---
_id: '6843'
abstract:
- lang: eng
text: The aim of this short paper is to offer a complete characterization of all
(not necessarily surjective) isometric embeddings of the Wasserstein space Wp(X),
where S is a countable discrete metric space and 0
Journal of Mathematical Analysis and Applications.
2019;480(2). doi:10.1016/j.jmaa.2019.123435
apa: Gehér, G. P., Titkos, T., & Virosztek, D. (2019). On isometric embeddings
of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis
and Applications. Elsevier. https://doi.org/10.1016/j.jmaa.2019.123435
chicago: Gehér, György Pál, Tamás Titkos, and Daniel Virosztek. “On Isometric Embeddings
of Wasserstein Spaces – the Discrete Case.” Journal of Mathematical Analysis
and Applications. Elsevier, 2019. https://doi.org/10.1016/j.jmaa.2019.123435.
ieee: G. P. Gehér, T. Titkos, and D. Virosztek, “On isometric embeddings of Wasserstein
spaces – the discrete case,” Journal of Mathematical Analysis and Applications,
vol. 480, no. 2. Elsevier, 2019.
ista: Gehér GP, Titkos T, Virosztek D. 2019. On isometric embeddings of Wasserstein
spaces – the discrete case. Journal of Mathematical Analysis and Applications.
480(2), 123435.
mla: Gehér, György Pál, et al. “On Isometric Embeddings of Wasserstein Spaces –
the Discrete Case.” Journal of Mathematical Analysis and Applications,
vol. 480, no. 2, 123435, Elsevier, 2019, doi:10.1016/j.jmaa.2019.123435.
short: G.P. Gehér, T. Titkos, D. Virosztek, Journal of Mathematical Analysis and
Applications 480 (2019).
date_created: 2019-09-01T22:01:01Z
date_published: 2019-12-15T00:00:00Z
date_updated: 2023-08-29T07:18:50Z
day: '15'
department:
- _id: LaEr
doi: 10.1016/j.jmaa.2019.123435
ec_funded: 1
external_id:
arxiv:
- '1809.01101'
isi:
- '000486563900031'
intvolume: ' 480'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.01101
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Mathematical Analysis and Applications
publication_identifier:
eissn:
- '10960813'
issn:
- 0022247X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On isometric embeddings of Wasserstein spaces – the discrete case
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2019'
...
---
_id: '6835'
abstract:
- lang: eng
text: We derive the Hasse principle and weak approximation for fibrations of certain
varieties in the spirit of work by Colliot-Thélène–Sansuc and Harpaz–Skorobogatov–Wittenberg.
Our varieties are defined through polynomials in many variables and part of our
work is devoted to establishing Schinzel's hypothesis for polynomials of this
kind. This last part is achieved by using arguments behind Birch's well-known
result regarding the Hasse principle for complete intersections with the notable
difference that we prove our result in 50% fewer variables than in the classical
Birch setting. We also study the problem of square-free values of an integer polynomial
with 66.6% fewer variables than in the Birch setting.
article_number: '102794'
article_processing_charge: No
article_type: original
author:
- first_name: Kevin N
full_name: Destagnol, Kevin N
id: 44DDECBC-F248-11E8-B48F-1D18A9856A87
last_name: Destagnol
- first_name: Efthymios
full_name: Sofos, Efthymios
last_name: Sofos
citation:
ama: Destagnol KN, Sofos E. Rational points and prime values of polynomials in moderately
many variables. Bulletin des Sciences Mathematiques. 2019;156(11). doi:10.1016/j.bulsci.2019.102794
apa: Destagnol, K. N., & Sofos, E. (2019). Rational points and prime values
of polynomials in moderately many variables. Bulletin Des Sciences Mathematiques.
Elsevier. https://doi.org/10.1016/j.bulsci.2019.102794
chicago: Destagnol, Kevin N, and Efthymios Sofos. “Rational Points and Prime Values
of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques.
Elsevier, 2019. https://doi.org/10.1016/j.bulsci.2019.102794.
ieee: K. N. Destagnol and E. Sofos, “Rational points and prime values of polynomials
in moderately many variables,” Bulletin des Sciences Mathematiques, vol.
156, no. 11. Elsevier, 2019.
ista: Destagnol KN, Sofos E. 2019. Rational points and prime values of polynomials
in moderately many variables. Bulletin des Sciences Mathematiques. 156(11), 102794.
mla: Destagnol, Kevin N., and Efthymios Sofos. “Rational Points and Prime Values
of Polynomials in Moderately Many Variables.” Bulletin Des Sciences Mathematiques,
vol. 156, no. 11, 102794, Elsevier, 2019, doi:10.1016/j.bulsci.2019.102794.
short: K.N. Destagnol, E. Sofos, Bulletin Des Sciences Mathematiques 156 (2019).
date_created: 2019-09-01T22:00:55Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T07:18:02Z
day: '01'
department:
- _id: TiBr
doi: 10.1016/j.bulsci.2019.102794
external_id:
arxiv:
- '1801.03082'
isi:
- '000496342100002'
intvolume: ' 156'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.03082
month: '11'
oa: 1
oa_version: Preprint
publication: Bulletin des Sciences Mathematiques
publication_identifier:
issn:
- 0007-4497
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rational points and prime values of polynomials in moderately many variables
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 156
year: '2019'
...
---
_id: '6837'
abstract:
- lang: eng
text: Migrasomes are a recently discovered type of extracellular vesicles that are
characteristically generated along retraction fibers in migrating cells. Two studies
now show how migrasomes are formed and how they function in the physiologically
relevant context of the developing zebrafish embryo.
article_processing_charge: No
author:
- first_name: Ste
full_name: Tavano, Ste
id: 2F162F0C-F248-11E8-B48F-1D18A9856A87
last_name: Tavano
orcid: 0000-0001-9970-7804
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Tavano S, Heisenberg C-PJ. Migrasomes take center stage. Nature Cell Biology.
2019;21(8):918-920. doi:10.1038/s41556-019-0369-3
apa: Tavano, S., & Heisenberg, C.-P. J. (2019). Migrasomes take center stage.
Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0369-3
chicago: Tavano, Ste, and Carl-Philipp J Heisenberg. “Migrasomes Take Center Stage.”
Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0369-3.
ieee: S. Tavano and C.-P. J. Heisenberg, “Migrasomes take center stage,” Nature
Cell Biology, vol. 21, no. 8. Springer Nature, pp. 918–920, 2019.
ista: Tavano S, Heisenberg C-PJ. 2019. Migrasomes take center stage. Nature Cell
Biology. 21(8), 918–920.
mla: Tavano, Ste, and Carl-Philipp J. Heisenberg. “Migrasomes Take Center Stage.”
Nature Cell Biology, vol. 21, no. 8, Springer Nature, 2019, pp. 918–20,
doi:10.1038/s41556-019-0369-3.
short: S. Tavano, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 918–920.
date_created: 2019-09-01T22:00:57Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-29T07:42:20Z
day: '01'
department:
- _id: CaHe
doi: 10.1038/s41556-019-0369-3
external_id:
isi:
- '000478029000003'
pmid:
- '31371826'
intvolume: ' 21'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 918-920
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Migrasomes take center stage
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2019'
...
---
_id: '6867'
abstract:
- lang: eng
text: A novel magnetic scratch method achieves repeatability, reproducibility and
geometric control greater than pipette scratch assays and closely approximating
the precision of cell exclusion assays while inducing the cell injury inherently
necessary for wound healing assays. The magnetic scratch is affordable, easily
implemented and standardisable and thus may contribute toward better comparability
of data generated in different studies and laboratories.
article_number: '12625'
article_processing_charge: No
author:
- first_name: M.
full_name: Fenu, M.
last_name: Fenu
- first_name: T.
full_name: Bettermann, T.
last_name: Bettermann
- first_name: C.
full_name: Vogl, C.
last_name: Vogl
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: J.
full_name: Schramel, J.
last_name: Schramel
- first_name: F.
full_name: Jenner, F.
last_name: Jenner
- first_name: I.
full_name: Ribitsch, I.
last_name: Ribitsch
citation:
ama: Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for
standardisation of wound-healing assays. Scientific Reports. 2019;9(1).
doi:10.1038/s41598-019-48930-7
apa: Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner,
F., & Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation
of wound-healing assays. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-48930-7
chicago: Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel,
F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation
of Wound-Healing Assays.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-48930-7.
ieee: M. Fenu et al., “A novel magnet-based scratch method for standardisation
of wound-healing assays,” Scientific Reports, vol. 9, no. 1. Springer Nature,
2019.
ista: Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch
I. 2019. A novel magnet-based scratch method for standardisation of wound-healing
assays. Scientific Reports. 9(1), 12625.
mla: Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of
Wound-Healing Assays.” Scientific Reports, vol. 9, no. 1, 12625, Springer
Nature, 2019, doi:10.1038/s41598-019-48930-7.
short: M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner,
I. Ribitsch, Scientific Reports 9 (2019).
date_created: 2019-09-15T22:00:42Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2023-08-29T07:55:15Z
day: '02'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1038/s41598-019-48930-7
external_id:
isi:
- '000483697800007'
pmid:
- '31477739'
file:
- access_level: open_access
checksum: 9cfd986d4108e288cc72276ef047ab0c
content_type: application/pdf
creator: dernst
date_created: 2019-09-16T12:42:40Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6879'
file_name: 2019_ScientificReports_Fenu.pdf
file_size: 3523795
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel magnet-based scratch method for standardisation of wound-healing assays
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6859'
abstract:
- lang: eng
text: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found
in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation
across theplasma membrane using the rotary-catalysis mechanism. They belong to
the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type
ATP synthasesin overall architecture. We solved cryo–electron microscopy structures
of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs,
in three rotationalstates and two substates. These structures indicate substantial
flexibility betweenV1and Voin a working enzyme, which results from mechanical
competition between centralshaft rotation and resistance from the peripheral stalks.
We also describedetails of adenosine diphosphate inhibition release, V1-Votorque
transmission, andproton translocation, which are relevant for the entire V-type
ATPase family.
acknowledged_ssus:
- _id: ScienComp
article_number: eaaw9144
article_processing_charge: No
author:
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus
thermophilus V/A-type ATPase. Science. 2019;365(6455). doi:10.1126/science.aaw9144
apa: Zhou, L., & Sazanov, L. A. (2019). Structure and conformational plasticity
of the intact Thermus thermophilus V/A-type ATPase. Science. AAAS. https://doi.org/10.1126/science.aaw9144
chicago: Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science. AAAS, 2019.
https://doi.org/10.1126/science.aaw9144.
ieee: L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the
intact Thermus thermophilus V/A-type ATPase,” Science, vol. 365, no. 6455.
AAAS, 2019.
ista: Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact
Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.
mla: Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity
of the Intact Thermus Thermophilus V/A-Type ATPase.” Science, vol. 365,
no. 6455, eaaw9144, AAAS, 2019, doi:10.1126/science.aaw9144.
short: L. Zhou, L.A. Sazanov, Science 365 (2019).
date_created: 2019-09-07T19:04:45Z
date_published: 2019-08-23T00:00:00Z
date_updated: 2023-08-29T07:52:02Z
day: '23'
department:
- _id: LeSa
doi: 10.1126/science.aaw9144
external_id:
isi:
- '000482464000043'
pmid:
- '31439765'
intvolume: ' 365'
isi: 1
issue: '6455'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/
scopus_import: '1'
status: public
title: Structure and conformational plasticity of the intact Thermus thermophilus
V/A-type ATPase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 365
year: '2019'
...
---
_id: '6858'
article_processing_charge: No
article_type: review
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. Is speciation driven by cycles of mixing and isolation? National
Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113
apa: Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation?
National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113
chicago: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.
ieee: N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National
Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.
ista: Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National
Science Review. 6(2), 291–292.
mla: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review, vol. 6, no. 2, Oxford University Press, 2019,
pp. 291–92, doi:10.1093/nsr/nwy113.
short: N.H. Barton, National Science Review 6 (2019) 291–292.
date_created: 2019-09-07T14:43:02Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-29T07:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/nsr/nwy113
external_id:
isi:
- '000467957400025'
file:
- access_level: open_access
checksum: 571d60fa21a568607d1fd04e119da88c
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T09:16:44Z
date_updated: 2020-10-02T09:16:44Z
file_id: '8595'
file_name: 2019_NSR_Barton.pdf
file_size: 106463
relation: main_file
success: 1
file_date_updated: 2020-10-02T09:16:44Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 291-292
publication: National Science Review
publication_identifier:
eissn:
- 2053-714X
issn:
- 2095-5138
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Is speciation driven by cycles of mixing and isolation?
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: 6
year: '2019'
...
---
_id: '6868'
abstract:
- lang: eng
text: "Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control
electrical rhythmicity and excitability in the heart and brain, but the function
of HCN channels at the subcellular level in axons remains poorly understood. Here,
we show that the action potential conduction velocity in both myelinated and unmyelinated
central axons can be bidirectionally modulated by a HCN channel blocker, cyclic
adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar
mossy fiber boutons show that HCN channels ensure reliable high-frequency firing
and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration
13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating
subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2
channels control conduction velocity primarily by altering the resting membrane
potential\r\nand are associated with significant metabolic costs. These results
suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity
to finely tune energy consumption and temporal delays across axons in the brain."
article_number: e42766
article_processing_charge: No
article_type: original
author:
- first_name: Niklas
full_name: Byczkowicz, Niklas
last_name: Byczkowicz
- first_name: Abdelmoneim
full_name: Eshra, Abdelmoneim
last_name: Eshra
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Andrea
full_name: Trevisiol, Andrea
last_name: Trevisiol
- first_name: Johannes
full_name: Hirrlinger, Johannes
last_name: Hirrlinger
- first_name: Maarten Hp
full_name: Kole, Maarten Hp
last_name: Kole
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Stefan
full_name: Hallermann, Stefan
last_name: Hallermann
citation:
ama: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated
neuromodulation can control action potential velocity and fidelity in central
axons. eLife. 2019;8. doi:10.7554/eLife.42766
apa: Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger,
J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation
can control action potential velocity and fidelity in central axons. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.42766
chicago: Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber,
Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and
Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential
Velocity and Fidelity in Central Axons.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/eLife.42766.
ieee: N. Byczkowicz et al., “HCN channel-mediated neuromodulation can control
action potential velocity and fidelity in central axons,” eLife, vol. 8.
eLife Sciences Publications, 2019.
ista: Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger
J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation
can control action potential velocity and fidelity in central axons. eLife. 8,
e42766.
mla: Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control
Action Potential Velocity and Fidelity in Central Axons.” ELife, vol. 8,
e42766, eLife Sciences Publications, 2019, doi:10.7554/eLife.42766.
short: N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger,
M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019).
date_created: 2019-09-15T22:00:43Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2023-08-30T06:17:06Z
day: '09'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.42766
external_id:
isi:
- '000485663900001'
file:
- access_level: open_access
checksum: c350b7861ef0fb537cae8a3232aec016
content_type: application/pdf
creator: dernst
date_created: 2019-09-16T13:14:33Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6880'
file_name: 2019_eLife_Byczkowicz.pdf
file_size: 4008137
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: HCN channel-mediated neuromodulation can control action potential velocity
and fidelity in central axons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6897'
abstract:
- lang: eng
text: The apical hook is a transiently formed structure that plays a protective
role when the germinating seedling penetrates through the soil towards the surface.
