---
_id: '8092'
abstract:
- lang: eng
text: Image translation refers to the task of mapping images from a visual domain
to another. Given two unpaired collections of images, we aim to learn a mapping
between the corpus-level style of each collection, while preserving semantic content
shared across the two domains. We introduce xgan, a dual adversarial auto-encoder,
which captures a shared representation of the common domain semantic content in
an unsupervised way, while jointly learning the domain-to-domain image translations
in both directions. We exploit ideas from the domain adaptation literature and
define a semantic consistency loss which encourages the learned embedding to preserve
semantics shared across domains. We report promising qualitative results for the
task of face-to-cartoon translation. The cartoon dataset we collected for this
purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic
style transfer at https://google.github.io/cartoonset/index.html.
article_processing_charge: No
arxiv: 1
author:
- first_name: Amélie
full_name: Royer, Amélie
id: 3811D890-F248-11E8-B48F-1D18A9856A87
last_name: Royer
orcid: 0000-0002-8407-0705
- first_name: Konstantinos
full_name: Bousmalis, Konstantinos
last_name: Bousmalis
- first_name: Stephan
full_name: Gouws, Stephan
last_name: Gouws
- first_name: Fred
full_name: Bertsch, Fred
last_name: Bertsch
- first_name: Inbar
full_name: Mosseri, Inbar
last_name: Mosseri
- first_name: Forrester
full_name: Cole, Forrester
last_name: Cole
- first_name: Kevin
full_name: Murphy, Kevin
last_name: Murphy
citation:
ama: 'Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation
for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain
Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3'
apa: 'Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., &
Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many
mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain
Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3'
chicago: 'Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar
Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image
Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding,
edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.'
ieee: 'A. Royer et al., “XGAN: Unsupervised image-to-image translation for
many-to-many mappings,” in Domain Adaptation for Visual Understanding,
R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp.
33–49.'
ista: 'Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN:
Unsupervised image-to-image translation for many-to-many mappings. In: Domain
Adaptation for Visual Understanding. , 33–49.'
mla: 'Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many
Mappings.” Domain Adaptation for Visual Understanding, edited by Richa
Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3.'
short: A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy,
in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual
Understanding, Springer Nature, 2020, pp. 33–49.
date_created: 2020-07-05T22:00:46Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2023-09-07T13:16:18Z
day: '08'
department:
- _id: ChLa
doi: 10.1007/978-3-030-30671-7_3
editor:
- first_name: Richa
full_name: Singh, Richa
last_name: Singh
- first_name: Mayank
full_name: Vatsa, Mayank
last_name: Vatsa
- first_name: Vishal M.
full_name: Patel, Vishal M.
last_name: Patel
- first_name: Nalini
full_name: Ratha, Nalini
last_name: Ratha
external_id:
arxiv:
- '1711.05139'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.05139
month: '01'
oa: 1
oa_version: Preprint
page: 33-49
publication: Domain Adaptation for Visual Understanding
publication_identifier:
isbn:
- '9783030306717'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8331'
relation: dissertation_contains
status: deleted
- id: '8390'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'XGAN: Unsupervised image-to-image translation for many-to-many mappings'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8093'
abstract:
- lang: eng
text: "Background: The activation of the EGFR/Ras-signalling pathway in tumour cells
induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods:
The effects of EGFR/Ras on the expression and translation of CCL20 were analysed
in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and
ELISA in vitro. CCL20 production was verified by immunohistochemistry in different
tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial
cell migration and tumour-associated vascularisation were comprehensively analysed
with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults:
Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression
of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased
lymph node metastasis and decreased survival in patients. Microvascular endothelial
cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in
endothelial cells induces angiogenesis. CCR6-deficient mice show significantly
decreased tumour growth and tumour-associated vascularisation. The observed phenotype
is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion:
We propose that the chemokine axis CCL20–CCR6 represents a novel and promising
target to interfere with the tumour microenvironment, and opens an innovative
multimodal strategy for cancer therapy."
acknowledgement: "The authors would like to thank A. van Lierop for technical assistance.
In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and
assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K.
Horst for advice on performing matrigel plug assays. This study has also been partially
presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190
‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis
project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1
of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was
supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and
J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research
Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia."
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Hippe, Andreas
last_name: Hippe
- first_name: Stephan Alexander
full_name: Braun, Stephan Alexander
last_name: Braun
- first_name: Péter
full_name: Oláh, Péter
last_name: Oláh
- first_name: Peter Arne
full_name: Gerber, Peter Arne
last_name: Gerber
- first_name: Anne
full_name: Schorr, Anne
last_name: Schorr
- first_name: Stephan
full_name: Seeliger, Stephan
last_name: Seeliger
- first_name: Stephanie
full_name: Holtz, Stephanie
last_name: Holtz
- first_name: Katharina
full_name: Jannasch, Katharina
last_name: Jannasch
- first_name: Andor
full_name: Pivarcsi, Andor
last_name: Pivarcsi
- first_name: Bettina
full_name: Buhren, Bettina
last_name: Buhren
- first_name: Holger
full_name: Schrumpf, Holger
last_name: Schrumpf
- first_name: Andreas
full_name: Kislat, Andreas
last_name: Kislat
- first_name: Erich
full_name: Bünemann, Erich
last_name: Bünemann
- first_name: Martin
full_name: Steinhoff, Martin
last_name: Steinhoff
- first_name: Jens
full_name: Fischer, Jens
last_name: Fischer
- first_name: Sérgio A.
full_name: Lira, Sérgio A.
last_name: Lira
- first_name: Petra
full_name: Boukamp, Petra
last_name: Boukamp
- first_name: Peter
full_name: Hevezi, Peter
last_name: Hevezi
- first_name: Nikolas Hendrik
full_name: Stoecklein, Nikolas Hendrik
last_name: Stoecklein
- first_name: Thomas
full_name: Hoffmann, Thomas
last_name: Hoffmann
- first_name: Frauke
full_name: Alves, Frauke
last_name: Alves
- first_name: Jonathan
full_name: Sleeman, Jonathan
last_name: Sleeman
- first_name: Thomas
full_name: Bauer, Thomas
last_name: Bauer
- first_name: Jörg
full_name: Klufa, Jörg
last_name: Klufa
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Maria
full_name: Sibilia, Maria
last_name: Sibilia
- first_name: Albert
full_name: Zlotnik, Albert
last_name: Zlotnik
- first_name: Anja
full_name: Müller-Homey, Anja
last_name: Müller-Homey
- first_name: Bernhard
full_name: Homey, Bernhard
last_name: Homey
citation:
ama: Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates
the tumour microenvironment. British Journal of Cancer. 2020;123:942-954.
doi:10.1038/s41416-020-0943-2
apa: Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S.,
… Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment.
