 1
publication: Complementary Strategies to Study Virus Structure and Function
publication_identifier:
isbn:
- '9780128184561'
issn:
- 0065-3527
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
series_title: Advances in Virus Research
status: public
title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron
tomography and subtomogram averaging
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2019'
...
---
_id: '6940'
abstract:
- lang: eng
text: "We study the effect of a linear tunneling coupling between two-dimensional
systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless
(BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the
one-body correlation functions are algebraically decaying and the other with\r\nexponential
decay. When the linear coupling is turned on, a third BKT-paired phase emerges,
in which one-body correlations are exponentially decaying, while two-body correlation
functions exhibit power-law\r\ndecay. We perform numerical simulations in the
paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences
that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent.
We provide a picture of the phase diagram using a renormalization group approach."
acknowledgement: "We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio
and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from
the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport
from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1
- 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative
Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021
Joint Project “Strongly interacting systems in confined geometries” is gratefully
acknowledged."
article_number: '100601'
article_processing_charge: No
article_type: original
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Nicolò
full_name: Defenu, Nicolò
last_name: Defenu
- first_name: István
full_name: Nándori, István
last_name: Nándori
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
- first_name: Andrea
full_name: Trombettoni, Andrea
last_name: Trombettoni
citation:
ama: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 2019;123(10).
doi:10.1103/physrevlett.123.100601
apa: Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019).
Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601
chicago: Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea
Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.”
Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601.
ieee: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models,” Physical Review Letters, vol. 123,
no. 10. American Physical Society, 2019.
ista: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.
mla: Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled
XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American
Physical Society, 2019, doi:10.1103/physrevlett.123.100601.
short: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical
Review Letters 123 (2019).
date_created: 2019-10-14T06:31:13Z
date_published: 2019-09-06T00:00:00Z
date_updated: 2023-08-30T06:57:53Z
day: '06'
department:
- _id: MiLe
doi: 10.1103/physrevlett.123.100601
external_id:
arxiv:
- '1907.06253'
isi:
- '000483587200004'
intvolume: ' 123'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.06253
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News auf IST Website
relation: press_release
url: https://ist.ac.at/en/news/new-form-of-magnetism-found/
scopus_import: '1'
status: public
title: Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 123
year: '2019'
...
---
_id: '6919'
article_number: eaaw6490
article_processing_charge: No
author:
- first_name: Chao
full_name: Qi, Chao
last_name: Qi
- first_name: Giulio Di
full_name: Minin, Giulio Di
last_name: Minin
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Anton
full_name: Wutz, Anton
last_name: Wutz
- first_name: Volodymyr M.
full_name: Korkhov, Volodymyr M.
last_name: Korkhov
citation:
ama: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol
recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9).
doi:10.1126/sciadv.aaw6490
apa: Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019).
Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490
chicago: Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr
M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor
PTCH1.” Science Advances. American Association for the Advancement of Science,
2019. https://doi.org/10.1126/sciadv.aaw6490.
ieee: C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural
basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances,
vol. 5, no. 9. American Association for the Advancement of Science, 2019.
ista: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of
sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490.
mla: Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog
Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association
for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.
short: C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances
5 (2019).
date_created: 2019-09-29T22:00:45Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2023-08-30T06:55:31Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1126/sciadv.aaw6490
external_id:
isi:
- '000491128800062'
file:
- access_level: open_access
checksum: b2256c9117655bc15f621ba0babf219f
content_type: application/pdf
creator: kschuh
date_created: 2019-10-02T11:13:54Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6928'
file_name: 2019_AAAS_Qi.pdf
file_size: 1236101
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of sterol recognition by human hedgehog receptor PTCH1
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2019'
...
---
_id: '6983'
abstract:
- lang: eng
text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when
Plasmodium-infected mosquitoes inject malaria sporozoites while searching for
blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes,
and form liver stages which in mice 48 h later escape into blood and cause clinical
malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating
and eliminating all liver stages in 48 h, thus preventing the blood-stage disease.