Crucial for proper bending is the local auxin maxima, which defines the concave
(inner) side of the hook curvature. As no sign of asymmetric auxin distribution
has been reported in embryonic hypocotyls prior to hook formation, the question
of how auxin asymmetry is established in the early phases of seedling germination
remains largely unanswered. Here, we analyzed the auxin distribution and expression
of PIN auxin efflux carriers from early phases of germination, and show that bending
of the root in response to gravity is the crucial initial cue that governs the
hypocotyl bending required for apical hook formation. Importantly, polar auxin
transport machinery is established gradually after germination starts as a result
of tight root-hypocotyl interaction and a proper balance between abscisic acid
and gibberellins.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Jiri Friml and Phillip Brewer for inspiring discussion
and for help in preparing the manuscript. This research was supported by the Scientific
Service Units (SSU) of IST-Austria through resources provided by the Bioimaging
Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by
grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg-
207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development
Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738)."
article_number: dev175919
article_processing_charge: No
article_type: original
author:
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Jiří
full_name: Pospíšil, Jiří
last_name: Pospíšil
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity
response module guides differential growth determining both root bending and apical
hook formation in Arabidopsis. Development. 2019;146(17). doi:10.1242/dev.175919
apa: Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., & Benková,
E. (2019). Root gravity response module guides differential growth determining
both root bending and apical hook formation in Arabidopsis. Development.
The Company of Biologists. https://doi.org/10.1242/dev.175919
chicago: Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad,
and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining
Both Root Bending and Apical Hook Formation in Arabidopsis.” Development.
The Company of Biologists, 2019. https://doi.org/10.1242/dev.175919.
ieee: Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková,
“Root gravity response module guides differential growth determining both root
bending and apical hook formation in Arabidopsis,” Development, vol. 146,
no. 17. The Company of Biologists, 2019.
ista: Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root
gravity response module guides differential growth determining both root bending
and apical hook formation in Arabidopsis. Development. 146(17), dev175919.
mla: Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth
Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” Development,
vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:10.1242/dev.175919.
short: Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development
146 (2019).
date_created: 2019-09-22T22:00:36Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:19:04Z
day: '12'
department:
- _id: EvBe
doi: 10.1242/dev.175919
ec_funded: 1
external_id:
isi:
- '000486297400011'
pmid:
- '31391194'
intvolume: ' 146'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.175919
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Development
publication_identifier:
eissn:
- '14779129'
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Root gravity response module guides differential growth determining both root
bending and apical hook formation in Arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 146
year: '2019'
...
---
_id: '6896'
abstract:
- lang: eng
text: "Until recently, a great amount of brain studies have been conducted in human
post mortem tissues, cell lines and model organisms. These researches provided
useful insights regarding cell-cell interactions occurring in the brain. However,
such approaches suffer from technical limitations and inaccurate modeling of the
tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background
essential for disease modeling. With the development of protocols to generate
human cerebral organoids, we are now closer to reproducing the early stages of
human brain development in vitro. As a result, more relevant cell-cell interaction
studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of
3D cultures over 2D in modulating brain cell-cell interactions during physiological
and pathological development, as well as the progress made in developing organoids
in which neurons, macroglia, microglia and vascularization are present. Finally,
we debate the limitations of those models and possible future directions."
article_number: '146458'
article_processing_charge: No
article_type: original
author:
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain
using cerebral organoids. Brain Research. 2019;1724. doi:10.1016/j.brainres.2019.146458
apa: Oliveira, B., Yahya, A. Ç., & Novarino, G. (2019). Modeling cell-cell interactions
in the brain using cerebral organoids. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2019.146458
chicago: Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell
Interactions in the Brain Using Cerebral Organoids.” Brain Research. Elsevier,
2019. https://doi.org/10.1016/j.brainres.2019.146458.
ieee: B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions
in the brain using cerebral organoids,” Brain Research, vol. 1724. Elsevier,
2019.
ista: Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in
the brain using cerebral organoids. Brain Research. 1724, 146458.
mla: Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using
Cerebral Organoids.” Brain Research, vol. 1724, 146458, Elsevier, 2019,
doi:10.1016/j.brainres.2019.146458.
short: B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019).
date_created: 2019-09-22T22:00:35Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T06:19:49Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.brainres.2019.146458
external_id:
isi:
- '000491646600033'
pmid:
- '31521639'
intvolume: ' 1724'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
publication: Brain Research
publication_identifier:
eissn:
- '18726240'
issn:
- '00068993'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling cell-cell interactions in the brain using cerebral organoids
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 1724
year: '2019'
...
---
_id: '9731'
abstract:
- lang: eng
text: OGs with putative pseudogenes by the number of affected genomes in different
chlamydial species. Frameshift and nonsense mutations located less than 60 bp
upstreamof the gene end or present in a single genome from the corresponding OG
were excluded. (CSV 31 kb)
article_processing_charge: No
author:
- first_name: Olga
full_name: Sigalova, Olga
last_name: Sigalova
- first_name: Andrei
full_name: Chaplin, Andrei
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel
full_name: Shelyakin, Pavel
last_name: Shelyakin
- first_name: Vsevolod
full_name: Filaretov, Vsevolod
last_name: Filaretov
- first_name: Evgeny
full_name: Akkuratov, Evgeny
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1
apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov,
E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.
Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1
chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod
Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional
File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.
ieee: O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.”
Springer Nature, 2019.
ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E,
Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808772.v1.
mla: Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.
short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov,
V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-07-27T14:09:11Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808772.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808772.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9783'
abstract:
- lang: eng
text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For
the analysis of putative pseudogenes, events located less than 60 bp. away from
gene end or present in a single genome from the corresponding OG were excluded.
(CSV 600 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.
ieee: O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.
mla: Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-06T07:59:56Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808760.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808760.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 10 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9897'
abstract:
- lang: eng
text: Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes.
Only 374 genes with typical length and domain composition were considered. (CSV
6 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808850.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808850.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808850.v1.
ieee: O. M. Sigalova et al., “Additional file 20 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 20 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808850.v1.
mla: Sigalova, Olga M., et al. Additional File 20 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808850.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:58:15Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808850.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808850.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 20 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9890'
abstract:
- lang: eng
text: Distribution of OGs with mosaic phyletic patterns across species (complete
genomes only). (CSV 7 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808802.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808802.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808802.v1.
ieee: O. M. Sigalova et al., “Additional file 15 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808802.v1.
mla: Sigalova, Olga M., et al. Additional File 15 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808802.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-11T14:26:40Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808802.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808802.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 15 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9892'
abstract:
- lang: eng
text: Distribution of OGs with mosaic phyletic patterns across species (all genomes).
(CSV 10 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V
full_name: Chaplin, Andrei V
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808814.v1
chicago: Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1.
ieee: O. M. Sigalova et al., “Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1.
mla: Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:11:53Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808814.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808814.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 16 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9893'
abstract:
- lang: eng
text: Summary of peripheral genesa phyletic patterns and tree concordance. (CSV
26 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808820.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808820.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808820.v1.
ieee: O. M. Sigalova et al., “Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808820.v1.
mla: Sigalova, Olga M., et al. Additional File 17 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808820.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:20:10Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808820.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808820.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 17 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9894'
abstract:
- lang: eng
text: Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808826.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808826.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808826.v1.
ieee: O. M. Sigalova et al., “Additional file 18 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 18 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808826.v1.
mla: Sigalova, Olga M., et al. Additional File 18 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808826.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:25:07Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808826.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808826.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 18 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9895'
abstract:
- lang: eng
text: Additional information on proteins from OG1. (CSV 30 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 19 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808835.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808835.v1.
ieee: O. M. Sigalova et al., “Additional file 19 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 19 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808835.v1.
mla: Sigalova, Olga M., et al. Additional File 19 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808835.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:44:52Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808835.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808835.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 19 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9896'
abstract:
- lang: eng
text: Summary of the analysed genomes. (CSV 24 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808841.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808841.v1.
ieee: O. M. Sigalova et al., “Additional file 1 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808841.v1.
mla: Sigalova, Olga M., et al. Additional File 1 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:50:53Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '02'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808841.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808841.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 1 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6899'
abstract:
- lang: eng
text: Intra-organ communication guides morphogenetic processes that are essential
for an organ to carry out complex physiological functions. In the heart, the growth
of the myocardium is tightly coupled to that of the endocardium, a specialized
endothelial tissue that lines its interior. Several molecular pathways have been
implicated in the communication between these tissues including secreted factors,
components of the extracellular matrix, or proteins involved in cell-cell communication.
Yet, it is unknown how the growth of the endocardium is coordinated with that
of the myocardium. Here, we show that an increased expansion of the myocardial
atrial chamber volume generates higher junctional forces within endocardial cells.
This leads to biomechanical signaling involving VE-cadherin, triggering nuclear
localization of the Hippo pathway transcriptional regulator Yap1 and endocardial
proliferation. Our work suggests that the growth of the endocardium results from
myocardial chamber volume expansion and ends when the tension on the tissue is
relaxed.
article_processing_charge: No
author:
- first_name: Dorothee
full_name: Bornhorst, Dorothee
last_name: Bornhorst
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Hiroyuki
full_name: Nakajima, Hiroyuki
last_name: Nakajima
- first_name: Chaitanya
full_name: Dingare, Chaitanya
last_name: Dingare
- first_name: Wiebke
full_name: Herzog, Wiebke
last_name: Herzog
- first_name: Virginie
full_name: Lecaudey, Virginie
last_name: Lecaudey
- first_name: Naoki
full_name: Mochizuki, Naoki
last_name: Mochizuki
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Deborah
full_name: Yelon, Deborah
last_name: Yelon
- first_name: Salim
full_name: Abdelilah-Seyfried, Salim
last_name: Abdelilah-Seyfried
citation:
ama: Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature
communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x
apa: Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V.,
… Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x
chicago: Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke
Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah
Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing
Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.”
Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.
ieee: D. Bornhorst et al., “Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions,”
Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113,
2019.
ista: Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki
N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling
within the developing zebrafish heart attunes endocardial growth to myocardial
chamber dimensions. Nature communications. 10(1), 4113.
mla: Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing
Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.”
Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p.
4113, doi:10.1038/s41467-019-12068-x.
short: D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N.
Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications
10 (2019) 4113.
date_created: 2019-09-22T22:00:37Z
date_published: 2019-09-11T00:00:00Z
date_updated: 2023-08-30T06:21:23Z
day: '11'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1038/s41467-019-12068-x
external_id:
isi:
- '000485216800009'
pmid:
- '31511517'
file:
- access_level: open_access
checksum: 62c2512712e16d27c1797d318d14ba9f
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T11:18:50Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6926'
file_name: 2019_Nature_Bornhorst.pdf
file_size: 3905793
relation: main_file
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has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '4113'
pmid: 1
publication: Nature communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Biomechanical signaling within the developing zebrafish heart attunes endocardial
growth to myocardial chamber dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6898'
abstract:
- lang: eng
text: "Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced,
though strikingly conserved genome. Despite their parasitic lifestyle and isolated
intracellular environment, these bacteria managed to avoid accumulation of deleterious
mutations leading to subsequent genome degradation characteristic for many parasitic
bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species
from genus Chlamydia including identification and functional annotation of orthologous
genes, and characterization of gene gains, losses, and rearrangements. We demonstrate
the overall genome stability of these bacteria as indicated by a large fraction
of common genes with conserved genomic locations. On the other hand, extreme evolvability
is confined to several paralogous gene families such as polymorphic membrane proteins
and phospholipase D, and likely is caused by the pressure from the host immune
system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome
and a small, evolvable periphery likely reflect the balance between the selective
pressure towards genome reduction and the need to adapt to escape from the host
immunity."
article_number: '710'
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.
BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.
BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central,
2019. https://doi.org/10.1186/s12864-019-6059-5.
ieee: O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance
between host adaptation and selective pressure to genome reduction,” BMC Genomics,
vol. 20, no. 1. BioMed Central, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance
between host adaptation and selective pressure to genome reduction. BMC Genomics.
20(1), 710.
mla: Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between
Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics,
vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).
date_created: 2019-09-22T22:00:36Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s12864-019-6059-5
external_id:
isi:
- '000485256100001'
file:
- access_level: open_access
checksum: b798773c5823012d31c812c9f7975da2
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T10:33:17Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6924'
file_name: 2019_BioMed_Sigalova.pdf
file_size: 4157175
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
eissn:
- '14712164'
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
related_material:
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- id: '9731'
relation: research_data
status: public
- id: '9783'
relation: research_data
status: public
- id: '9890'
relation: research_data
status: public
- id: '9892'
relation: research_data
status: public
- id: '9893'
relation: research_data
status: public
- id: '9894'
relation: research_data
status: public
- id: '9895'
relation: research_data
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- id: '9896'
relation: research_data
status: public
- id: '9897'
relation: research_data
status: public
- id: '9898'
relation: research_data
status: public
- id: '9899'
relation: research_data
status: public
- id: '9900'
relation: research_data
status: public
- id: '9901'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Chlamydia pan-genomic analysis reveals balance between host adaptation and
selective pressure to genome reduction
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: 20
year: '2019'
...
---
_id: '6920'
article_processing_charge: No
article_type: original
author:
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation.
Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003
apa: Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in
root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003
chicago: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners
in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003.
ieee: C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth
regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314,
2019.
ista: Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth
regulation. Molecular Plant. 12(10), 1312–1314.
mla: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root
Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019,
pp. 1312–14, doi:10.1016/j.molp.2019.09.003.
short: C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.
date_created: 2019-09-30T10:00:40Z
date_published: 2019-10-07T00:00:00Z
date_updated: 2023-08-30T06:55:02Z
day: '07'
department:
- _id: EvBe
doi: 10.1016/j.molp.2019.09.003
external_id:
isi:
- '000489132500002'
pmid:
- '31541740'
intvolume: ' 12'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1312-1314
pmid: 1
project:
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
- 1752-9867
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene and cytokinin - partners in root growth regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2019'
...
---
_id: '9898'
abstract:
- lang: eng
text: All polyN tracts of length 5 or more nucleotides in sequences of genes from
OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts
implemented in the RAST pipeline. (CSV 133 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.
ieee: O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1.
mla: Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:10:23Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808859.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808859.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 21 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9901'
abstract:
- lang: eng
text: Clusters of Orthologous Genes (COGs) and corresponding functional categories
assigned to OGs. (CSV 117 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1.
ieee: O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808907.v1.
mla: Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T10:54:03Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808907.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808907.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 9 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9899'
abstract:
- lang: eng
text: Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV
362 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1.
ieee: O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808865.v1.
mla: Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:18:09Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808865.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808865.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 2 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9900'
abstract:
- lang: eng
text: Pan-genome statistics by species. (CSV 3 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.
ieee: O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808886.v1.
mla: Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:44:49Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808886.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808886.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 5 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6936'
abstract:
- lang: eng
text: "A key challenge for community ecology is to understand to what extent observational
data can be used to infer the underlying community assembly processes. As different
processes can lead to similar or even identical patterns, statistical analyses
of non‐manipulative observational data never yield undisputable causal inference
on the underlying processes. Still, most empirical studies in community ecology
are based on observational data, and hence understanding under which circumstances
such data can shed light on assembly processes is a central concern for community
ecologists. We simulated a spatial agent‐based model that generates variation
in metacommunity dynamics across multiple axes, including the four classic metacommunity
paradigms as special cases. We further simulated a virtual ecologist who analysed
snapshot data sampled from the simulations using eighteen output metrics derived
from beta‐diversity and habitat variation indices, variation partitioning and
joint species distribution modelling. Our results indicated two main axes of variation
in the output metrics. The first axis of variation described whether the landscape
has patchy or continuous variation, and thus was essentially independent of the
properties of the species community. The second axis of variation related to the
level of predictability of the metacommunity. The most predictable communities
were niche‐based metacommunities inhabiting static landscapes with marked environmental
heterogeneity, such as metacommunities following the species sorting paradigm
or the mass effects paradigm. The most unpredictable communities were neutral‐based
metacommunities inhabiting dynamics landscapes with little spatial heterogeneity,
such as metacommunities following the neutral or patch sorting paradigms. The
output metrics from joint species distribution modelling yielded generally the
highest resolution to disentangle among the simulated scenarios. Yet, the different
types of statistical approaches utilized in this study carried complementary information,
and thus our results suggest that the most comprehensive evaluation of metacommunity
structure can be obtained by combining them.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Otso
full_name: Ovaskainen, Otso
last_name: Ovaskainen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Nerea
full_name: Abrego, Nerea
last_name: Abrego
citation:
ama: Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about
metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444
apa: Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational
data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444
chicago: Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational
Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.
ieee: O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal
about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp.
1877–1886, 2019.
ista: Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal
about metacommunity processes? Ecography. 42(11), 1877–1886.
mla: Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity
Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444.
short: O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.
date_created: 2019-10-08T13:01:24Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:57:25Z
day: '01'
ddc:
- '577'
department:
- _id: DaAl
doi: 10.1111/ecog.04444
ec_funded: 1
external_id:
isi:
- '000486348700001'
file:
- access_level: open_access
checksum: 6c9fbbd5ea8ce10ae93e55ad560a7bf9
content_type: application/pdf
creator: jrybicki
date_created: 2019-10-08T13:07:44Z
date_updated: 2020-07-14T12:47:45Z
file_id: '6937'
file_name: ecog.04444.pdf
file_size: 1682718
relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1877-1886
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Ecography
publication_identifier:
eissn:
- 1600-0587
issn:
- 0906-7590
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: What can observational data reveal about metacommunity processes?
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: 42
year: '2019'
...
---
_id: '6857'
abstract:
- lang: eng
text: "Gene Drives are regarded as future tools with a high potential for population
control. Due to their inherent ability to overcome the rules of Mendelian inheritance,
gene drives (GD) may spread genes rapidly through populations of sexually reproducing
organisms. A release of organisms carrying a GD would constitute a paradigm shift
in the handling of genetically modified organisms because gene drive organisms
(GDO) are designed to drive their transgenes into wild populations and thereby
increase the number of GDOs. The rapid development in this field and its focus
on wild populations demand a prospective risk assessment with a focus on exposure
related aspects. Presently, it is unclear how adequate risk management could be
guaranteed to limit the spread of GDs in time and space, in order to avoid potential
adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the
“Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute
of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight
into the potential population dynamic behavior of GDs and appropriate measures
of control. Scientists from France, Germany, England, and the USA discussed both
topics in this meeting on April 4–5, 2019. This article summarizes results of
the workshop."
article_number: '1900151'
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Giese, B
last_name: Giese
- first_name: J L
full_name: Friess, J L
last_name: Friess
- first_name: 'M F '
full_name: 'Schetelig, M F '
last_name: Schetelig
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Philip
full_name: Messer, Philip
last_name: Messer
- first_name: Florence
full_name: Debarre, Florence
last_name: Debarre
- first_name: H
full_name: Meimberg, H
last_name: Meimberg
- first_name: N
full_name: Windbichler, N
last_name: Windbichler
- first_name: C
full_name: Boete, C
last_name: Boete
citation:
ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory
matters – A report from the workshop “Evaluation of spatial and temporal control
of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151'
apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre,
F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report
from the workshop “Evaluation of spatial and temporal control of Gene Drives”,
4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151'
chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer,
Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics
and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and
Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays.
Wiley, 2019. https://doi.org/10.1002/bies.201900151.'
ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A
report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’,
4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.'
ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg
H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters
– A report from the workshop “Evaluation of spatial and temporal control of Gene
Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.'
mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report
from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’,
4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley,
2019, doi:10.1002/bies.201900151.'
short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre,
H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).
date_created: 2019-09-07T14:40:03Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/bies.201900151
external_id:
isi:
- '000489502000001'
file:
- access_level: open_access
checksum: 8cc7551bff70b2658f8d5630f228ee12
content_type: application/pdf
creator: dernst
date_created: 2019-10-11T06:59:26Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6939'
file_name: 2019_BioEssays_Giese.pdf
file_size: 193248
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop
“Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna'
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: 41
year: '2019'
...
---
_id: '6890'
abstract:
- lang: eng
text: Describing the protein interactions that form pleomorphic and asymmetric viruses
represents a considerable challenge to most structural biology techniques, including
X-ray crystallography and single particle cryo-electron microscopy. Obtaining
a detailed understanding of these interactions is nevertheless important, considering
the number of relevant human pathogens that do not follow strict icosahedral or
helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide
structural insights into complex biological environments and are well suited to
go beyond structures of perfectly symmetric viruses. This chapter discusses recent
developments showing that cryo-ET and subtomogram averaging can provide high-resolution
insights into hitherto unknown structural features of pleomorphic and asymmetric
virus particles. It also describes how these methods have significantly added
to our understanding of retrovirus capsid assemblies in immature and mature viruses.
Additional examples of irregular viruses and their associated proteins, whose
structures have been studied via cryo-ET and subtomogram averaging, further support
the versatility of these methods.
article_processing_charge: No
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary
Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus
Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008'
apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and
asymmetric viruses using cryo-electron tomography and subtomogram averaging. In
F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function
(Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008
chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic
and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
In Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.
ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric
viruses using cryo-electron tomography and subtomogram averaging,” in Complementary
Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed.
Elsevier, 2019, pp. 117–159.
ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies
to Study Virus Structure and Function. vol. 105, 117–159.'
mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and
Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.
short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study
Virus Structure and Function, Elsevier, 2019, pp. 117–159.
date_created: 2019-09-18T08:15:37Z
date_published: 2019-08-27T00:00:00Z
date_updated: 2023-08-30T06:56:00Z
day: '27'
department:
- _id: FlSc
doi: 10.1016/bs.aivir.2019.07.008
editor:
- first_name: Félix A.
full_name: Rey, Félix A.
last_name: Rey
external_id:
isi:
- '000501594500006'
pmid:
- ' 31522703'
intvolume: ' 105'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 117-159
pmid: 1
publication: Complementary Strategies to Study Virus Structure and Function
publication_identifier:
isbn:
- '9780128184561'
issn:
- 0065-3527
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
series_title: Advances in Virus Research
status: public
title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron
tomography and subtomogram averaging
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2019'
...
---
_id: '6940'
abstract:
- lang: eng
text: "We study the effect of a linear tunneling coupling between two-dimensional
systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless
(BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the
one-body correlation functions are algebraically decaying and the other with\r\nexponential
decay. When the linear coupling is turned on, a third BKT-paired phase emerges,
in which one-body correlations are exponentially decaying, while two-body correlation
functions exhibit power-law\r\ndecay. We perform numerical simulations in the
paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences
that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent.
We provide a picture of the phase diagram using a renormalization group approach."
acknowledgement: "We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio
and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from
the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport
from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1
- 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative
Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021
Joint Project “Strongly interacting systems in confined geometries” is gratefully
acknowledged."
article_number: '100601'
article_processing_charge: No
article_type: original
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Nicolò
full_name: Defenu, Nicolò
last_name: Defenu
- first_name: István
full_name: Nándori, István
last_name: Nándori
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
- first_name: Andrea
full_name: Trombettoni, Andrea
last_name: Trombettoni
citation:
ama: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 2019;123(10).
doi:10.1103/physrevlett.123.100601
apa: Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019).
Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601
chicago: Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea
Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.”
Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601.
ieee: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models,” Physical Review Letters, vol. 123,
no. 10. American Physical Society, 2019.
ista: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.
mla: Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled
XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American
Physical Society, 2019, doi:10.1103/physrevlett.123.100601.
short: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical
Review Letters 123 (2019).
date_created: 2019-10-14T06:31:13Z
date_published: 2019-09-06T00:00:00Z
date_updated: 2023-08-30T06:57:53Z
day: '06'
department:
- _id: MiLe
doi: 10.1103/physrevlett.123.100601
external_id:
arxiv:
- '1907.06253'
isi:
- '000483587200004'
intvolume: ' 123'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.06253
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News auf IST Website
relation: press_release
url: https://ist.ac.at/en/news/new-form-of-magnetism-found/
scopus_import: '1'
status: public
title: Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 123
year: '2019'
...
---
_id: '6919'
article_number: eaaw6490
article_processing_charge: No
author:
- first_name: Chao
full_name: Qi, Chao
last_name: Qi
- first_name: Giulio Di
full_name: Minin, Giulio Di
last_name: Minin
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Anton
full_name: Wutz, Anton
last_name: Wutz
- first_name: Volodymyr M.
full_name: Korkhov, Volodymyr M.
last_name: Korkhov
citation:
ama: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol
recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9).
doi:10.1126/sciadv.aaw6490
apa: Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019).
Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490
chicago: Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr
M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor
PTCH1.” Science Advances. American Association for the Advancement of Science,
2019. https://doi.org/10.1126/sciadv.aaw6490.
ieee: C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural
basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances,
vol. 5, no. 9. American Association for the Advancement of Science, 2019.
ista: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of
sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490.
mla: Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog
Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association
for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.
short: C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances
5 (2019).
date_created: 2019-09-29T22:00:45Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2023-08-30T06:55:31Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1126/sciadv.aaw6490
external_id:
isi:
- '000491128800062'
file:
- access_level: open_access
checksum: b2256c9117655bc15f621ba0babf219f
content_type: application/pdf
creator: kschuh
date_created: 2019-10-02T11:13:54Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6928'
file_name: 2019_AAAS_Qi.pdf
file_size: 1236101
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of sterol recognition by human hedgehog receptor PTCH1
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2019'
...
---
_id: '6983'
abstract:
- lang: eng
text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when
Plasmodium-infected mosquitoes inject malaria sporozoites while searching for
blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes,
and form liver stages which in mice 48 h later escape into blood and cause clinical
malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating
and eliminating all liver stages in 48 h, thus preventing the blood-stage disease.
However, the rules of how CD8 T cells are able to locate all liver stages within
a relatively short time period remains poorly understood. We recently reported
formation of clusters consisting of variable numbers of activated CD8 T cells
around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental
data and mathematical models we now provide additional insights into mechanisms
of formation of these clusters. First, we show that a model in which cluster formation
is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness”
of different liver stages, cannot explain distribution of cluster sizes in different
experimental conditions. In contrast, the model in which cluster formation is
driven by the positive feedback loop (i.e., larger clusters attract more CD8 T
cells) can accurately explain the available data. Second, while both Py-specific
CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are
attracted to the clusters, we found no evidence that non-specific CD8 T cells
play a role in cluster formation. Third and finally, mathematical modeling suggested
that formation of clusters occurs rapidly, within few hours after adoptive transfer
of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their
targets in complex peripheral organs, such as the liver. Taken together, our analysis
provides novel insights into and attempts to discriminate between alternative
mechanisms driving the formation of clusters of antigen-specific CD8 T cells in
the liver.
article_number: '2153'
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: H
full_name: Rajakaruna, H
last_name: Rajakaruna
- first_name: IA
full_name: Cockburn, IA
last_name: Cockburn
- first_name: VV
full_name: Ganusov, VV
last_name: Ganusov
citation:
ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8
T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153
apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering
of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153
chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering
of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven
by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.
ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of
activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers,
2019.
ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated
CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 10, 2153.
mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected
Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in
Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.
short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology
10 (2019).
date_created: 2019-11-04T15:50:06Z
date_published: 2019-09-20T00:00:00Z
date_updated: 2023-08-30T07:18:23Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3389/fimmu.2019.02153
external_id:
isi:
- '000487187000001'
pmid:
- '31616407'
file:
- access_level: open_access
checksum: 68d1708f7aa412544159b498ef17a6b9
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:54:00Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6984'
file_name: 2019_FrontiersImmonology_Kelemen.pdf
file_size: 2083061
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is
rapid and is driven by antigen-specific cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6972'
abstract:
- lang: eng
text: 'We give fault-tolerant algorithms for establishing synchrony in distributed
systems in which each of thennodes has its own clock. Our algorithms operate in
a very strong fault model: we require self-stabilisation, i.e.,the initial state
of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471
apa: Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471
chicago: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock
Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM,
2019. https://doi.org/10.1145/3339471.
ieee: C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM,
2019.
ista: Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. 66(5), 32.
mla: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation
Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32,
ACM, 2019, doi:10.1145/3339471.
short: C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).
date_created: 2019-10-24T17:12:48Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-30T07:07:23Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3339471
ec_funded: 1
external_id:
arxiv:
- '1705.06173'
isi:
- '000496514100001'
file:
- access_level: open_access
checksum: 7e5d95c478e0e393f4927fcf7e48194e
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:58:38Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6975'
file_name: 2019_JACM_Lenzen.pdf
file_size: 2183085
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-stabilising Byzantine clock synchronisation is almost as easy as consensus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 66
year: '2019'
...
---
_id: '6942'
abstract:
- lang: eng
text: "Graph games and Markov decision processes (MDPs) are standard models in reactive
synthesis and verification of probabilistic systems with nondeterminism. The class
of \U0001D714 -regular winning conditions; e.g., safety, reachability, liveness,
parity conditions; provides a robust and expressive specification formalism for
properties that arise in analysis of reactive systems. The resolutions of nondeterminism
in games and MDPs are represented as strategies, and we consider succinct representation
of such strategies. The decision-tree data structure from machine learning retains
the flavor of decisions of strategies and allows entropy-based minimization to
obtain succinct trees. However, in contrast to traditional machine-learning problems
where small errors are allowed, for winning strategies in graph games and MDPs
no error is allowed, and the decision tree must represent the entire strategy.
In this work we propose decision trees with linear classifiers for representation
of strategies in graph games and MDPs. We have implemented strategy representation
using this data structure and we present experimental results for problems on
graph games and MDPs, which show that this new data structure presents a much
more efficient strategy representation as compared to standard decision trees."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jan
full_name: Křetínský, Jan
last_name: Křetínský
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy
representation by decision trees with linear classifiers. In: 16th International
Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature;
2019:109-128. doi:10.1007/978-3-030-30281-8_7'
apa: 'Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., &
Toman, V. (2019). Strategy representation by decision trees with linear classifiers.
In 16th International Conference on Quantitative Evaluation of Systems
(Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7'
chicago: Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph
Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear
Classifiers.” In 16th International Conference on Quantitative Evaluation of
Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7.
ieee: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman,
“Strategy representation by decision trees with linear classifiers,” in 16th
International Conference on Quantitative Evaluation of Systems, Glasgow, United
Kingdom, 2019, vol. 11785, pp. 109–128.
ista: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019.
Strategy representation by decision trees with linear classifiers. 16th International
Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation
of Systems, LNCS, vol. 11785, 109–128.'
mla: Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear
Classifiers.” 16th International Conference on Quantitative Evaluation of Systems,
vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.
short: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman,
in:, 16th International Conference on Quantitative Evaluation of Systems, Springer
Nature, 2019, pp. 109–128.
conference:
end_date: 2019-09-12
location: Glasgow, United Kingdom
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2019-09-10
date_created: 2019-10-14T06:57:49Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2023-08-30T06:59:36Z
day: '04'
department:
- _id: KrCh
- _id: ChLa
doi: 10.1007/978-3-030-30281-8_7
external_id:
arxiv:
- '1906.08178'
isi:
- '000679281300007'
intvolume: ' 11785'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.08178
month: '09'
oa: 1
oa_version: Preprint
page: 109-128
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: 16th International Conference on Quantitative Evaluation of Systems
publication_identifier:
eisbn:
- '9783030302818'
isbn:
- '9783030302801'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy representation by decision trees with linear classifiers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11785
year: '2019'
...
---
_id: '6955'
abstract:
- lang: eng
text: We study few-body bound states of charged particles subject to attractive
zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic
length scales of the system at zero energy are set by the Coulomb length scale
D and the Coulomb-modified effective range r eff. We study shallow bound states
of charged particles with D >> r eff and show that these systems obey universal
scaling laws different from neutral particles. An accurate description of these
states requires both the Coulomb-modified scattering length and the effective
range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant
for bound states whose spatial extent is significantly larger than the range of
the attractive potential. These states enjoy universality – their character is
independent of the shape of the short-range potential.
article_number: '135016'
article_processing_charge: No
article_type: original
author:
- first_name: C.H.
full_name: Schmickler, C.H.
last_name: Schmickler
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of
a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016
apa: Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics
of bound states of a few charged particles. Physics Letters B. Elsevier.
https://doi.org/10.1016/j.physletb.2019.135016
chicago: Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics
of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier,
2019. https://doi.org/10.1016/j.physletb.2019.135016.
ieee: C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound
states of a few charged particles,” Physics Letters B, vol. 798. Elsevier,
2019.
ista: Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states
of a few charged particles. Physics Letters B. 798, 135016.
mla: Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged
Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016.
short: C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).
date_created: 2019-10-18T18:33:32Z
date_published: 2019-11-10T00:00:00Z
date_updated: 2023-08-30T07:06:42Z
day: '10'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1016/j.physletb.2019.135016
external_id:
arxiv:
- '1904.00913'
isi:
- '000494939000086'
file:
- access_level: open_access
checksum: d27f983b34ea7dafdf356afbf9472fbf
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:47:04Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6974'
file_name: 2019_PhysicsLettersB_Schmickler.pdf
file_size: 528362
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 798'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Physics Letters B
publication_identifier:
issn:
- 0370-2693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal physics of bound states of a few charged particles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 798
year: '2019'
...
---
_id: '7005'
abstract:
- lang: eng
text: Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during
intense neuronal activity via a two-step process. First, bulk endosomes are formed
direct from the plasma membrane from which SVs are then generated. SV generation
from bulk endosomes requires the efflux of previously accumulated calcium and
activation of the protein phosphatase calcineurin. However, it is still unknown
how calcineurin mediates SV generation. We addressed this question using a series
of acute interventions that decoupled the generation of SVs from bulk endosomes
in rat primary neuronal culture. This was achieved by either disruption of protein–protein
interactions via delivery of competitive peptides, or inhibition of enzyme activity
by known inhibitors. SV generation was monitored using either a morphological
horseradish peroxidase assay or an optical assay that monitors the replenishment
of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides
that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity
and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin
I interaction. Peptides that disrupted syndapin I interactions with eps15 homology
domain-containing proteins had no effect. This revealed that (i) calcineurin must
be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity
is essential for SV fission and (iii) the calcineurin-dependent interaction between
dynamin I and syndapin I is essential for SV generation. We therefore propose
that a calcineurin-dependent dephosphorylation cascade that requires both dynamin
I GTPase and syndapin I lipid-deforming activity is essential for SV generation
from bulk endosomes.
article_processing_charge: No
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Michael A.
full_name: Cousin, Michael A.
last_name: Cousin
citation:
ama: Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk
endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862
apa: Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from
activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin
interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862
chicago: Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation
from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent
Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019.
https://doi.org/10.1111/jnc.14862.
ieee: G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,”
Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.
ista: Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent
bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction.
Journal of Neurochemistry. 151(5), 570–583.
mla: Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from
Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin
Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019,
pp. 570–83, doi:10.1111/jnc.14862.
short: G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.
date_created: 2019-11-12T14:37:08Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:21:50Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1111/jnc.14862
external_id:
isi:
- '000490703100001'
pmid:
- '31479508'
file:
- access_level: open_access
checksum: ec1fb2aebb874009bc309adaada6e1d7
content_type: application/pdf
creator: dernst
date_created: 2020-02-05T10:30:02Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7452'
file_name: 2019_JournNeurochemistry_Cheung.pdf
file_size: 4334962
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 570-583
pmid: 1
publication: Journal of Neurochemistry
publication_identifier:
eissn:
- 1471-4159
issn:
- 0022-3042
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synaptic vesicle generation from activity‐dependent bulk endosomes requires
a dephosphorylation‐dependent dynamin–syndapin interaction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 151
year: '2019'
...
---
_id: '7000'
abstract:
- lang: eng
text: The main contributions of this paper are the proposition and the convergence
analysis of a class of inertial projection-type algorithm for solving variational
inequality problems in real Hilbert spaces where the underline operator is monotone
and uniformly continuous. We carry out a unified analysis of the proposed method
under very mild assumptions. In particular, weak convergence of the generated
sequence is established and nonasymptotic O(1 / n) rate of convergence is established,
where n denotes the iteration counter. We also present some experimental results
to illustrate the profits gained by introducing the inertial extrapolation steps.
article_number: '161'
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Xiao-Huan
full_name: Li, Xiao-Huan
last_name: Li
- first_name: Qiao-Li
full_name: Dong, Qiao-Li
last_name: Dong
citation:
ama: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method
for variational inequalities. Computational and Applied Mathematics. 2019;38(4).
doi:10.1007/s40314-019-0955-9
apa: Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence
analysis of projection method for variational inequalities. Computational and
Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9
chicago: Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence
Analysis of Projection Method for Variational Inequalities.” Computational
and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9.
ieee: Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of
projection method for variational inequalities,” Computational and Applied
Mathematics, vol. 38, no. 4. Springer Nature, 2019.
ista: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection
method for variational inequalities. Computational and Applied Mathematics. 38(4),
161.
mla: Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational
Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161,
Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.
short: Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics
38 (2019).
date_created: 2019-11-12T12:41:44Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:20:32Z
day: '01'
ddc:
- '510'
- '515'
- '518'
department:
- _id: VlKo
doi: 10.1007/s40314-019-0955-9
ec_funded: 1
external_id:
arxiv:
- '2101.09081'
isi:
- '000488973100005'
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s40314-019-0955-9
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Computational and Applied Mathematics
publication_identifier:
eissn:
- 1807-0302
issn:
- 2238-3603
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence analysis of projection method for variational inequalities
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '7009'
abstract:
- lang: eng
text: Cell migration is essential for physiological processes as diverse as development,
immune defence and wound healing. It is also a hallmark of cancer malignancy.
Thousands of publications have elucidated detailed molecular and biophysical mechanisms
of cultured cells migrating on flat, 2D substrates of glass and plastic. However,
much less is known about how cells successfully navigate the complex 3D environments
of living tissues. In these more complex, native environments, cells use multiple
modes of migration, including mesenchymal, amoeboid, lobopodial and collective,
and these are governed by the local extracellular microenvironment, specific modalities
of Rho GTPase signalling and non- muscle myosin contractility. Migration through
3D environments is challenging because it requires the cell to squeeze through
complex or dense extracellular structures. Doing so requires specific cellular
adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling.
In addition, besides navigating through diverse ECM environments and overcoming
extracellular barriers, cells often interact with neighbouring cells and tissues
through physical and signalling interactions. Accordingly, cells need to call
on an impressively wide diversity of mechanisms to meet these challenges. This
Review examines how cells use both classical and novel mechanisms of locomotion
as they traverse challenging 3D matrices and cellular environments. It focuses
on principles rather than details of migratory mechanisms and draws comparisons
between 1D, 2D and 3D migration.
article_processing_charge: No
article_type: review
author:
- first_name: KM
full_name: Yamada, KM
last_name: Yamada
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular
Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9
apa: Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature
Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9
chicago: Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature
Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.
ieee: K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews
Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.
ista: Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular
Cell Biology. 20(12), 738–752.
mla: Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature
Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp.
738–752, doi:10.1038/s41580-019-0172-9.
short: K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.
date_created: 2019-11-12T14:54:42Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-30T07:22:20Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41580-019-0172-9
external_id:
isi:
- '000497966900007'
pmid:
- '31582855'
intvolume: ' 20'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 738–752
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
eissn:
- 1471-0080
issn:
- 1471-0072
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms of 3D cell migration
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2019'
...
---
_id: '6988'
abstract:
- lang: eng
text: 'Platelets are central players in thrombosis and hemostasis but are increasingly
recognized as key components of the immune system. They shape ensuing immune responses
by recruiting leukocytes, and support the development of adaptive immunity. Recent
data shed new light on the complex role of platelets in immunity. Here, we summarize
experimental and clinical data on the role of platelets in host defense against
bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet
proinflammatory effector functions and cross-talk with the coagulation system,
can also result in damage to the host (e.g., acute lung injury and sepsis). Novel
clinical insights support this dichotomy: platelet inhibition/thrombocytopenia
can be either harmful or protective, depending on pathophysiological context.
Clinical studies are currently addressing this aspect in greater depth.'
article_processing_charge: No
article_type: review
author:
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: 'Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004'
apa: 'Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host
defense: Experimental and clinical insights. Trends in Immunology. Cell
Press. https://doi.org/10.1016/j.it.2019.08.004'
chicago: 'Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host
Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell
Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.'
ieee: 'L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental
and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press,
pp. 922–938, 2019.'
ista: 'Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental
and clinical insights. Trends in Immunology. 40(10), 922–938.'
mla: 'Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical
Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp.
922–38, doi:10.1016/j.it.2019.08.004.'
short: L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.
date_created: 2019-11-04T16:27:36Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:19:23Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.it.2019.08.004
ec_funded: 1
external_id:
isi:
- '000493292100005'
pmid:
- '31601520'
intvolume: ' 40'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 922-938
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Trends in Immunology
publication_identifier:
issn:
- 1471-4906
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Platelets in host defense: Experimental and clinical insights'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2019'
...
---
_id: '7002'
abstract:
- lang: eng
text: Multiple Importance Sampling (MIS) is a key technique for achieving robustness
of Monte Carlo estimators in computer graphics and other fields. We derive optimal
weighting functions for MIS that provably minimize the variance of an MIS estimator,
given a set of sampling techniques. We show that the resulting variance reduction
over the balance heuristic can be higher than predicted by the variance bounds
derived by Veach and Guibas, who assumed only non-negative weights in their proof.