British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2
chicago: Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber,
Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20
Production Modulates the Tumour Microenvironment.” British Journal of Cancer.
Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.
ieee: A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour
microenvironment,” British Journal of Cancer, vol. 123. Springer Nature,
pp. 942–954, 2020.
ista: Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch
K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer
J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J,
Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020.
EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British
Journal of Cancer. 123, 942–954.
mla: Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour
Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature,
2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.
short: A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz,
K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff,
J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F.
Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey,
B. Homey, British Journal of Cancer 123 (2020) 942–954.
date_created: 2020-07-05T22:00:46Z
date_published: 2020-09-15T00:00:00Z
date_updated: 2023-08-22T07:51:12Z
day: '15'
ddc:
- '610'
department:
- _id: SiHi
doi: 10.1038/s41416-020-0943-2
external_id:
isi:
- '000544152500001'
pmid:
- '32601464'
file:
- access_level: open_access
checksum: 05a8e65d49c3f5b8e37ac4afe68287e2
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-02T12:35:12Z
date_updated: 2021-12-02T12:35:12Z
file_id: '10398'
file_name: 2020_BrJournalCancer_Hippe.pdf
file_size: 3620691
relation: main_file
success: 1
file_date_updated: 2021-12-02T12:35:12Z
has_accepted_license: '1'
intvolume: ' 123'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 942-954
pmid: 1
publication: British Journal of Cancer
publication_identifier:
eissn:
- 1532-1827
issn:
- 0007-0920
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41416-021-01563-y
record:
- id: '10170'
relation: later_version
status: deleted
scopus_import: '1'
status: public
title: EGFR/Ras-induced CCL20 production modulates the tumour microenvironment
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: 123
year: '2020'
...
---
_id: '8097'
abstract:
- lang: eng
text: 'Antibiotics that interfere with translation, when combined, interact in diverse
and difficult-to-predict ways. Here, we explain these interactions by "translation
bottlenecks": points in the translation cycle where antibiotics block ribosomal
progression. To elucidate the underlying mechanisms of drug interactions between
translation inhibitors, we generate translation bottlenecks genetically using
inducible control of translation factors that regulate well-defined translation
cycle steps. These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks causes these
interactions. We further show that growth laws, combined with drug uptake and
binding kinetics, enable the direct prediction of a large fraction of observed
interactions, yet fail to predict suppression. However, varying two translation
bottlenecks simultaneously supports that dense traffic of ribosomes and competition
for translation factors account for the previously unexplained suppression. These
results highlight the importance of "continuous epistasis" in bacterial physiology.'
acknowledged_ssus:
- _id: LifeSc
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug
interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097
apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms
of drug interactions between translation-inhibiting antibiotics.” Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097
chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms
of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of
Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.
ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of
drug interactions between translation-inhibiting antibiotics.’” Institute of Science
and Technology Austria, 2020.
ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms
of drug interactions between translation-inhibiting antibiotics’, Institute of
Science and Technology Austria, 10.15479/AT:ISTA:8097.
mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms
of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.
short: B. Kavcic, (2020).
contributor:
- contributor_type: research_group
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- contributor_type: research_group
first_name: Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
date_created: 2020-07-06T20:40:19Z
date_published: 2020-07-15T00:00:00Z
date_updated: 2024-02-21T12:40:51Z
day: '15'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8097
file:
- access_level: open_access
checksum: 5c321dbbb6d4b3c85da786fd3ebbdc98
content_type: application/zip
creator: bkavcic
date_created: 2020-07-06T20:38:27Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8098'
file_name: natComm_2020_scripts.zip
file_size: 255770756
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- antibiotic combinations
- translation
- growth laws
- drug interactions
- bacterial physiology
- translation inhibitors
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Analysis scripts and research data for the paper "Mechanisms of drug interactions
between translation-inhibiting antibiotics"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8099'
abstract:
- lang: eng
text: Sewall Wright developed FST for describing population differentiation and
it has since been extended to many novel applications, including the detection
of homomorphic sex chromosomes. However, there has been confusion regarding the
expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome
when comparing males and females. Here, we attempt to resolve this confusion by
contrasting two common FST estimators and explain why they yield different estimates
when applied to the case of sex chromosomes. We show that this difference is true
for many allele frequencies, but the situation characterized by fixed differences
between the X‐ and Y‐chromosome is among the most extreme. To avoid additional
confusion, we recommend that all authors using FST clearly state which estimator
of FST their work uses.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case
study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525.
doi:10.1111/1755-0998.13210'
apa: 'Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in
FST estimators: A case study from sex chromosomes. Molecular Ecology Resources.
Wiley. https://doi.org/10.1111/1755-0998.13210'
chicago: 'Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement
in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources.
Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.'
ieee: 'W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators:
A case study from sex chromosomes,” Molecular Ecology Resources, vol.
20, no. 6. Wiley, pp. 1517–1525, 2020.'
ista: 'Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators:
A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.'
mla: 'Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study
from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley,
2020, pp. 1517–25, doi:10.1111/1755-0998.13210.'
short: W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20
(2020) 1517–1525.
date_created: 2020-07-07T08:56:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-09-05T16:07:08Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/1755-0998.13210
ec_funded: 1
external_id:
isi:
- '000545451200001'
pmid:
- '32543001'
file:
- access_level: open_access
checksum: 3d87ebb8757dcd504f20c618b72e6575
content_type: application/pdf
creator: dernst
date_created: 2020-11-26T11:46:43Z
date_updated: 2020-11-26T11:46:43Z
file_id: '8814'
file_name: 2020_MolecularEcologyRes_Gammerdinger.pdf
file_size: 820428
relation: main_file
success: 1
file_date_updated: 2020-11-26T11:46:43Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1517-1525
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
issn:
- 1755-098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Disagreement in FST estimators: A case study from sex chromosomes'
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: 20
year: '2020'
...