However, the rules of how CD8 T cells are able to locate all liver stages within
a relatively short time period remains poorly understood. We recently reported
formation of clusters consisting of variable numbers of activated CD8 T cells
around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental
data and mathematical models we now provide additional insights into mechanisms
of formation of these clusters. First, we show that a model in which cluster formation
is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness”
of different liver stages, cannot explain distribution of cluster sizes in different
experimental conditions. In contrast, the model in which cluster formation is
driven by the positive feedback loop (i.e., larger clusters attract more CD8 T
cells) can accurately explain the available data. Second, while both Py-specific
CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are
attracted to the clusters, we found no evidence that non-specific CD8 T cells
play a role in cluster formation. Third and finally, mathematical modeling suggested
that formation of clusters occurs rapidly, within few hours after adoptive transfer
of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their
targets in complex peripheral organs, such as the liver. Taken together, our analysis
provides novel insights into and attempts to discriminate between alternative
mechanisms driving the formation of clusters of antigen-specific CD8 T cells in
the liver.
article_number: '2153'
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: H
full_name: Rajakaruna, H
last_name: Rajakaruna
- first_name: IA
full_name: Cockburn, IA
last_name: Cockburn
- first_name: VV
full_name: Ganusov, VV
last_name: Ganusov
citation:
ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8
T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153
apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering
of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153
chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering
of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven
by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.
ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of
activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers,
2019.
ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated
CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 10, 2153.
mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected
Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in
Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.
short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology
10 (2019).
date_created: 2019-11-04T15:50:06Z
date_published: 2019-09-20T00:00:00Z
date_updated: 2023-08-30T07:18:23Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3389/fimmu.2019.02153
external_id:
isi:
- '000487187000001'
pmid:
- '31616407'
file:
- access_level: open_access
checksum: 68d1708f7aa412544159b498ef17a6b9
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:54:00Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6984'
file_name: 2019_FrontiersImmonology_Kelemen.pdf
file_size: 2083061
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is
rapid and is driven by antigen-specific cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6972'
abstract:
- lang: eng
text: 'We give fault-tolerant algorithms for establishing synchrony in distributed
systems in which each of thennodes has its own clock. Our algorithms operate in
a very strong fault model: we require self-stabilisation, i.e.,the initial state
of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471
apa: Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471
chicago: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock
Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM,
2019. https://doi.org/10.1145/3339471.
ieee: C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM,
2019.
ista: Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. 66(5), 32.
mla: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation
Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32,
ACM, 2019, doi:10.1145/3339471.
short: C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).
date_created: 2019-10-24T17:12:48Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-30T07:07:23Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3339471
ec_funded: 1
external_id:
arxiv:
- '1705.06173'
isi:
- '000496514100001'
file:
- access_level: open_access
checksum: 7e5d95c478e0e393f4927fcf7e48194e
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:58:38Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6975'
file_name: 2019_JACM_Lenzen.pdf
file_size: 2183085
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-stabilising Byzantine clock synchronisation is almost as easy as consensus
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: 66
year: '2019'
...
---
_id: '6942'
abstract:
- lang: eng
text: "Graph games and Markov decision processes (MDPs) are standard models in reactive
synthesis and verification of probabilistic systems with nondeterminism. The class
of \U0001D714 -regular winning conditions; e.g., safety, reachability, liveness,
parity conditions; provides a robust and expressive specification formalism for
properties that arise in analysis of reactive systems. The resolutions of nondeterminism
in games and MDPs are represented as strategies, and we consider succinct representation
of such strategies. The decision-tree data structure from machine learning retains
the flavor of decisions of strategies and allows entropy-based minimization to
obtain succinct trees. However, in contrast to traditional machine-learning problems
where small errors are allowed, for winning strategies in graph games and MDPs
no error is allowed, and the decision tree must represent the entire strategy.
In this work we propose decision trees with linear classifiers for representation
of strategies in graph games and MDPs. We have implemented strategy representation
using this data structure and we present experimental results for problems on
graph games and MDPs, which show that this new data structure presents a much
more efficient strategy representation as compared to standard decision trees."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jan
full_name: Křetínský, Jan
last_name: Křetínský
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy
representation by decision trees with linear classifiers. In: 16th International
Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature;
2019:109-128. doi:10.1007/978-3-030-30281-8_7'
apa: 'Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., &
Toman, V. (2019). Strategy representation by decision trees with linear classifiers.
In 16th International Conference on Quantitative Evaluation of Systems
(Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7'
chicago: Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph
Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear
Classifiers.” In 16th International Conference on Quantitative Evaluation of
Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7.
ieee: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman,
“Strategy representation by decision trees with linear classifiers,” in 16th
International Conference on Quantitative Evaluation of Systems, Glasgow, United
Kingdom, 2019, vol. 11785, pp. 109–128.
ista: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019.