We theoretically analyze the variance of the optimal MIS weights and show the
relation to the variance of the balance heuristic. Furthermore, we establish a
connection between the new weighting functions and control variates as previously
applied to mixture sampling. We apply the new optimal weights to integration problems
in light transport and show that they allow for new design considerations when
choosing the appropriate sampling techniques for a given integration problem.
article_number: '37'
article_processing_charge: No
article_type: original
author:
- first_name: Ivo
full_name: Kondapaneni, Ivo
last_name: Kondapaneni
- first_name: Petr
full_name: Vevoda, Petr
last_name: Vevoda
- first_name: Pascal
full_name: Grittmann, Pascal
last_name: Grittmann
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Philipp
full_name: Slusallek, Philipp
last_name: Slusallek
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
citation:
ama: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal
multiple importance sampling. ACM Transactions on Graphics. 2019;38(4).
doi:10.1145/3306346.3323009
apa: Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., &
Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3306346.3323009
chicago: Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp
Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM
Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.
ieee: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J.
Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics,
vol. 38, no. 4. ACM, 2019.
ista: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J.
2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4),
37.
mla: Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions
on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009.
short: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek,
ACM Transactions on Graphics 38 (2019).
date_created: 2019-11-12T13:05:40Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-30T07:21:25Z
day: '01'
department:
- _id: ChWo
doi: 10.1145/3306346.3323009
ec_funded: 1
external_id:
isi:
- '000475740600011'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal multiple importance sampling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6978'
abstract:
- lang: eng
text: In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent
work, we study numerically the localized turbulence in pipe flow and elucidate
astate space structure that gives rise to transient chaos. Starting from the basin
boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence
of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe
homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which
wasconjectured in various earlier studies. By mapping the transverse intersections
between thestable and unstable manifold of a periodic orbit, we identify the gateways
that promote anescape from turbulence.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Akshunna
full_name: Dogra, Akshunna
last_name: Dogra
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401
apa: Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos
in streamwise-localized pipe flow turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401
chicago: Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient
Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids.
American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401.
ieee: N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized
pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American
Physical Society, p. 102401, 2019.
ista: Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized
pipe flow turbulence. Physical Review Fluids. 4(10), 102401.
mla: Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized
Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American
Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401.
short: N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.
date_created: 2019-11-04T10:04:01Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-30T07:20:03Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.4.102401
external_id:
arxiv:
- '1810.02211'
isi:
- '000493510400001'
intvolume: ' 4'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.02211
month: '10'
oa: 1
oa_version: Preprint
page: '102401'
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of transient chaos in streamwise-localized pipe flow turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '7026'
abstract:
- lang: eng
text: Effective design of combination therapies requires understanding the changes
in cell physiology that result from drug interactions. Here, we show that the
genome-wide transcriptional response to combinations of two drugs, measured at
a rigorously controlled growth rate, can predict higher-order antagonism with
a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90%
of the variation in cellular response can be decomposed into three principal components
(PCs) that have clear biological interpretations. We demonstrate that the third
PC captures emergent transcriptional programs that are dependent on both drugs
and can predict antagonism with a third drug targeting the emergent pathway. We
further show that emergent gene expression patterns are most pronounced at a drug
ratio where the drug interaction is strongest, providing a guideline for future
measurements. Our results provide a readily applicable recipe for uncovering emergent
responses in other systems and for higher-order drug combinations. A record of
this paper’s transparent peer review process is included in the Supplemental Information.
acknowledged_ssus:
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations
predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3.
doi:10.1016/j.cels.2019.10.004
apa: Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses
to drug combinations predict higher-order drug interactions. Cell Systems.
Cell Press. https://doi.org/10.1016/j.cels.2019.10.004
chicago: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression
Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell
Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004.
ieee: M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to
drug combinations predict higher-order drug interactions,” Cell Systems,
vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.
ista: Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug
combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.
mla: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses
to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems,
vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.
short: M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.
date_created: 2019-11-15T10:51:42Z
date_published: 2019-11-27T00:00:00Z
date_updated: 2023-08-30T07:24:58Z
day: '27'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.cels.2019.10.004
external_id:
isi:
- '000499495400003'
file:
- access_level: open_access
checksum: 7a11d6c2f9523d65b049512d61733178
content_type: application/pdf
creator: dernst
date_created: 2019-11-15T10:57:42Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7027'
file_name: 2019_CellSystems_Lukacisin.pdf
file_size: 4238460
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 423-433.e1-e3
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- 2405-4712
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent gene expression responses to drug combinations predict higher-order
drug interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '7034'
abstract:
- lang: eng
text: We find a graph of genus 5 and its drawing on the orientable surface of genus
4 with every pair of independent edges crossing an even number of times. This
shows that the strong Hanani–Tutte theorem cannot be extended to the orientable
surface of genus 4. As a base step in the construction we use a counterexample
to an extension of the unified Hanani–Tutte theorem on the torus.
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem
on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7
apa: Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7
chicago: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the
Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer
Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7.
ieee: R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer
Nature, pp. 1267–1279, 2019.
ista: Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte
theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.
mla: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte
Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer
Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.
short: R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.
date_created: 2019-11-18T14:29:50Z
date_published: 2019-10-29T00:00:00Z
date_updated: 2023-08-30T07:26:25Z
day: '29'
department:
- _id: UlWa
doi: 10.1007/s00493-019-3905-7
ec_funded: 1
external_id:
arxiv:
- '1709.00508'
isi:
- '000493267200003'
intvolume: ' 39'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.00508
month: '10'
oa: 1
oa_version: Preprint
page: 1267-1279
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Combinatorica
publication_identifier:
eissn:
- 1439-6912
issn:
- 0209-9683
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counterexample to an extension of the Hanani-Tutte theorem on the surface of
genus 4
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2019'
...
---
_id: '7032'
abstract:
- lang: eng
text: Optical frequency combs (OFCs) are light sources whose spectra consists of
equally spaced frequency lines in the optical domain [1]. They have great potential
for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy,
and high-precision measurements [2].
article_number: '8873300'
article_processing_charge: No
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Madhuri
full_name: Kuamri, Madhuri
last_name: Kuamri
- first_name: Harald G. L.
full_name: Schwefel, Harald G. L.
last_name: Schwefel
citation:
ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic
frequency comb generation in lithium niobate whispering gallery mode resonators.
In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300'
apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel,
H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering
gallery mode resonators. In 2019 Conference on Lasers and Electro-Optics Europe
& European Quantum Electronics Conference. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300'
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri,
and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium
Niobate Whispering Gallery Mode Resonators.” In 2019 Conference on Lasers and
Electro-Optics Europe & European Quantum Electronics Conference. IEEE,
2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel,
“Electro-optic frequency comb generation in lithium niobate whispering gallery
mode resonators,” in 2019 Conference on Lasers and Electro-Optics Europe &
European Quantum Electronics Conference, Munich, Germany, 2019.
ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic
frequency comb generation in lithium niobate whispering gallery mode resonators.
2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics
Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.'
mla: Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation
in Lithium Niobate Whispering Gallery Mode Resonators.” 2019 Conference on
Lasers and Electro-Optics Europe & European Quantum Electronics Conference,
8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300.
short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:,
2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics
Conference, IEEE, 2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: 'CLEO: Conference on Lasers and Electro-Optics Europe'
start_date: 2019-06-23
date_created: 2019-11-18T13:58:22Z
date_published: 2019-10-17T00:00:00Z
date_updated: 2023-08-30T07:26:01Z
day: '17'
department:
- _id: JoFi
doi: 10.1109/cleoe-eqec.2019.8873300
external_id:
isi:
- '000630002701617'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference
publication_identifier:
isbn:
- '9781728104690'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electro-optic frequency comb generation in lithium niobate whispering gallery
mode resonators
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7095'
abstract:
- lang: eng
text: BAX, a member of the BCL2 gene family, controls the committed step of the
intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed
feature of apoptosis, which occurs through the process of mitochondrial fission.
BAX has consistently been associated with mitochondrial fission, yet how BAX participates
in the process of mitochondrial fragmentation during apoptosis remains to be tested.
Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates
that rapid mitochondrial fragmentation during apoptosis occurs after the complete
recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement
of a fully functioning BAX protein for the fission process was demonstrated further
in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant
performed fusion to restore the mitochondrial network. but was not demonstrably
recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial
fragmentation was blocked. Additionally, we show that loss of the fission protein,
dynamin-like protein 1 (DRP1), does not temporally affect the initiation time
or rate of BAX recruitment, but does reduce the final level of BAX recruited to
the MOM during the late phase of BAX recruitment. These correlative observations
suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial
fragmentation machinery in apoptotic cells.
article_number: '16565'
article_processing_charge: No
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: J. A.
full_name: Grosser, J. A.
last_name: Grosser
- first_name: R. L.
full_name: Fehrman, R. L.
last_name: Fehrman
- first_name: C. L.
full_name: Schlamp, C. L.
last_name: Schlamp
- first_name: R. W.
full_name: Nickells, R. W.
last_name: Nickells
citation:
ama: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX
recruitment correlates with mitochondrial fission during apoptosis. Scientific
Reports. 2019;9. doi:10.1038/s41598-019-53049-w
apa: Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells,
R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission
during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w
chicago: Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W.
Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission
during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w.
ieee: M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells,
“Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,”
Scientific Reports, vol. 9. Springer Nature, 2019.
ista: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion
of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific
Reports. 9, 16565.
mla: Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial
Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer
Nature, 2019, doi:10.1038/s41598-019-53049-w.
short: M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific
Reports 9 (2019).
date_created: 2019-11-25T07:45:17Z
date_published: 2019-11-12T00:00:00Z
date_updated: 2023-08-30T07:26:54Z
day: '12'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41598-019-53049-w
external_id:
isi:
- '000495857600019'
pmid:
- '31719602'
file:
- access_level: open_access
checksum: 9ab397ed9c1c454b34bffb8cc863d734
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T07:49:52Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7096'
file_name: 2019_ScientificReports_Maes.pdf
file_size: 6467393
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Completion of BAX recruitment correlates with mitochondrial fission during
apoptosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '7097'
abstract:
- lang: eng
text: Early endosomes, also called sorting endosomes, are known to mature into late
endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early
endosome existence isthought to be maintained by the continual fusion of transport
vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show
instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial
for the formation of endosomes andthe subsequent endolysosomal traffic regulated
by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide
exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p
and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components
is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and
the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation
and identify the TGN as a critical location forregulating progress through the
endolysosomal trafficking pathway.
article_number: '419'
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation
is regulated at the trans-Golgi network. Communications Biology. 2019;2(1).
doi:10.1038/s42003-019-0670-5
apa: Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated
endosome formation is regulated at the trans-Golgi network. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5
chicago: Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated
Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications
Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.
ieee: M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome
formation is regulated at the trans-Golgi network,” Communications Biology,
vol. 2, no. 1. Springer Nature, 2019.
ista: Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome
formation is regulated at the trans-Golgi network. Communications Biology. 2(1),
419.
mla: Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the
Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer
Nature, 2019, doi:10.1038/s42003-019-0670-5.
short: M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology
2 (2019).
date_created: 2019-11-25T07:55:01Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2023-08-30T07:27:55Z
day: '15'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1038/s42003-019-0670-5
external_id:
isi:
- '000496767800005'
file:
- access_level: open_access
checksum: c63c69a264fc8a0e52f2b0d482f3bdae
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T07:58:05Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7098'
file_name: 2019_CommunicBiology_Nagano.pdf
file_size: 2626069
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rab5-mediated endosome formation is regulated at the trans-Golgi network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2
year: '2019'
...
---
_id: '7099'
acknowledgement: "The authors thank Gabi Schmid for excellent technical support. We
also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the
specificity\r\nof some of the antibodies used in this study on replicas. Funding
was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung)
Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.),
and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National
Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous
version of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Kasugai, Yu
last_name: Kasugai
- first_name: Elisabeth
full_name: Vogel, Elisabeth
last_name: Vogel
- first_name: Heide
full_name: Hörtnagl, Heide
last_name: Hörtnagl
- first_name: Sabine
full_name: Schönherr, Sabine
last_name: Schönherr
- first_name: Enrica
full_name: Paradiso, Enrica
last_name: Paradiso
- first_name: Markus
full_name: Hauschild, Markus
last_name: Hauschild
- first_name: Georg
full_name: Göbel, Georg
last_name: Göbel
- first_name: Ivan
full_name: Milenkovic, Ivan
last_name: Milenkovic
- first_name: Yvan
full_name: Peterschmitt, Yvan
last_name: Peterschmitt
- first_name: Ramon
full_name: Tasan, Ramon
last_name: Tasan
- first_name: Günther
full_name: Sperk, Günther
last_name: Sperk
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Werner
full_name: Sieghart, Werner
last_name: Sieghart
- first_name: Nicolas
full_name: Singewald, Nicolas
last_name: Singewald
- first_name: Andreas
full_name: Lüthi, Andreas
last_name: Lüthi
- first_name: Francesco
full_name: Ferraguti, Francesco
last_name: Ferraguti
citation:
ama: Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling
of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4.
doi:10.1016/j.neuron.2019.08.013
apa: Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild,
M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic
synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013
chicago: Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica
Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling
of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier,
2019. https://doi.org/10.1016/j.neuron.2019.08.013.
ieee: Y. Kasugai et al., “Structural and functional remodeling of amygdala
GABAergic synapses in associative fear learning,” Neuron, vol. 104, no.
4. Elsevier, p. 781–794.e4, 2019.
ista: Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel
G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald
N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala
GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.
mla: Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic
Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier,
2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013.
short: Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild,
G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W.
Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.
date_created: 2019-11-25T08:02:39Z
date_published: 2019-11-20T00:00:00Z
date_updated: 2023-08-30T07:28:22Z
day: '20'
ddc:
- '571'
- '599'
department:
- _id: RySh
doi: 10.1016/j.neuron.2019.08.013
external_id:
isi:
- '000497963500017'
pmid:
- '31543297'
has_accepted_license: '1'
intvolume: ' 104'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.08.013
month: '11'
oa: 1
oa_version: Published Version
page: 781-794.e4
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural and functional remodeling of amygdala GABAergic synapses in associative
fear learning
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2019'
...