---
_id: '8101'
abstract:
- lang: eng
text: By rigorously accounting for mesoscale spatial correlations in donor/acceptor
surface properties, we develop a scale-spanning model for same-material tribocharging.
We find that mesoscale correlations affect not only the magnitude of charge transfer
but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability
that is not observed experimentally. We furthermore propose a generic theoretical
mechanism by which the mesoscale features might emerge, which is qualitatively
consistent with other proposals in the literature.
acknowledgement: "We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin,
and Bilge Baytekin for helpful discussions.\r\nThis project has received funding
from the European Unions Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411."
article_number: '082602'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
- first_name: Juan Carlos A
full_name: Sobarzo Ponce, Juan Carlos A
id: 4B807D68-AE37-11E9-AC72-31CAE5697425
last_name: Sobarzo Ponce
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent
scale-spanning model for same-material tribocharging. Physical Review Materials.
2020;4(8). doi:10.1103/PhysRevMaterials.4.082602
apa: Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R.
(2020). Quantitatively consistent scale-spanning model for same-material tribocharging.
Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602
chicago: Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott
R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material
Tribocharging.” Physical Review Materials. American Physical Society, 2020.
https://doi.org/10.1103/PhysRevMaterials.4.082602.
ieee: G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively
consistent scale-spanning model for same-material tribocharging,” Physical
Review Materials, vol. 4, no. 8. American Physical Society, 2020.
ista: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively
consistent scale-spanning model for same-material tribocharging. Physical Review
Materials. 4(8), 082602.
mla: Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model
for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no.
8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.
short: G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical
Review Materials 4 (2020).
date_created: 2020-07-07T11:33:54Z
date_published: 2020-08-17T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '17'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevMaterials.4.082602
ec_funded: 1
external_id:
arxiv:
- '2006.07120'
isi:
- '000561897000001'
file:
- access_level: open_access
checksum: 288fef1eeb6540c6344bb8f7c8159dc9
content_type: application/pdf
creator: ggrosjea
date_created: 2020-08-17T15:54:20Z
date_updated: 2020-08-17T15:54:20Z
file_id: '8277'
file_name: Grosjean2020.pdf
file_size: 853753
relation: main_file
success: 1
file_date_updated: 2020-08-17T15:54:20Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '8'
keyword:
- electric charge
- tribocharging
- soft matter
- granular materials
- polymers
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Materials
publication_identifier:
issn:
- 2475-9953
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '12697'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Quantitatively consistent scale-spanning model for same-material tribocharging
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: 4
year: '2020'
...
---
_id: '8105'
abstract:
- lang: eng
text: Physical and biological systems often exhibit intermittent dynamics with bursts
or avalanches (active states) characterized by power-law size and duration distributions.
These emergent features are typical of systems at the critical point of continuous
phase transitions, and have led to the hypothesis that such systems may self-organize
at criticality, i.e. without any fine tuning of parameters. Since the introduction
of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality
(SOC) has been very fruitful for the analysis of emergent collective behaviors
in a number of systems, including the brain. Although considerable effort has
been devoted in identifying and modeling scaling features of burst and avalanche
statistics, dynamical aspects related to the temporal organization of bursts remain
often poorly understood or controversial. Of crucial importance to understand
the mechanisms responsible for emergent behaviors is the relationship between
active and quiet periods, and the nature of the correlations. Here we investigate
the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity
during the sleep-wake cycle. We show the duality of power-law (θ, active phase)
and exponential-like (δ, quiescent phase) duration distributions, typical of SOC,
jointly emerge with power-law temporal correlations and anti-correlated coupling
between active and quiet states. Importantly, we demonstrate that such temporal
organization shares important similarities with earthquake dynamics, and propose
that specific power-law correlations and coupling between active and quiet states
are distinctive characteristics of a class of systems with self-organization at
criticality.
article_number: '00005'
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Jilin W.J.L.
full_name: Wang, Jilin W.J.L.
last_name: Wang
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Plamen Ch
full_name: Ivanov, Plamen Ch
last_name: Ivanov
citation:
ama: Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling
of active and quiet states underlie a class of complex systems with self-organization
at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005
apa: Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). Power-law
correlations and coupling of active and quiet states underlie a class of complex
systems with self-organization at criticality. EPJ Web of Conferences.
EDP Sciences. https://doi.org/10.1051/epjconf/202023000005
chicago: Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov.
“Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class
of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences.
EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.
ieee: F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations
and coupling of active and quiet states underlie a class of complex systems with
self-organization at criticality,” EPJ Web of Conferences, vol. 230. EDP
Sciences, 2020.
ista: Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and
coupling of active and quiet states underlie a class of complex systems with self-organization
at criticality. EPJ Web of Conferences. 230, 00005.
mla: Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and
Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.”
EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005.
short: F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences
230 (2020).
date_created: 2020-07-12T16:20:33Z
date_published: 2020-03-11T00:00:00Z
date_updated: 2021-01-12T08:16:55Z
day: '11'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1051/epjconf/202023000005
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:17:11Z
date_updated: 2020-07-22T06:17:11Z
file_id: '8144'
file_name: 2020_EPJWebConf_Lombardi.pdf
file_size: 2197543
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:17:11Z
has_accepted_license: '1'
intvolume: ' 230'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: EPJ Web of Conferences
publication_identifier:
issn:
- 2100-014X
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
status: public
title: Power-law correlations and coupling of active and quiet states underlie a class
of complex systems with self-organization at criticality
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: 230
year: '2020'
...