Strategy representation by decision trees with linear classifiers. 16th International
Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation
of Systems, LNCS, vol. 11785, 109–128.'
mla: Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear
Classifiers.” 16th International Conference on Quantitative Evaluation of Systems,
vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.
short: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman,
in:, 16th International Conference on Quantitative Evaluation of Systems, Springer
Nature, 2019, pp. 109–128.
conference:
end_date: 2019-09-12
location: Glasgow, United Kingdom
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2019-09-10
date_created: 2019-10-14T06:57:49Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2023-08-30T06:59:36Z
day: '04'
department:
- _id: KrCh
- _id: ChLa
doi: 10.1007/978-3-030-30281-8_7
external_id:
arxiv:
- '1906.08178'
isi:
- '000679281300007'
intvolume: ' 11785'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.08178
month: '09'
oa: 1
oa_version: Preprint
page: 109-128
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: 16th International Conference on Quantitative Evaluation of Systems
publication_identifier:
eisbn:
- '9783030302818'
isbn:
- '9783030302801'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy representation by decision trees with linear classifiers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11785
year: '2019'
...
---
_id: '6955'
abstract:
- lang: eng
text: We study few-body bound states of charged particles subject to attractive
zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic
length scales of the system at zero energy are set by the Coulomb length scale
D and the Coulomb-modified effective range r eff. We study shallow bound states
of charged particles with D >> r eff and show that these systems obey universal
scaling laws different from neutral particles. An accurate description of these
states requires both the Coulomb-modified scattering length and the effective
range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant
for bound states whose spatial extent is significantly larger than the range of
the attractive potential. These states enjoy universality – their character is
independent of the shape of the short-range potential.
article_number: '135016'
article_processing_charge: No
article_type: original
author:
- first_name: C.H.
full_name: Schmickler, C.H.
last_name: Schmickler
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of
a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016
apa: Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics
of bound states of a few charged particles. Physics Letters B. Elsevier.
https://doi.org/10.1016/j.physletb.2019.135016
chicago: Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics
of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier,
2019. https://doi.org/10.1016/j.physletb.2019.135016.
ieee: C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound
states of a few charged particles,” Physics Letters B, vol. 798. Elsevier,
2019.
ista: Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states
of a few charged particles. Physics Letters B. 798, 135016.
mla: Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged
Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016.
short: C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).
date_created: 2019-10-18T18:33:32Z
date_published: 2019-11-10T00:00:00Z
date_updated: 2023-08-30T07:06:42Z
day: '10'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1016/j.physletb.2019.135016
external_id:
arxiv:
- '1904.00913'
isi:
- '000494939000086'
file:
- access_level: open_access
checksum: d27f983b34ea7dafdf356afbf9472fbf
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:47:04Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6974'
file_name: 2019_PhysicsLettersB_Schmickler.pdf
file_size: 528362
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 798'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Physics Letters B
publication_identifier:
issn:
- 0370-2693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal physics of bound states of a few charged particles
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: 798
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: '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
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: '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: '6988'
abstract:
- lang: eng
text: 'Platelets are central players in thrombosis and hemostasis but are increasingly
recognized as key components of the immune system. They shape ensuing immune responses
by recruiting leukocytes, and support the development of adaptive immunity. Recent
data shed new light on the complex role of platelets in immunity. Here, we summarize
experimental and clinical data on the role of platelets in host defense against
bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet
proinflammatory effector functions and cross-talk with the coagulation system,
can also result in damage to the host (e.g., acute lung injury and sepsis). Novel
clinical insights support this dichotomy: platelet inhibition/thrombocytopenia
can be either harmful or protective, depending on pathophysiological context.
Clinical studies are currently addressing this aspect in greater depth.'
article_processing_charge: No
article_type: review
author:
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: 'Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004'
apa: 'Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host
defense: Experimental and clinical insights. Trends in Immunology. Cell
Press. https://doi.org/10.1016/j.it.2019.08.004'
chicago: 'Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host
Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell
Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.'
ieee: 'L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental
and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press,
pp. 922–938, 2019.'
ista: 'Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 40(10), 922–938.'
mla: 'Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical
Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp.