---
_id: '6455'
abstract:
- lang: eng
text: During corticogenesis, distinct subtypes of neurons are sequentially born
from ventricular zone progenitors. How these cells are molecularly temporally
patterned is poorly understood. We used single-cell RNA sequencing at high temporal
resolution to trace the lineage of the molecular identities of successive generations
of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified
a core set of evolutionarily conserved, temporally patterned genes that drive
APs from internally driven to more exteroceptive states. We found that the Polycomb
repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic
age–dependent AP molecular states are transmitted to their progeny as successive
ground states, onto which essentially conserved early postmitotic differentiation
programs are applied, and are complemented by later-occurring environment-dependent
signals. Thus, epigenetically regulated temporal molecular birthmarks present
in progenitors act in their postmitotic progeny to seed adult neuronal diversity.
article_number: eaav2522
article_processing_charge: No
article_type: original
author:
- first_name: L
full_name: Telley, L
last_name: Telley
- first_name: G
full_name: Agirman, G
last_name: Agirman
- first_name: J
full_name: Prados, J
last_name: Prados
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: S
full_name: Fièvre, S
last_name: Fièvre
- first_name: P
full_name: Oberst, P
last_name: Oberst
- first_name: G
full_name: Bartolini, G
last_name: Bartolini
- first_name: I
full_name: Vitali, I
last_name: Vitali
- first_name: C
full_name: Cadilhac, C
last_name: Cadilhac
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: L
full_name: Nguyen, L
last_name: Nguyen
- first_name: A
full_name: Dayer, A
last_name: Dayer
- first_name: D
full_name: Jabaudon, D
last_name: Jabaudon
citation:
ama: Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors
and their daughter neurons in the developing neocortex. Science. 2019;364(6440).
doi:10.1126/science.aav2522
apa: Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., …
Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter
neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522
chicago: Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini,
et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in
the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.
ieee: L. Telley et al., “Temporal patterning of apical progenitors and their
daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440.
AAAS, 2019.
ista: Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G,
Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal
patterning of apical progenitors and their daughter neurons in the developing
neocortex. Science. 364(6440), eaav2522.
mla: Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter
Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522,
AAAS, 2019, doi:10.1126/science.aav2522.
short: L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini,
I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science
364 (2019).
date_created: 2019-05-14T13:07:47Z
date_published: 2019-05-10T00:00:00Z
date_updated: 2023-09-05T11:51:09Z
day: '10'
department:
- _id: SiHi
doi: 10.1126/science.aav2522
ec_funded: 1
external_id:
isi:
- '000467631800034'
pmid:
- '31073041'
intvolume: ' 364'
isi: 1
issue: '6440'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/
scopus_import: '1'
status: public
title: Temporal patterning of apical progenitors and their daughter neurons in the
developing neocortex
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 364
year: '2019'
...
---
_id: '6586'
abstract:
- lang: eng
text: The bottom-up assembly of colloidal nanocrystals is a versatile methodology
to produce composite nanomaterials with precisely tuned electronic properties.
Beyond the synthetic control over crystal domain size, shape, crystal phase, and
composition, solution-processed nanocrystals allow exquisite surface engineering.
This provides additional means to modulate the nanomaterial characteristics and
particularly its electronic transport properties. For instance, inorganic surface
ligands can be used to tune the type and concentration of majority carriers or
to modify the electronic band structure. Herein, we report the thermoelectric
properties of SnTe nanocomposites obtained from the consolidation of surface-engineered
SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to
(i) converge the light and heavy bands through partial Cd alloying and (ii) generate
CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing
the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric
figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge,
the highest thermoelectric figure of merit reported for solution-processed SnTe.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Beatrice
full_name: Kuster, Beatrice
last_name: Kuster
- first_name: Maximilian
full_name: Schuster, Maximilian
last_name: Schuster
- first_name: Oleksandr
full_name: Dobrozhan, Oleksandr
last_name: Dobrozhan
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Maksym V.
full_name: Kovalenko, Maksym V.
last_name: Kovalenko
citation:
ama: Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up
assembled SnTe nanocomposites for thermoelectric energy conversion. Journal
of the American Chemical Society. 2019;141(20):8025-8029. doi:10.1021/jacs.9b01394
apa: Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko,
M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites
for thermoelectric energy conversion. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/jacs.9b01394
chicago: Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian
Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up
Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal
of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b01394.
ieee: M. Ibáñez et al., “Ligand-mediated band engineering in bottom-up assembled
SnTe nanocomposites for thermoelectric energy conversion,” Journal of the American
Chemical Society, vol. 141, no. 20. American Chemical Society, pp. 8025–8029,
2019.
ista: Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid
D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in
bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion.
Journal of the American Chemical Society. 141(20), 8025–8029.
mla: Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled
SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American
Chemical Society, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29,
doi:10.1021/jacs.9b01394.
short: M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan,
D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical
Society 141 (2019) 8025–8029.
date_created: 2019-06-25T11:53:35Z
date_published: 2019-04-19T00:00:00Z
date_updated: 2023-09-05T12:03:45Z
day: '19'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/jacs.9b01394
ec_funded: 1
external_id:
isi:
- '000469292300004'
pmid:
- '31017419 '
file:
- access_level: open_access
checksum: 34d7ec837869cc6a07996b54f75696b7
content_type: application/pdf
creator: cpetz
date_created: 2019-06-25T11:59:00Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6587'
file_name: JACS_April2019.pdf
file_size: 6234004
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 141'
isi: 1
issue: '20'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 8025-8029
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites
for thermoelectric energy conversion
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2019'
...
---
_id: '6174'
abstract:
- lang: eng
text: We propose a scaling theory for the many-body localization (MBL) phase transition
in one dimension, building on the idea that it proceeds via a “quantum avalanche.”
We argue that the critical properties can be captured at a coarse-grained level
by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological
grounds, we identify the scaling variables as the density of thermal regions and
the length scale that controls the decay of typical matrix elements. Within this
KT picture, the MBL phase is a line of fixed points that terminates at the delocalization
transition. We discuss two possible scenarios distinguished by the distribution
of rare, fractal thermal inclusions within the MBL phase. In the first scenario,
these regions have a stretched exponential distribution in the MBL phase. In the
second scenario, the near-critical MBL phase hosts rare thermal regions that are
power-law-distributed in size. This points to the existence of a second transition
within the MBL phase, at which these power laws change to the stretched exponential
form expected at strong disorder. We numerically simulate two different phenomenological
RGs previously proposed to describe the MBL transition. Both RGs display a universal
power-law length distribution of thermal regions at the transition with a critical
exponent αc=2, and continuously varying exponents in the MBL phase consistent
with the KT picture.
article_number: '094205'
article_processing_charge: No
article_type: original
author:
- first_name: Philipp T.
full_name: Dumitrescu, Philipp T.
last_name: Dumitrescu
- first_name: Anna
full_name: Goremykina, Anna
last_name: Goremykina
- first_name: Siddharth A.
full_name: Parameswaran, Siddharth A.
last_name: Parameswaran
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Romain
full_name: Vasseur, Romain
last_name: Vasseur
citation:
ama: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless
scaling at many-body localization phase transitions. Physical Review B.
2019;99(9). doi:10.1103/physrevb.99.094205
apa: Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., & Vasseur,
R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions.
Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.094205
chicago: Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym
Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization
Phase Transitions.” Physical Review B. American Physical Society, 2019.
https://doi.org/10.1103/physrevb.99.094205.
ieee: P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur,
“Kosterlitz-Thouless scaling at many-body localization phase transitions,” Physical
Review B, vol. 99, no. 9. American Physical Society, 2019.
ista: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless
scaling at many-body localization phase transitions. Physical Review B. 99(9),
094205.
mla: Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization
Phase Transitions.” Physical Review B, vol. 99, no. 9, 094205, American
Physical Society, 2019, doi:10.1103/physrevb.99.094205.
short: P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur,
Physical Review B 99 (2019).
date_created: 2019-03-25T07:32:08Z
date_published: 2019-03-22T00:00:00Z
date_updated: 2023-09-05T12:11:13Z
day: '22'
department:
- _id: MaSe
doi: 10.1103/physrevb.99.094205
external_id:
arxiv:
- '1811.03103'
isi:
- '000462883200001'
intvolume: ' 99'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.03103
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Kosterlitz-Thouless scaling at many-body localization phase transitions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 99
year: '2019'
...
---
_id: '6366'
abstract:
- lang: eng
text: Plants have a remarkable capacity to adjust their growth and development to
elevated ambient temperatures. Increased elongation growth of roots, hypocotyls
and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis.
In the last decade, significant progress has been made to identify the molecular
signaling components regulating these growth responses. Increased ambient temperature
utilizes diverse components of the light sensing and signal transduction network
to trigger growth adjustments. However, it remains unknown whether temperature
sensing and responses are universal processes that occur uniformly in all plant
organs. Alternatively, temperature sensing may be confined to specific tissues
or organs, which would require a systemic signal that mediates responses in distal
parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings
show organ-specific transcriptome responses to elevated temperatures, and that
thermomorphogenesis involves both autonomous and organ-interdependent temperature
sensing and signaling. Seedling roots can sense and respond to temperature in
a shoot-independent manner, whereas shoot temperature responses require both local
and systemic processes. The induction of cell elongation in hypocotyls requires
temperature sensing in cotyledons, followed by generation of a mobile auxin signal.
Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced
cell elongation in seedling stems, which depends upon a distinct, permissive temperature
sensor in the hypocotyl.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Bellstaedt, Julia
last_name: Bellstaedt
- first_name: Jana
full_name: Trenner, Jana
last_name: Trenner
- first_name: Rebecca
full_name: Lippmann, Rebecca
last_name: Lippmann
- first_name: Yvonne
full_name: Poeschl, Yvonne
last_name: Poeschl
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Marcel
full_name: Quint, Marcel
last_name: Quint
- first_name: Carolin
full_name: Delker, Carolin
last_name: Delker
citation:
ama: Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects
temperature sensing in cotyledons with growth responses in hypocotyls. Plant
Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377
apa: Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J.,
… Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377
chicago: Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi
Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects
Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant
Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.
ieee: J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing
in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol.
180, no. 2. ASPB, pp. 757–766, 2019.
ista: Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M,
Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.
mla: Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing
in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol.
180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.
short: J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M.
Quint, C. Delker, Plant Physiology 180 (2019) 757–766.
date_created: 2019-04-30T15:24:22Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-05T12:25:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01377
external_id:
isi:
- '000470086100019'
pmid:
- '31000634'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1104/pp.18.01377
month: '06'
oa: 1
oa_version: Published Version
page: 757-766
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: A mobile auxin signal connects temperature sensing in cotyledons with growth
responses in hypocotyls
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
_id: '6986'
abstract:
- lang: eng
text: 'Li-Nadler proposed a conjecture about traces of Hecke categories, which implies
the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler
in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds
in the natural generality of reflection groups in Euclidean or hyperbolic space.
As a corollary, we give an expression of the centralizer of a finite order element
in a reflection group using homotopy theory. '
article_processing_charge: No
article_type: original
author:
- first_name: Penghui
full_name: Li, Penghui
id: 42A24CCC-F248-11E8-B48F-1D18A9856A87
last_name: Li
citation:
ama: Li P. A colimit of traces of reflection groups. Proceedings of the American
Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586
apa: Li, P. (2019). A colimit of traces of reflection groups. Proceedings of
the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586
chicago: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings
of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586.
ieee: P. Li, “A colimit of traces of reflection groups,” Proceedings of the American
Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.
ista: Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American
Mathematical Society. 147(11), 4597–4604.
mla: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of
the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604,
doi:10.1090/proc/14586.
short: P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.
date_created: 2019-11-04T16:10:50Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-05T12:22:21Z
day: '01'
department:
- _id: TaHa
doi: 10.1090/proc/14586
ec_funded: 1
external_id:
arxiv:
- '1810.07039'
isi:
- '000488621700004'
intvolume: ' 147'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.07039
month: '11'
oa: 1
oa_version: Preprint
page: 4597-4604
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Proceedings of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6826
issn:
- 0002-9939
publication_status: published
publisher: AMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: A colimit of traces of reflection groups
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 147
year: '2019'
...
---
_id: '6454'
abstract:
- lang: eng
text: 'Adult neural stem cells and multiciliated ependymalcells are glial cells
essential for neurological func-tions. Together, they make up the adult neurogenicniche.
Using both high-throughput clonal analysisand single-cell resolution of progenitor
division pat-terns and fate, we show that these two componentsof the neurogenic
niche are lineally related: adult neu-ral stem cells are sister cells to ependymal
cells,whereas most ependymal cells arise from the termi-nal symmetric divisions
of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation,
GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells.
Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and
identify the Geminin familymembers as key regulators of the initial pool of adultneural
stem cells.'
article_processing_charge: No
author:
- first_name: G
full_name: Ortiz-Álvarez, G
last_name: Ortiz-Álvarez
- first_name: M
full_name: Daclin, M
last_name: Daclin
- first_name: A
full_name: Shihavuddin, A
last_name: Shihavuddin
- first_name: P
full_name: Lansade, P
last_name: Lansade
- first_name: A
full_name: Fortoul, A
last_name: Fortoul
- first_name: M
full_name: Faucourt, M
last_name: Faucourt
- first_name: S
full_name: Clavreul, S
last_name: Clavreul
- first_name: ME
full_name: Lalioti, ME
last_name: Lalioti
- first_name: S
full_name: Taraviras, S
last_name: Taraviras
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: J
full_name: Livet, J
last_name: Livet
- first_name: A
full_name: Meunier, A
last_name: Meunier
- first_name: A
full_name: Genovesio, A
last_name: Genovesio
- first_name: N
full_name: Spassky, N
last_name: Spassky
citation:
ama: Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and
multiciliated ependymal cells share a common lineage regulated by the Geminin
family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051
apa: Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt,
M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal
cells share a common lineage regulated by the Geminin family members. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051
chicago: Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt,
S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells
Share a Common Lineage Regulated by the Geminin Family Members.” Neuron.
Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.
ieee: G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated
ependymal cells share a common lineage regulated by the Geminin family members,”
Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.
ista: Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M,
Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio
A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells
share a common lineage regulated by the Geminin family members. Neuron. 102(1),
159–172.e7.
mla: Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal
Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron,
vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051.
short: G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt,
S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A.
Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.
date_created: 2019-05-14T13:06:30Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2023-09-05T13:02:21Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2019.01.051
ec_funded: 1
external_id:
isi:
- '000463337900018'
pmid:
- '30824354'
file:
- access_level: open_access
checksum: 1fb6e195c583eb0c5cabf26f69ff6675
content_type: application/pdf
creator: dernst
date_created: 2019-05-15T09:28:41Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6457'
file_name: 2019_Neuron_Ortiz.pdf
file_size: 7288572
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 102'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 159-172.e7
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adult neural stem cells and multiciliated ependymal cells share a common lineage
regulated by the Geminin family members
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 102
year: '2019'
...