---
_id: '8112'
article_number: '20190530'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. On the completion of speciation. Philosophical Transactions
of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530'
apa: 'Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530'
chicago: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0530.'
ieee: 'N. H. Barton, “On the completion of speciation,” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The
Royal Society, 2020.'
ista: 'Barton NH. 2020. On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.'
mla: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530,
The Royal Society, 2020, doi:10.1098/rstb.2019.0530.'
short: 'N.H. Barton, Philosophical Transactions of the Royal Society. Series B:
Biological Sciences 375 (2020).'
date_created: 2020-07-13T03:41:39Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T07:53:52Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0530
external_id:
isi:
- '000552662100002'
pmid:
- '32654647'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the completion of speciation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8126'
abstract:
- lang: eng
text: Cortical areas comprise multiple types of inhibitory interneurons with stereotypical
connectivity motifs, but their combined effect on postsynaptic dynamics has been
largely unexplored. Here, we analyse the response of a single postsynaptic model
neuron receiving tuned excitatory connections alongside inhibition from two plastic
populations. Depending on the inhibitory plasticity rule, synapses remain unspecific
(flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the
neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on
the modulatory state of inhibition. When both inhibitory populations are active,
inhibition balances excitation, resulting in uncorrelated postsynaptic responses
regardless of the inhibitory tuning profiles. Modulating the activity of a given
inhibitory population produces strong correlations to either preferred or non-preferred
inputs, in line with recent experimental findings showing dramatic context-dependent
changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive
field doesn’t follow directly from the weight profiles of its presynaptic afferents.
article_processing_charge: No
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Andrea I.
full_name: Luppi, Andrea I.
last_name: Luppi
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge
from plasticity and allow attentional switching of receptive fields. The Journal
of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020
apa: Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory
weight profiles emerge from plasticity and allow attentional switching of receptive
fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020
chicago: Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory
Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive
Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.
ieee: E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight
profiles emerge from plasticity and allow attentional switching of receptive fields,”
The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience,
pp. 9634–9649, 2020.
ista: Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles
emerge from plasticity and allow attentional switching of receptive fields. The
Journal of Neuroscience. 40(50), 9634–9649.
mla: Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge
from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal
of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49,
doi:10.1523/JNEUROSCI.0276-20.2020.
short: E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020)
9634–9649.
date_created: 2020-07-16T12:25:04Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T07:54:26Z
day: '09'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0276-20.2020
external_id:
isi:
- '000606706400009'
pmid:
- '33168622'
file:
- access_level: open_access
checksum: 7977e4dd6b89357d1a5cc88babac56da
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:31:47Z
date_updated: 2020-12-28T08:31:47Z
file_id: '8977'
file_name: 2020_JourNeuroscience_Agnes.pdf
file_size: 2750920
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:31:47Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 9634-9649
pmid: 1
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complementary inhibitory weight profiles emerge from plasticity and allow attentional
switching of receptive fields
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: 40
year: '2020'
...
---
_id: '8127'
abstract:
- lang: eng
text: Mechanistic modeling in neuroscience aims to explain observed phenomena in
terms of underlying causes. However, determining which model parameters agree
with complex and stochastic neural data presents a significant challenge. We address
this challenge with a machine learning tool which uses deep neural density estimators—trained
using model simulations—to carry out Bayesian inference and retrieve the full
space of parameters compatible with raw data or selected data features. Our method
is scalable in parameters and data features and can rapidly analyze new data after
initial training. We demonstrate the power and flexibility of our approach on
receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize
the space of circuit configurations giving rise to rhythmic activity in the crustacean
stomatogastric ganglion, and use these results to derive hypotheses for underlying
compensation mechanisms. Our approach will help close the gap between data-driven
and theory-driven models of neural dynamics.
acknowledgement: We thank Mahmood S Hoseini and Michael Stryker for sharing their
data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham,
Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid
Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the
manuscript. This work was supported by the German Research Foundation (DFG) through
SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041
‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1
– Project number 390727645 and the German Federal Ministry of Education and Research
(BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome
Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant
(SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological
Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge
the Leibniz Supercomputing Centre for funding this project by providing computing
time on its Linux-Cluster.
article_number: e56261
article_processing_charge: No
article_type: original
author:
- first_name: Pedro J.
full_name: Gonçalves, Pedro J.
last_name: Gonçalves
orcid: 0000-0002-6987-4836
- first_name: Jan-Matthis
full_name: Lueckmann, Jan-Matthis
last_name: Lueckmann
orcid: 0000-0003-4320-4663
- first_name: Michael
full_name: Deistler, Michael
last_name: Deistler
orcid: 0000-0002-3573-0404
- first_name: Marcel
full_name: Nonnenmacher, Marcel
last_name: Nonnenmacher
orcid: 0000-0001-6044-6627
- first_name: Kaan
full_name: Öcal, Kaan
last_name: Öcal
orcid: 0000-0002-8528-6858
- first_name: Giacomo
full_name: Bassetto, Giacomo
last_name: Bassetto
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Sara A.
full_name: Haddad, Sara A.
last_name: Haddad
orcid: 0000-0003-0807-0823
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: David S.
full_name: Greenberg, David S.
last_name: Greenberg
- first_name: Jakob H.
full_name: Macke, Jakob H.
last_name: Macke
orcid: 0000-0001-5154-8912
citation:
ama: Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density
estimators to identify mechanistic models of neural dynamics. eLife. 2020;9.
doi:10.7554/eLife.56261
apa: Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K.,
Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to
identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.56261
chicago: Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher,
Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural
Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.
ieee: P. J. Gonçalves et al., “Training deep neural density estimators to
identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto
G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020.
Training deep neural density estimators to identify mechanistic models of neural
dynamics. eLife. 9, e56261.
mla: Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify
Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences
Publications, 2020, doi:10.7554/eLife.56261.
short: P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G.
Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg,
J.H. Macke, ELife 9 (2020).
date_created: 2020-07-16T12:26:04Z
date_published: 2020-09-17T00:00:00Z
date_updated: 2023-08-22T07:54:52Z
day: '17'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.7554/eLife.56261
ec_funded: 1
external_id:
isi:
- '000584989400001'
pmid:
- '32940606'
file:
- access_level: open_access
checksum: c4300ddcd93ed03fc9c6cdf1f77890be
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T11:37:32Z
date_updated: 2020-10-27T11:37:32Z
file_id: '8709'
file_name: 2020_eLife_Gonçalves.pdf
file_size: 17355867
relation: main_file
success: 1
file_date_updated: 2020-10-27T11:37:32Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Training deep neural density estimators to identify mechanistic models of neural
dynamics
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: '2020'
...