922–38, doi:10.1016/j.it.2019.08.004.'
short: L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.
date_created: 2019-11-04T16:27:36Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:19:23Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.it.2019.08.004
ec_funded: 1
external_id:
isi:
- '000493292100005'
pmid:
- '31601520'
intvolume: ' 40'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 922-938
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Trends in Immunology
publication_identifier:
issn:
- 1471-4906
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Platelets in host defense: Experimental and clinical insights'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
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: '6978'
abstract:
- lang: eng
text: In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent
work, we study numerically the localized turbulence in pipe flow and elucidate
astate space structure that gives rise to transient chaos. Starting from the basin
boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence
of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe
homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which
wasconjectured in various earlier studies. By mapping the transverse intersections
between thestable and unstable manifold of a periodic orbit, we identify the gateways
that promote anescape from turbulence.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Akshunna
full_name: Dogra, Akshunna
last_name: Dogra
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401
apa: Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos
in streamwise-localized pipe flow turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401
chicago: Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient
Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids.
American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.
ieee: N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized
pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American
Physical Society, p. 102401, 2019.
ista: Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 4(10), 102401.
mla: Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized
Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American
Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.
short: N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.
date_created: 2019-11-04T10:04:01Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:20:03Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.4.102401
external_id:
arxiv:
- '1810.02211'
isi:
- '000493510400001'
intvolume: ' 4'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.02211
month: '10'
oa: 1
oa_version: Preprint
page: '102401'
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of transient chaos in streamwise-localized pipe flow turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
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: '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
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: '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: '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
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
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:
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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: '6455'
abstract:
- lang: eng
text: During corticogenesis, distinct subtypes of neurons are sequentially born
from ventricular zone progenitors. How these cells are molecularly temporally
patterned is poorly understood. We used single-cell RNA sequencing at high temporal
resolution to trace the lineage of the molecular identities of successive generations
of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified
a core set of evolutionarily conserved, temporally patterned genes that drive
APs from internally driven to more exteroceptive states. We found that the Polycomb
repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic
age–dependent AP molecular states are transmitted to their progeny as successive
ground states, onto which essentially conserved early postmitotic differentiation
programs are applied, and are complemented by later-occurring environment-dependent
signals. Thus, epigenetically regulated temporal molecular birthmarks present
in progenitors act in their postmitotic progeny to seed adult neuronal diversity.
article_number: eaav2522
article_processing_charge: No
article_type: original
author:
- first_name: L
full_name: Telley, L
last_name: Telley
- first_name: G
full_name: Agirman, G
last_name: Agirman
- first_name: J
full_name: Prados, J
last_name: Prados
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: S
full_name: Fièvre, S
last_name: Fièvre
- first_name: P
full_name: Oberst, P
last_name: Oberst
- first_name: G
full_name: Bartolini, G
last_name: Bartolini
- first_name: I
full_name: Vitali, I
last_name: Vitali
- first_name: C
full_name: Cadilhac, C
last_name: Cadilhac
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: L
full_name: Nguyen, L
last_name: Nguyen
- first_name: A
full_name: Dayer, A
last_name: Dayer
- first_name: D
full_name: Jabaudon, D
last_name: Jabaudon
citation:
ama: Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors
and their daughter neurons in the developing neocortex. Science. 2019;364(6440).
doi:10.1126/science.aav2522
apa: Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., …
Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter
neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522
chicago: Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini,
et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in
the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.
ieee: L. Telley et al., “Temporal patterning of apical progenitors and their
daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440.
AAAS, 2019.
ista: Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G,
Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal
patterning of apical progenitors and their daughter neurons in the developing
neocortex. Science. 364(6440), eaav2522.
mla: Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter
Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522,
AAAS, 2019, doi:10.1126/science.aav2522.
short: L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini,
I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science
364 (2019).
date_created: 2019-05-14T13:07:47Z
date_published: 2019-05-10T00:00:00Z
date_updated: 2023-09-05T11:51:09Z
day: '10'
department:
- _id: SiHi
doi: 10.1126/science.aav2522
ec_funded: 1
external_id:
isi:
- '000467631800034'
pmid:
- '31073041'
intvolume: ' 364'
isi: 1
issue: '6440'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/
scopus_import: '1'
status: public
title: Temporal patterning of apical progenitors and their daughter neurons in the
developing neocortex
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 364
year: '2019'
...