---
_id: '6979'
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial
cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068'
apa: 'Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal
epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068'
chicago: 'Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of
Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press,
2019. https://doi.org/10.1016/j.cub.2019.08.068.'
ieee: 'A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal
epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20.
Cell Press, pp. R1091–R1093, 2019.'
ista: 'Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial
cells in tissue renewal. Current Biology. 29(20), R1091–R1093.'
mla: 'Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal
Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20,
Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068.'
short: A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.
date_created: 2019-11-04T15:18:29Z
date_published: 2019-10-21T00:00:00Z
date_updated: 2023-09-05T12:43:43Z
day: '21'
department:
- _id: MiSi
doi: 10.1016/j.cub.2019.08.068
external_id:
isi:
- '000491286200016'
pmid:
- '31639357'
intvolume: ' 29'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa_version: None
page: R1091-R1093
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gut homeostasis: Active migration of intestinal epithelial cells in tissue
renewal'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '6980'
abstract:
- lang: eng
text: Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal
coordination of mechanical and chemical signals. Extensive work on how mechanical
forces together with the well‐established morphogen signalling pathways can actively
shape living tissues has revealed evolutionary conserved mechanochemical features
of embryonic development. More recently, attention has been drawn to the description
of tissue material properties and how they can influence certain morphogenetic
processes. Interestingly, besides the role of tissue material properties in determining
how much tissues deform in response to force application, there is increasing
theoretical and experimental evidence, suggesting that tissue material properties
can abruptly and drastically change in development. These changes resemble phase
transitions, pointing at the intriguing possibility that important morphogenetic
processes in development, such as symmetry breaking and self‐organization, might
be mediated by tissue phase transitions. In this review, we summarize recent findings
on the regulation and role of tissue material properties in the context of the
developing embryo. We posit that abrupt changes of tissue rheological properties
may have important implications in maintaining the balance between robustness
and adaptability during embryonic development.
article_number: e102497
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Nicoletta
full_name: Petridou, Nicoletta
id: 2A003F6C-F248-11E8-B48F-1D18A9856A87
last_name: Petridou
orcid: 0000-0002-8451-1195
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The
EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497
apa: Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic
organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497
chicago: Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in
Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497.
ieee: N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,”
The EMBO Journal, vol. 38, no. 20. EMBO, 2019.
ista: Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization.
The EMBO Journal. 38(20), e102497.
mla: Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic
Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019,
doi:10.15252/embj.2019102497.
short: N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).
date_created: 2019-11-04T15:24:29Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-09-05T13:04:13Z
day: '15'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.15252/embj.2019102497
ec_funded: 1
external_id:
isi:
- '000485561900001'
pmid:
- '31512749'
file:
- access_level: open_access
checksum: 76f7f4e79ab6d850c30017a69726fd85
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:30:08Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6981'
file_name: 2019_Embo_Petridou.pdf
file_size: 847356
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2693FD8C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00736
name: Tissue material properties in embryonic development
publication: The EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: EMBO
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tissue rheology in embryonic organization
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: 38
year: '2019'
...
---
_id: '6554'
abstract:
- lang: eng
text: Due to the importance of zero-shot learning, i.e. classifying images where
there is a lack of labeled training data, the number of proposed approaches has
recently increased steadily. We argue that it is time to take a step back and
to analyze the status quo of the area. The purpose of this paper is three-fold.
First, given the fact that there is no agreed upon zero-shot learning benchmark,
we first define a new benchmark by unifying both the evaluation protocols and
data splits of publicly available datasets used for this task. This is an important
contribution as published results are often not comparable and sometimes even
flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose
a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset
which we make publicly available both in terms of image features and the images
themselves. Second, we compare and analyze a significant number of the state-of-the-art
methods in depth, both in the classic zero-shot setting but also in the more realistic
generalized zero-shot setting. Finally, we discuss in detail the limitations of
the current status of the area which can be taken as a basis for advancing it.
article_processing_charge: No
article_type: original
author:
- first_name: Yongqin
full_name: Xian, Yongqin
last_name: Xian
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0002-4561-241X
- first_name: Bernt
full_name: Schiele, Bernt
last_name: Schiele
- first_name: Zeynep
full_name: Akata, Zeynep
last_name: Akata
citation:
ama: Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive
evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern
Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768
apa: Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning
- A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions
on Pattern Analysis and Machine Intelligence. Institute of Electrical and
Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768
chicago: Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot
Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE
Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical
and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768.
ieee: Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive
evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical
and Electronics Engineers (IEEE), pp. 2251–2265, 2019.
ista: Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive
evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 41(9), 2251–2265.
mla: Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the
Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine
Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers
(IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768.
short: Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis
and Machine Intelligence 41 (2019) 2251–2265.
date_created: 2019-06-11T14:05:59Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-09-05T13:18:09Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/tpami.2018.2857768
external_id:
arxiv:
- '1707.00600'
isi:
- '000480343900015'
intvolume: ' 41'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1707.00600
month: '09'
oa: 1
oa_version: Preprint
page: 2251 - 2265
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_identifier:
eissn:
- 1939-3539
issn:
- 0162-8828
publication_status: published
publisher: Institute of Electrical and Electronics Engineers (IEEE)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zero-shot learning - A comprehensive evaluation of the good, the bad and the
ugly
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2019'
...
---
_id: '6259'
abstract:
- lang: eng
text: The plant hormone auxin has crucial roles in almost all aspects of plant growth
and development. Concentrations of auxin vary across different tissues, mediating
distinct developmental outcomes and contributing to the functional diversity of
auxin. However, the mechanisms that underlie these activities are poorly understood.
Here we identify an auxin signalling mechanism, which acts in parallel to the
canonical auxin pathway based on the transport inhibitor response1 (TIR1) and
other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that
translates levels of cellular auxin to mediate differential growth during apical-hook
development. This signalling mechanism operates at the concave side of the apical
hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase
1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically
interacts with and phosphorylates two non-canonical transcriptional repressors
of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby
regulating ARF transcription factors. In contrast to the degradation of Aux/IAA
transcriptional repressors in the canonical pathway, the newly identified mechanism
stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate
gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway
originates at the cell surface, is triggered by high levels of auxin and shares
a partially overlapping set of transcription factors with the TIR1/AFB signalling
pathway. This allows distinct interpretations of different concentrations of cellular
auxin, and thus enables this versatile signalling molecule to mediate complex
developmental outcomes.
article_processing_charge: No
article_type: original
author:
- first_name: Min
full_name: Cao, Min
last_name: Cao
- first_name: Rong
full_name: Chen, Rong
last_name: Chen
- first_name: Pan
full_name: Li, Pan
last_name: Li
- first_name: Yongqiang
full_name: Yu, Yongqiang
last_name: Yu
- first_name: Rui
full_name: Zheng, Rui
last_name: Zheng
- first_name: Danfeng
full_name: Ge, Danfeng
last_name: Ge
- first_name: Wei
full_name: Zheng, Wei
last_name: Zheng
- first_name: Xuhui
full_name: Wang, Xuhui
last_name: Wang
- first_name: Yangtao
full_name: Gu, Yangtao
last_name: Gu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Heng
full_name: Zhang, Heng
last_name: Zhang
- first_name: Renyi
full_name: Liu, Renyi
last_name: Liu
- first_name: Jun
full_name: He, Jun
last_name: He
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
citation:
ama: Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential
growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7
apa: Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated
auxin signalling regulates differential growth of the apical hook. Nature.
Springer Nature. https://doi.org/10.1038/s41586-019-1069-7
chicago: Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng,
et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical
Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.
ieee: M. Cao et al., “TMK1-mediated auxin signalling regulates differential
growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243,
2019.
ista: Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z,
Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates
differential growth of the apical hook. Nature. 568, 240–243.
mla: Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth
of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43,
doi:10.1038/s41586-019-1069-7.
short: M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu,
Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.
date_created: 2019-04-09T08:37:05Z
date_published: 2019-04-11T00:00:00Z
date_updated: 2023-09-05T14:58:41Z
day: '11'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-019-1069-7
ec_funded: 1
external_id:
isi:
- '000464412700050'
pmid:
- '30944466'
file:
- access_level: open_access
checksum: 6b84ab602a34382cf0340a37a1378c75
content_type: application/pdf
creator: dernst
date_created: 2020-11-13T07:37:41Z
date_updated: 2020-11-13T07:37:41Z
file_id: '8751'
file_name: 2019_Nature _Cao_accepted.pdf
file_size: 4321328
relation: main_file
success: 1
file_date_updated: 2020-11-13T07:37:41Z
has_accepted_license: '1'
intvolume: ' 568'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 240-243
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
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/
scopus_import: '1'
status: public
title: TMK1-mediated auxin signalling regulates differential growth of the apical
hook
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 568
year: '2019'
...
---
_id: '6987'
abstract:
- lang: eng
text: Cells are arranged into species-specific patterns during early embryogenesis.
Such cell division patterns are important since they often reflect the distribution
of localized cortical factors from eggs/fertilized eggs to specific cells as well
as the emergence of organismal form. However, it has proven difficult to reveal
the mechanisms that underlie the emergence of cell positioning patterns that underlie
embryonic shape, likely because a systems-level approach is required that integrates
cell biological, genetic, developmental, and mechanical parameters. The choice
of organism to address such questions is also important. Because ascidians display
the most extreme form of invariant cleavage pattern among the metazoans, we have
been analyzing the cell biological mechanisms that underpin three aspects of cell
division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous
cell cycles) which affect the overall shape of the blastula-stage ascidian embryo
composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell
stage that in turn undergo two further successive rounds of UCD. Starting at the
16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides
before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages.
Perturbing either UCD or the alternate cell division rhythm perturbs cell position.
We propose that dynamic cell shape changes propagate throughout the embryo via
cell-cell contacts to create the ascidian-specific invariant cleavage pattern.
alternative_title:
- RESULTS
article_processing_charge: No
author:
- first_name: Alex
full_name: McDougall, Alex
last_name: McDougall
- first_name: Janet
full_name: Chenevert, Janet
last_name: Chenevert
- first_name: Benoit G
full_name: Godard, Benoit G
id: 33280250-F248-11E8-B48F-1D18A9856A87
last_name: Godard
- first_name: Remi
full_name: Dumollard, Remi
last_name: Dumollard
citation:
ama: 'McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape
during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model
Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154.
doi:10.1007/978-3-030-23459-1_6'
apa: 'McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence
of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski
(Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol.
68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6'
chicago: 'McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard.
“Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model
Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and
Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.'
ieee: 'A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of
embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in
cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski,
Eds. Springer Nature, 2019, pp. 127–154.'
ista: 'McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo
shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental
biology. RESULTS, vol. 68, 127–154.'
mla: 'McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.”
Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by
Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp.
127–54, doi:10.1007/978-3-030-23459-1_6.'
short: 'A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo,
S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology,
Springer Nature, 2019, pp. 127–154.'
date_created: 2019-11-04T16:20:19Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-05T15:01:12Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1007/978-3-030-23459-1_6
editor:
- first_name: Waclaw
full_name: Tworzydlo, Waclaw
last_name: Tworzydlo
- first_name: Szczepan M.
full_name: Bilinski, Szczepan M.
last_name: Bilinski
external_id:
pmid:
- '31598855'
file:
- access_level: open_access
checksum: 7f43e1e3706d15061475c5c57efc2786
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T10:09:30Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7829'
file_name: 2019_RESULTS_McDougall.pdf
file_size: 19317348
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 68'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 127-154
pmid: 1
publication: 'Evo-Devo: Non-model species in cell and developmental biology'
publication_identifier:
eissn:
- 1861-0412
isbn:
- '9783030234584'
- '9783030234591'
issn:
- 0080-1844
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of embryo shape during cleavage divisions
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 68
year: '2019'
...
---
_id: '6762'
abstract:
- lang: eng
text: "We present and study novel optimal control problems motivated by the search
for photovoltaic materials with high power-conversion efficiency. The material
must perform the first step: convert light (photons) into electronic excitations.
We formulate various desirable properties of the excitations as mathematical control
goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by
the nuclear charge distribution. We prove that nuclear distributions exist which
give rise to optimal HOMO-LUMO excitations, and present illustrative numerical
simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features
such as large electron-hole separation, and a hierarchy of length scales: internal
HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the
doping profiles < system size."
article_processing_charge: No
author:
- first_name: Gero
full_name: Friesecke, Gero
last_name: Friesecke
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Friesecke G, Kniely M. New optimal control problems in density functional theory
motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947.
doi:10.1137/18M1207272
apa: Friesecke, G., & Kniely, M. (2019). New optimal control problems in density
functional theory motivated by photovoltaics. Multiscale Modeling and Simulation.
SIAM. https://doi.org/10.1137/18M1207272
chicago: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation.
SIAM, 2019. https://doi.org/10.1137/18M1207272.
ieee: G. Friesecke and M. Kniely, “New optimal control problems in density functional
theory motivated by photovoltaics,” Multiscale Modeling and Simulation,
vol. 17, no. 3. SIAM, pp. 926–947, 2019.
ista: Friesecke G, Kniely M. 2019. New optimal control problems in density functional
theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3),
926–947.
mla: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density
Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation,
vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.
short: G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.
date_created: 2019-08-04T21:59:21Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2023-09-05T15:05:45Z
day: '16'
department:
- _id: JuFi
doi: 10.1137/18M1207272
external_id:
arxiv:
- '1808.04200'
isi:
- '000487931800002'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04200
month: '07'
oa: 1
oa_version: Preprint
page: 926-947
publication: Multiscale Modeling and Simulation
publication_identifier:
eissn:
- '15403467'
issn:
- '15403459'
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: New optimal control problems in density functional theory motivated by photovoltaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2019'
...