---
_id: '8130'
abstract:
- lang: eng
text: We study the dynamics of a system of N interacting bosons in a disc-shaped
trap, which is realised by an external potential that confines the bosons in one
spatial dimension to an interval of length of order ε. The interaction is non-negative
and scaled in such a way that its scattering length is of order ε/N, while its
range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the
simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein
condensation. We prove that condensation is preserved by the N-body dynamics,
where the time-evolved condensate wave function is the solution of a two-dimensional
non-linear equation. The strength of the non-linearity depends on the scaling
parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger
equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the
scattering length of the interaction. In both cases, the coupling parameter depends
on the confining potential.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement
in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo
and Nikolai Leopold are gratefully acknowledged. This work was supported by the
German Research Foundation within the Research Training Group 1838 “Spectral Theory
and Dynamics of Quantum Systems” and has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
citation:
ama: Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined
3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606.
doi:10.1007/s00205-020-01548-w
apa: Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly
confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer
Nature. https://doi.org/10.1007/s00205-020-01548-w
chicago: Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly
Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer
Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w.
ieee: L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly
confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol.
238, no. 11. Springer Nature, pp. 541–606, 2020.
ista: Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly
confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.
mla: Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly
Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol.
238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w.
short: L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606.
date_created: 2020-07-18T15:06:35Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-09-05T14:19:06Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00205-020-01548-w
ec_funded: 1
external_id:
arxiv:
- '1907.04547'
isi:
- '000550164400001'
file:
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checksum: cc67a79a67bef441625fcb1cd031db3d
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creator: dernst
date_created: 2020-12-02T08:50:38Z
date_updated: 2020-12-02T08:50:38Z
file_id: '8826'
file_name: 2020_ArchiveRatMech_Bossmann.pdf
file_size: 942343
relation: main_file
success: 1
file_date_updated: 2020-12-02T08:50:38Z
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intvolume: ' 238'
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language:
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month: '11'
oa: 1
oa_version: Published Version
page: 541-606
project:
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call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons
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: 238
year: '2020'
...
---
_id: '8131'
abstract:
- lang: eng
text: The possibility to generate construct valid animal models enabled the development
and testing of therapeutic strategies targeting the core features of autism spectrum
disorders (ASDs). At the same time, these studies highlighted the necessity of
identifying sensitive developmental time windows for successful therapeutic interventions.
Animal and human studies also uncovered the possibility to stratify the variety
of ASDs in molecularly distinct subgroups, potentially facilitating effective
treatment design. Here, we focus on the molecular pathways emerging as commonly
affected by mutations in diverse ASD-risk genes, on their role during critical
windows of brain development and the potential treatments targeting these biological
processes.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD
treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137.
doi:10.1016/j.gde.2020.06.004
apa: Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms
for targeted ASD treatments. Current Opinion in Genetics and Development.
Elsevier. https://doi.org/10.1016/j.gde.2020.06.004
chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms
for Targeted ASD Treatments.” Current Opinion in Genetics and Development.
Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.
ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted
ASD treatments,” Current Opinion in Genetics and Development, vol. 65,
no. 12. Elsevier, pp. 126–137, 2020.
ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted
ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.
mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.”
Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier,
2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.
short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development
65 (2020) 126–137.
date_created: 2020-07-19T22:00:58Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-09-10T12:04:25Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.gde.2020.06.004
ec_funded: 1
external_id:
isi:
- '000598918900019'
pmid:
- '32659636'
file:
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content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:47:45Z
date_updated: 2020-07-22T06:47:45Z
file_id: '8146'
file_name: 2020_CurrentOpGenetics_Basilico.pdf
file_size: 1381545
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:47:45Z
has_accepted_license: '1'
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issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 126-137
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F07807
name: Neural stem cells in autism and epilepsy
publication: Current Opinion in Genetics and Development
publication_identifier:
eissn:
- '18790380'
issn:
- 0959437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Molecular mechanisms for targeted ASD treatments
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 65
year: '2020'
...
---
_id: '8132'
abstract:
- lang: eng
text: The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral
branched actin network constituting one of the main drivers of eukaryotic cell
migration. Here, we uncover an essential role of the hematopoietic-specific WRC
component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies
an inborn error of immunity with systemic autoimmunity, at cellular level marked
by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia.
Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In
the absence of Hem1, B cells become deprived of extracellular stimuli necessary
to maintain the strength of B cell receptor signaling at a level permissive for
survival of non-autoreactive B cells. This shifts the balance of B cell fate choices
toward autoreactive B cells and thus autoimmunity.
article_number: eabc3979
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Samaneh
full_name: Zoghi, Samaneh
last_name: Zoghi
- first_name: Máté G.
full_name: Kiss, Máté G.
last_name: Kiss
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Christina
full_name: Rashkova, Christina
last_name: Rashkova
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Matthias
full_name: Haimel, Matthias
last_name: Haimel
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Rico Chandra
full_name: Ardy, Rico Chandra
last_name: Ardy
- first_name: Birgit
full_name: Hoeger, Birgit
last_name: Hoeger
- first_name: Jana
full_name: Block, Jana
last_name: Block
- first_name: David
full_name: Medgyesi, David
last_name: Medgyesi
- first_name: Celine
full_name: Sin, Celine
last_name: Sin
- first_name: Sepideh
full_name: Shahkarami, Sepideh
last_name: Shahkarami
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Vahid
full_name: Ziaee, Vahid
last_name: Ziaee
- first_name: Peter
full_name: Hammerl, Peter
last_name: Hammerl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Loïc
full_name: Dupré, Loïc
last_name: Dupré
- first_name: Johannes B.
full_name: Huppa, Johannes B.
last_name: Huppa
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alexis
full_name: Lomakin, Alexis
last_name: Lomakin
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Christoph J.
full_name: Binder, Christoph J.
last_name: Binder
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
- first_name: Nima
full_name: Rezaei, Nima
last_name: Rezaei
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs
B cell development and prevents autoimmunity. Science Immunology. 2020;5(49).
doi:10.1126/sciimmunol.abc3979
apa: Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., …
Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979
chicago: Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina
Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator
HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology.
AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.
ieee: E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.
ista: Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer
R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain
R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A,
Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal
regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology.
5(49), eabc3979.
mla: Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development
and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979,
AAAS, 2020, doi:10.1126/sciimmunol.abc3979.
short: E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel,
R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S.
Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B.
Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei,
K. Boztug, Science Immunology 5 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-10T00:00:00Z
date_updated: 2023-08-22T07:56:04Z
day: '10'
department:
- _id: MiSi
doi: 10.1126/sciimmunol.abc3979
external_id:
isi:
- '000546994600004'
pmid:
- '32646852'
intvolume: ' 5'
isi: 1
issue: '49'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Science Immunology
publication_identifier:
eissn:
- '24709468'
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '8133'
abstract:
- lang: eng
text: The molecular factors which control circulating levels of inflammatory proteins
are not well understood. Furthermore, association studies between molecular probes
and human traits are often performed by linear model-based methods which may fail
to account for complex structure and interrelationships within molecular datasets.In
this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS)
on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy
older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel).
We employ a Bayesian framework (BayesR+) which can account for issues pertaining
to data structure and unknown confounding variables (with sensitivity analyses
using ordinary least squares- (OLS) and mixed model-based approaches). We identified
13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and
Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG
each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged
genetic variants accounted for up to 45% of variance in protein levels (for MCP2,
36% of variance alone attributable to 1 polymorphism). Methylation data accounted
for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation
in protein levels (for VEGFA) was explained using genetic and epigenetic data
combined. We demonstrated putative causal relationships between CD6 and IL18R1
with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data
may aid understanding of the molecular regulation of the circulating inflammatory
proteome as well as causal relationships between inflammatory mediators and disease.
article_number: '60'
article_processing_charge: No
article_type: original
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Allan F.
full_name: Mcrae, Allan F.
last_name: Mcrae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
2020;12(1). doi:10.1186/s13073-020-00754-1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
Springer Nature. https://doi.org/10.1186/s13073-020-00754-1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method
Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older
Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.
ieee: R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies
of inflammatory protein levels in healthy older adults,” Genome Medicine,
vol. 12, no. 1. Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Genome Medicine. 12(1), 60.
mla: Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies
of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine,
vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T07:55:37Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-020-00754-1
external_id:
isi:
- '000551778400001'
pmid:
- '32641083'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:27:38Z
date_updated: 2020-07-22T06:27:38Z
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intvolume: ' 12'
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issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Medicine
publication_identifier:
eissn:
- 1756994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9706'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-method genome- and epigenome-wide studies of inflammatory protein levels
in healthy older adults
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: 12
year: '2020'
...
---
_id: '8134'
abstract:
- lang: eng
text: We prove an upper bound on the free energy of a two-dimensional homogeneous
Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the
free energy per unit volume differs from the one of the non-interacting system
by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering
length of the two-body interaction potential, ρ is the density, β is the inverse
temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature
for superfluidity. In combination with the corresponding matching lower bound
proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality
in the asymptotic expansion.
article_number: '061901'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas.
II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950
apa: Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional
dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP
Publishing. https://doi.org/10.1063/5.0005950
chicago: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP
Publishing, 2020. https://doi.org/10.1063/5.0005950.
ieee: S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute
Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no.
6. AIP Publishing, 2020.
ista: Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute
Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.
mla: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol.
61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.
short: S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).
date_created: 2020-07-19T22:00:59Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-08-22T08:12:40Z
day: '22'
department:
- _id: RoSe
doi: 10.1063/5.0005950
ec_funded: 1
external_id:
arxiv:
- '2002.08281'
isi:
- '000544595100001'
intvolume: ' 61'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.08281
month: '06'
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: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free energy of the two-dimensional dilute Bose gas. II. Upper bound
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8135'
abstract:
- lang: eng
text: Discrete Morse theory has recently lead to new developments in the theory
of random geometric complexes. This article surveys the methods and results obtained
with this new approach, and discusses some of its shortcomings. It uses simulations
to illustrate the results and to form conjectures, getting numerical estimates
for combinatorial, topological, and geometric properties of weighted and unweighted
Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes
contained in the mosaics.
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreements No 78818 Alpha and No 638176). It is also partially supported
by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and
Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).
alternative_title:
- Abel Symposia
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
citation:
ama: 'Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. Radius functions on Poisson–Delaunay
mosaics and related complexes experimentally. In: Topological Data Analysis.
Vol 15. Springer Nature; 2020:181-218. doi:10.1007/978-3-030-43408-3_8'
apa: Edelsbrunner, H., Nikitenko, A., Ölsböck, K., & Synak, P. (2020). Radius
functions on Poisson–Delaunay mosaics and related complexes experimentally. In
Topological Data Analysis (Vol. 15, pp. 181–218). Springer Nature. https://doi.org/10.1007/978-3-030-43408-3_8
chicago: Edelsbrunner, Herbert, Anton Nikitenko, Katharina Ölsböck, and Peter Synak.
“Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.”
In Topological Data Analysis, 15:181–218. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-43408-3_8.
ieee: H. Edelsbrunner, A. Nikitenko, K. Ölsböck, and P. Synak, “Radius functions
on Poisson–Delaunay mosaics and related complexes experimentally,” in Topological
Data Analysis, 2020, vol. 15, pp. 181–218.
ista: Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. 2020. Radius functions on
Poisson–Delaunay mosaics and related complexes experimentally. Topological Data
Analysis. , Abel Symposia, vol. 15, 181–218.
mla: Edelsbrunner, Herbert, et al. “Radius Functions on Poisson–Delaunay Mosaics
and Related Complexes Experimentally.” Topological Data Analysis, vol.
15, Springer Nature, 2020, pp. 181–218, doi:10.1007/978-3-030-43408-3_8.
short: H. Edelsbrunner, A. Nikitenko, K. Ölsböck, P. Synak, in:, Topological Data
Analysis, Springer Nature, 2020, pp. 181–218.
date_created: 2020-07-19T22:00:59Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2021-01-12T08:17:06Z
day: '22'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/978-3-030-43408-3_8
ec_funded: 1
file:
- access_level: open_access
checksum: 7b5e0de10675d787a2ddb2091370b8d8
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T08:56:14Z
date_updated: 2020-10-08T08:56:14Z
file_id: '8628'
file_name: 2020-B-01-PoissonExperimentalSurvey.pdf
file_size: 2207071
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:56:14Z
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 181-218
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Topological Data Analysis
publication_identifier:
eissn:
- '21978549'
isbn:
- '9783030434076'
issn:
- '21932808'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Radius functions on Poisson–Delaunay mosaics and related complexes experimentally
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2020'
...
---
_id: '8138'
abstract:
- lang: eng
text: Directional transport of the phytohormone auxin is a versatile, plant-specific
mechanism regulating many aspects of plant development. The recently identified
plant hormones, strigolactones (SLs), are implicated in many plant traits; among
others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters
for fine-tuning of growth and developmental responses. Here, we show in pea and
Arabidopsis that SLs target processes dependent on the canalization of auxin flow,
which involves auxin feedback on PIN subcellular distribution. D14 receptor- and
MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels
after wounding or from artificial auxin sources, during vasculature de novo formation
and regeneration. At the cellular level, SLs interfere with auxin effects on PIN
polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis.
Our results identify a non-transcriptional mechanism of SL action, uncoupling
auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue
formation and regeneration.
acknowledgement: We are grateful to David Nelson for providing published materials
and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful
discussions. The research leading to these results has received funding from the
European Research Council (ERC) under the European Union's Horizon 2020 research
and innovation programme (742985). This work was also supported by the Beijing Municipal
Natural Science Foundation (5192011), Beijing Outstanding University Discipline
Program, the National Natural Science Foundation of China (31370309), CEITEC 2020
(LQ1601) project with financial contribution made by the Ministry of Education,
Youth and Sports of the Czech Republic within special support paid from the National
Program of Sustainability II funds, Australian Research Council (FT180100081), and
China Postdoctoral Science Foundation (2019M660864).
article_processing_charge: No
article_type: original
author:
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: J
full_name: Balla, J
last_name: Balla
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: P
full_name: Kalousek, P
last_name: Kalousek
- first_name: Z
full_name: Medveďová, Z
last_name: Medveďová
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: V
full_name: Reinöhl, V
last_name: Reinöhl
- first_name: S
full_name: Procházka, S
last_name: Procházka
- first_name: R
full_name: Halouzka, R
last_name: Halouzka
- first_name: P
full_name: Tarkowski, P
last_name: Tarkowski
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
- first_name: PB
full_name: Brewer, PB
last_name: Brewer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on
PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508.
doi:10.1038/s41467-020-17252-y
apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z.,
… Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin
transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y
chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová,
Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport
Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.
ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer
Nature, p. 3508, 2020.
ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang
Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig
C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization. Nature Communications. 11(1), 3508.
mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin
Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer
Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.
short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y.
Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P.
Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.
date_created: 2020-07-21T08:58:07Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2023-08-22T08:13:44Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17252-y
ec_funded: 1
external_id:
isi:
- '000550062200004'
pmid:
- '32665554'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T08:32:55Z
date_updated: 2020-07-22T08:32:55Z
file_id: '8148'
file_name: 2020_NatureComm_Zhang.pdf
file_size: 1759490
relation: main_file
success: 1
file_date_updated: 2020-07-22T08:32:55Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '3508'
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8139'
abstract:
- lang: eng
text: 'Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated
in many aspects of plant growth, development, intra- and inter-cellular signaling,
nutrient uptake and pathogen defense. Despite these significant roles, little
is known about the precise molecular details of how it functions in planta. In
order to facilitate the direct quantitative study of plant CME, here we review
current routinely used methods and present refined, standardized quantitative
imaging protocols which allow the detailed characterization of CME at multiple
scales in plant tissues. These include: (i) an efficient electron microscopy protocol
for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for
the detailed characterization of the ultra-structure of clathrin-coated vesicles;
(ii) a detailed protocol and analysis for quantitative live-cell fluorescence
microscopy to precisely examine the temporal interplay of endocytosis components
during single CME events; (iii) a semi-automated analysis to allow the quantitative
characterization of global internalization of cargos in whole plant tissues; and
(iv) an overview and validation of useful genetic and pharmacological tools to
interrogate the molecular mechanisms and function of CME in intact plant samples.'
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
acknowledgement: "This paper is dedicated to the memory of Christien Merrifield. He
pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship
inspired the development of all\r\nthe analysis methods presented here. His joy
in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant
inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP
plants used in this manuscript. We further thank the\r\nScientific Service Units
at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical
assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility
for access to equipment. "
article_number: jcs248062
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: G
full_name: Vert, G
last_name: Vert
- first_name: SY
full_name: Bednarek, SY
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative
evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal
of Cell Science. 2020;133(15). doi:10.1242/jcs.248062
apa: Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek,
S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of
clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell
Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062
chicago: Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan,
G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation
of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of
Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.
ieee: A. J. Johnson et al., “Experimental toolbox for quantitative evaluation
of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of
Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.
ista: Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml
J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated
endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15),
jcs248062.
mla: Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation
of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of
Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020,
doi:10.1242/jcs.248062.
short: A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek,
J. Friml, Journal of Cell Science 133 (2020).
date_created: 2020-07-21T08:58:19Z
date_published: 2020-08-06T00:00:00Z
date_updated: 2023-12-01T13:51:07Z
day: '06'
ddc:
- '575'
department:
- _id: JiFr
- _id: EM-Fac
doi: 10.1242/jcs.248062
ec_funded: 1
external_id:
isi:
- '000561047900021'
pmid:
- '32616560'
file:
- access_level: open_access
checksum: 2d11f79a0b4e0a380fb002b933da331a
content_type: application/pdf
creator: ajohnson
date_created: 2020-11-26T17:12:51Z
date_updated: 2021-08-08T22:30:03Z
embargo: 2021-08-07
file_id: '8815'
file_name: 2020 - Johnson - JSC - plant CME toolbox.pdf
file_size: 15150403
relation: main_file
file_date_updated: 2021-08-08T22:30:03Z
has_accepted_license: '1'
intvolume: ' 133'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14510'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis
in the plant model Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 133
year: '2020'
...
---
_id: '8142'
abstract:
- lang: eng
text: Cell production and differentiation for the acquisition of specific functions
are key features of living systems. The dynamic network of cellular microtubules
provides the necessary platform to accommodate processes associated with the transition
of cells through the individual phases of cytogenesis. Here, we show that the
plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton
during cell differentiation and counteracts microtubular rearrangements driven
by the hormone auxin. The endogenous upward gradient of cytokinin activity along
the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust
rearrangements of the microtubule cytoskeleton in epidermal cells progressing
from the proliferative to the differentiation stage. Controlled increases in cytokinin
activity result in premature re‐organization of the microtubule network from transversal
to an oblique disposition in cells prior to their differentiation, whereas attenuated
hormone perception delays cytoskeleton conversion into a configuration typical
for differentiated cells. Intriguingly, cytokinin can interfere with microtubules
also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive
control pathway for the microtubular cytoskeleton may be at least partially conserved
between plant and animal cells.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing
material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring
discussions, and Martine De Cock for help in preparing the manuscript. This research
was supported by the Scientific Service Units (SSUs) of IST Austria through resources
provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the
Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship
(ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738
to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.
article_number: e104238
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: A
full_name: Abuzeineh, A
last_name: Abuzeineh
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Alba
full_name: Juanes Garcia, Alba
id: 40F05888-F248-11E8-B48F-1D18A9856A87
last_name: Juanes Garcia
orcid: 0000-0002-1009-9652
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: J
full_name: Petrášek, J
last_name: Petrášek
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides
microtubule dynamics during cell progression from proliferative to differentiated
stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238
apa: Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös,
K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule
dynamics during cell progression from proliferative to differentiated stage. The
Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238
chicago: Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia,
Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin
Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated
Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238.
ieee: J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule
dynamics during cell progression from proliferative to differentiated stage,”
The Embo Journal, vol. 39, no. 17. Embo Press, 2020.
ista: Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek
J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics
during cell progression from proliferative to differentiated stage. The Embo Journal.
39(17), e104238.
mla: Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule
Dynamics during Cell Progression from Proliferative to Differentiated Stage.”
The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238.
short: J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös,
J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).
date_created: 2020-07-21T09:08:38Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-09-05T13:05:47Z
day: '01'
ddc:
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department:
- _id: MiSi
- _id: EvBe
doi: 10.15252/embj.2019104238
external_id:
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pmid:
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pmid: 1
project:
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grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: The Embo Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phytohormone cytokinin guides microtubule dynamics during cell progression
from proliferative to differentiated stage
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: 39
year: '2020'
...
---
_id: '8151'
abstract:
- lang: eng
text: The main idea behind the Core Project is to teach first year students at IST
scientific communication skills and let them practice by presenting their research
within an interdisciplinary environment. Over the course of the first semester,
students participated in seminars, where they shared their results with the colleagues
from other fields and took part in discussions on relevant subjects. The main
focus during this sessions was on delivering the information in a simplified and
comprehensible way, going into the very basics of a subject if necessary. At the
end, the students were asked to present their research in the written form to
exercise their writing skills. The reports were gathered in this document. All
of them were reviewed by the teaching assistants and write-ups illustrating unique
stylistic features and, in general, an outstanding level of writing skills, were
honorably mentioned in the section "Selected Reports".
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Maslov M, Kondrashov F, Artner C, et al. Core Project Proceedings. IST
Austria; 2020.
apa: Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik,
N. N., … Tomanek, I. (2020). Core Project Proceedings. IST Austria.
chicago: Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen,
Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. Core
Project Proceedings. IST Austria, 2020.
ieee: M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
ista: Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN,
Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p.
mla: Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
short: M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N.
Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
date_created: 2020-07-22T14:48:14Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-02-23T13:26:00Z
day: '01'
ddc:
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extern: '1'
file:
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content_type: application/pdf
creator: dernst
date_created: 2020-07-22T14:45:07Z
date_updated: 2020-07-22T14:45:07Z
file_id: '8152'
file_name: Core_Project_Proceedings_mod.pdf
file_size: 169620437
relation: main_file
file_date_updated: 2020-07-22T14:45:07Z
has_accepted_license: '1'
language:
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month: '06'
oa_version: None
page: '425'
publication_status: published
publisher: IST Austria
status: public
title: Core Project Proceedings
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8155'
abstract:
- lang: eng
text: "In the thesis we focus on the interplay of the biophysics and evolution of
gene regulation. We start by addressing how the type of prokaryotic gene regulation
– activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional
crosstalk. We propose that regulatory interference caused by excess regulatory
proteins in the dense cellular medium – global crosstalk – could be a factor in
determining which type of gene regulatory network is evolutionarily preferred.
Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium
enhancer models that optimize so-called regulatory phenotypes. We find a class
of models that differ from standard thermodynamic equilibrium models by a single
parameter that notably increases the regulatory performance. Next chapter addresses
the question of genotype-phenotype-fitness maps of higher dimensional phenotypes.
We show that our biophysically realistic approach allows us to understand how
the mechanisms of promoter function constrain genotypephenotype maps, and how
they affect the evolutionary trajectories of promoters.\r\nIn the last chapter
we ask whether the intrinsic instability of gene duplication and amplification
provides a generic alternative to canonical gene regulation. Using mathematical
modeling, we show that amplifications can tune gene expression in many environments,
including those where transcription factor-based schemes are\r\nhard to evolve
or maintain. "
acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship
of the Austrian Academy of Sciences.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
citation:
ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution.
2020. doi:10.15479/AT:ISTA:8155
apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155
chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints
Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape
evolution,” Institute of Science and Technology Austria, 2020.
ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria.
mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.
short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-07-23T09:51:28Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-09-07T13:13:27Z
day: '24'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:8155
file:
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content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
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creator: rgrah
date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
file_id: '8177'
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '310'
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7675'
relation: part_of_dissertation
status: public
- id: '7569'
relation: part_of_dissertation
status: public
- id: '7652'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Gene regulation across scales – how biophysical constraints shape evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...