---
_id: '10874'
abstract:
- lang: eng
text: In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler,
and Zykin, which allows us to connect invariants of binary octics to Siegel modular
forms of genus 3. We use this connection to show that certain modular functions,
when restricted to the hyperelliptic locus, assume values whose denominators are
products of powers of primes of bad reduction for the associated hyperelliptic
curves. We illustrate our theorem with explicit computations. This work is motivated
by the study of the values of these modular functions at CM points of the Siegel
upper half-space, which, if their denominators are known, can be used to effectively
compute models of (hyperelliptic, in our case) curves with CM.
acknowledgement: "The authors would like to thank the Lorentz Center in Leiden for
hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable
environment for our initial work on this project. We are grateful to the organizers
of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference
and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler
for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund
of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s
work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky
Universität Oldenburg. Massierer was supported by the Australian Research Council
(DP150101689). Vincent is supported by the National Science Foundation under Grant
No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the
United States and the FACE Foundation. "
article_number: '9'
article_processing_charge: No
article_type: original
author:
- first_name: Sorina
full_name: Ionica, Sorina
last_name: Ionica
- first_name: Pınar
full_name: Kılıçer, Pınar
last_name: Kılıçer
- first_name: Kristin
full_name: Lauter, Kristin
last_name: Lauter
- first_name: Elisa
full_name: Lorenzo García, Elisa
last_name: Lorenzo García
- first_name: Maria-Adelina
full_name: Manzateanu, Maria-Adelina
id: be8d652e-a908-11ec-82a4-e2867729459c
last_name: Manzateanu
- first_name: Maike
full_name: Massierer, Maike
last_name: Massierer
- first_name: Christelle
full_name: Vincent, Christelle
last_name: Vincent
citation:
ama: Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic
curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6
apa: Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A.,
Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic
curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6
chicago: Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina
Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus
3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019.
https://doi.org/10.1007/s40993-018-0146-6.
ieee: S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,”
Research in Number Theory, vol. 5. Springer Nature, 2019.
ista: Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer
M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research
in Number Theory. 5, 9.
mla: Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.”
Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.
short: S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M.
Massierer, C. Vincent, Research in Number Theory 5 (2019).
date_created: 2022-03-18T12:09:48Z
date_published: 2019-01-02T00:00:00Z
date_updated: 2023-09-05T15:39:31Z
day: '02'
department:
- _id: TiBr
doi: 10.1007/s40993-018-0146-6
external_id:
arxiv:
- '1807.08986'
intvolume: ' 5'
keyword:
- Algebra and Number Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.08986
month: '01'
oa: 1
oa_version: Preprint
publication: Research in Number Theory
publication_identifier:
eissn:
- 2363-9555
issn:
- 2522-0160
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modular invariants for genus 3 hyperelliptic curves
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7100'
abstract:
- lang: eng
text: We present microscopic derivations of the defocusing two-dimensional cubic
nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman
interacting N-particle system of bosons. We consider the interaction potential
to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx),
for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R).
In both cases we prove the convergence of the reduced density corresponding to
the exact time evolution to the projector onto the solution of the corresponding
nonlinear Schrödinger equation in trace norm. For the latter potential VN we show
that it is crucial to take the microscopic structure of the condensate into account
in order to obtain the correct dynamics.
acknowledgement: OA fund by IST Austria
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maximilian
full_name: Jeblick, Maximilian
last_name: Jeblick
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69.
doi:10.1007/s00220-019-03599-x
apa: Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time
dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x
chicago: Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of
the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications
in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x.
ieee: M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent
Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical
Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.
ista: Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii
equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.
mla: Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii
Equation in Two Dimensions.” Communications in Mathematical Physics, vol.
372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x.
short: M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics
372 (2019) 1–69.
date_created: 2019-11-25T08:08:02Z
date_published: 2019-11-08T00:00:00Z
date_updated: 2023-09-06T10:47:43Z
day: '08'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03599-x
ec_funded: 1
external_id:
isi:
- '000495193700002'
file:
- access_level: open_access
checksum: cd283b475dd739e04655315abd46f528
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:11:11Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7101'
file_name: 2019_CommMathPhys_Jeblick.pdf
file_size: 884469
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 372'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1-69
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Derivation of the time dependent Gross–Pitaevskii equation in two dimensions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 372
year: '2019'
...
---
_id: '7106'
abstract:
- lang: eng
text: PIN-FORMED (PIN) transporters mediate directional, intercellular movement
of the phytohormone auxin in land plants. To elucidate the evolutionary origins
of this developmentally crucial mechanism, we analysed the single PIN homologue
of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized
auxin exporter in land plants and heterologous models. While its role in algae
remains unclear, PIN-driven auxin export is probably an ancient and conserved
trait within streptophytes.
article_processing_charge: No
article_type: original
author:
- first_name: Roman
full_name: Skokan, Roman
last_name: Skokan
- first_name: Eva
full_name: Medvecká, Eva
last_name: Medvecká
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Stanislav
full_name: Vosolsobě, Stanislav
last_name: Vosolsobě
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Karel
full_name: Müller, Karel
last_name: Müller
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Yuzhou
full_name: Zhang, Yuzhou
last_name: Zhang
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early
in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5
apa: Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K.,
… Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution.
Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5
chicago: Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka,
Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in
Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.
ieee: R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte
evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119,
2019.
ista: Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P,
Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml
J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature
Plants. 5(11), 1114–1119.
mla: Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte
Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19,
doi:10.1038/s41477-019-0542-5.
short: R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P.
Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński,
J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.
date_created: 2019-11-25T09:08:04Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:09:49Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-019-0542-5
ec_funded: 1
external_id:
isi:
- '000496526100010'
pmid:
- '31712756'
file:
- access_level: open_access
checksum: 94e0426856aad9a9bd0135d5436efbf1
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T08:54:49Z
date_updated: 2020-10-14T08:54:49Z
file_id: '8660'
file_name: 2019_NaturePlants_Skokan_accepted.pdf
file_size: 1980851
relation: main_file
success: 1
file_date_updated: 2020-10-14T08:54:49Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1114-1119
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 Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN-driven auxin transport emerged early in streptophyte evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7105'
abstract:
- lang: eng
text: Cell migration is hypothesized to involve a cycle of behaviours beginning
with leading edge extension. However, recent evidence suggests that the leading
edge may be dispensable for migration, raising the question of what actually controls
cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages
to bridge the different temporal scales of the behaviours controlling motility.
This approach reveals that edge fluctuations during random motility are not persistent
and are weakly correlated with motion. In contrast, flow of the actin network
behind the leading edge is highly persistent. Quantification of actin flow structure
during migration reveals a stable organization and asymmetry in the cell-wide
flowfield that strongly correlates with cell directionality. This organization
is regulated by a gradient of actin network compression and destruction, which
is controlled by myosin contraction and cofilin-mediated disassembly. It is this
stable actin-flow polarity, which integrates rapid fluctuations of the leading
edge, that controls inherent cellular persistence.
article_processing_charge: No
article_type: original
author:
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Mubarik
full_name: Burki, Mubarik
last_name: Burki
- first_name: Stefania
full_name: Marcotti, Stefania
last_name: Marcotti
- first_name: Andrei
full_name: Luchici, Andrei
last_name: Luchici
- first_name: Fiona N.
full_name: Kenny, Fiona N.
last_name: Kenny
- first_name: John Robert
full_name: Davis, John Robert
last_name: Davis
- first_name: Eduardo
full_name: Serna-Morales, Eduardo
last_name: Serna-Morales
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- 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: Andrew
full_name: Davidson, Andrew
last_name: Davidson
- first_name: Will
full_name: Wood, Will
last_name: Wood
- first_name: Linus J.
full_name: Schumacher, Linus J.
last_name: Schumacher
- first_name: Robert G.
full_name: Endres, Robert G.
last_name: Endres
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Brian M.
full_name: Stramer, Brian M.
last_name: Stramer
citation:
ama: Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin
flow is essential for directionality during cell migration. Nature Cell Biology.
2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5
apa: Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J.
R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential
for directionality during cell migration. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/s41556-019-0411-5
chicago: Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona
N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized
Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature
Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.
ieee: L. Yolland et al., “Persistent and polarized global actin flow is essential
for directionality during cell migration,” Nature Cell Biology, vol. 21,
no. 11. Springer Nature, pp. 1370–1381, 2019.
ista: Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales
E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik
M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for
directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.
mla: Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential
for Directionality during Cell Migration.” Nature Cell Biology, vol. 21,
no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.
short: L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E.
Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G.
Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.
date_created: 2019-11-25T08:55:00Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:08:52Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41556-019-0411-5
external_id:
isi:
- '000495888300009'
pmid:
- '31685997'
intvolume: ' 21'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891
month: '11'
oa: 1
oa_version: Submitted Version
page: 1370-1381
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent and polarized global actin flow is essential for directionality
during cell migration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2019'
...
---
_id: '7109'
abstract:
- lang: eng
text: We show how to construct temporal testers for the logic MITL, a prominent
linear-time logic for real-time systems. A temporal tester is a transducer that
inputs a signal holding the Boolean value of atomic propositions and outputs the
truth value of a formula along time. Here we consider testers over continuous-time
Boolean signals that use clock variables to enforce duration constraints, as in
timed automata. We first rewrite the MITL formula into a “simple” formula using
a limited set of temporal modalities. We then build testers for these specific
modalities and show how to compose testers for simple formulae into complex ones.
Temporal testers can be turned into acceptors, yielding a compositional translation
from MITL to timed automata. This construction is much simpler than previously
known and remains asymptotically optimal. It supports both past and future operators
and can easily be extended.
article_number: '19'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Amir
full_name: Pnueli, Amir
last_name: Pnueli
citation:
ama: Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata.
Journal of the ACM. 2019;66(3). doi:10.1145/3286976
apa: Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time
logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976
chicago: Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time
Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.
ieee: T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to
timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed
automata. Journal of the ACM. 66(3), 19.
mla: Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal
of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.
short: T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).
date_created: 2019-11-26T10:22:32Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-09-06T11:11:56Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3286976
external_id:
isi:
- '000495406300005'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: From real-time logic to timed automata
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7108'
abstract:
- lang: eng
text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial
complex is shellable is NP-hard, hence NP-complete. This resolves a question raised,
e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d
≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable
is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible
pure d-dimensional complexes. Another simple corollary of our result is that it
is NP-hard to decide whether a given poset is CL-shellable.
article_number: '21'
article_processing_charge: No
article_type: original
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete.
Journal of the ACM. 2019;66(3). doi:10.1145/3314024
apa: Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability
is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024
chicago: Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.
ieee: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is
NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete.
Journal of the ACM. 66(3), 21.
mla: Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM,
vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.
short: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM
66 (2019).
date_created: 2019-11-26T10:13:59Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-06T11:10:58Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3314024
external_id:
arxiv:
- '1711.08436'
isi:
- '000495406300007'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1711.08436.pdf
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '184'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Shellability is NP-complete
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7147'
abstract:
- lang: eng
text: "The expression of a gene is characterised by its transcription factors and
the function processing them. If the transcription factors are not affected by
gene products, the regulating function is often represented as a combinational
logic circuit, where the outputs (product) are determined by current input values
(transcription factors) only, and are hence independent on their relative arrival
times. However, the simultaneous arrival of transcription factors (TFs) in genetic
circuits is a strong assumption, given that the processes of transcription and
translation of a gene into a protein introduce intrinsic time delays and that
there is no global synchronisation among the arrival times of different molecular
species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally
implementable genetic circuit with two inputs and a single output, such that,
in presence of small delays in input arrival, the circuit exhibits qualitatively
distinct observable phenotypes. In particular, these phenotypes are long lived
transients: they all converge to a single value, but so slowly, that they seem
stable for an extended time period, longer than typical experiment duration. We
used rule-based language to prototype our circuit, and we implemented a search
for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe
behaviour of our prototype circuit has wide implications. First, it suggests that
GRNs can exploit event timing to create phenotypes. Second, it opens the possibility
that GRNs are using event timing to react to stimuli and memorise events, without
explicit feedback in regulation. From the modelling perspective, our prototype
circuit demonstrates the critical importance of analysing the transient dynamics
at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."
alternative_title:
- LNCS
article_processing_charge: No
author:
- 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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene
regulation. In: 17th International Conference on Computational Methods in Systems
Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9'
apa: 'Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019).
Transient memory in gene regulation. In 17th International Conference on Computational
Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer
Nature. https://doi.org/10.1007/978-3-030-31304-3_9'
chicago: Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali
Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference
on Computational Methods in Systems Biology, 11773:155–87. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-31304-3_9.
ieee: C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient
memory in gene regulation,” in 17th International Conference on Computational
Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.
ista: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory
in gene regulation. 17th International Conference on Computational Methods in
Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773,
155–187.'
mla: Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International
Conference on Computational Methods in Systems Biology, vol. 11773, Springer
Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.
short: C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International
Conference on Computational Methods in Systems Biology, Springer Nature, 2019,
pp. 155–187.
conference:
end_date: 2019-09-20
location: Trieste, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2019-09-18
date_created: 2019-12-04T16:07:50Z
date_published: 2019-09-17T00:00:00Z
date_updated: 2023-09-06T11:18:08Z
day: '17'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-030-31304-3_9
external_id:
isi:
- '000557875100009'
intvolume: ' 11773'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 155-187
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture
publication: 17th International Conference on Computational Methods in Systems Biology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030313036'
- '9783030313043'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient memory in gene regulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11773
year: '2019'
...
---
_id: '7136'
abstract:
- lang: eng
text: "It is well established that the notion of min-entropy fails to satisfy the
\\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy.
Such a property would help to analyze how min-entropy is split among smaller blocks.
Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe
show that any sequence of variables exhibits a very strong strong block-source
structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil
few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination
properties} hold. In particular, we have many nice properties that min-entropy
doesn't obey in general, for example strong chain rules, \"information can't hurt\"
inequalities, equivalences of average and worst-case conditional entropy definitions
and others. Quantitatively, for any sequence X1,…,Xt of random variables over
an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt)
bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240'
apa: 'Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled.
In 2019 IEEE International Symposium on Information Theory. Paris, France:
IEEE. https://doi.org/10.1109/isit.2019.8849240'
chicago: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
In 2019 IEEE International Symposium on Information Theory. IEEE, 2019.
https://doi.org/10.1109/isit.2019.8849240.
ieee: M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in
2019 IEEE International Symposium on Information Theory, Paris, France,
2019.
ista: 'Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled.
2019 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 8849240.'
mla: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
2019 IEEE International Symposium on Information Theory, 8849240, IEEE,
2019, doi:10.1109/isit.2019.8849240.
short: M. Skórski, in:, 2019 IEEE International Symposium on Information Theory,
IEEE, 2019.
conference:
end_date: 2019-07-12
location: Paris, France
name: 'ISIT: International Symposium on Information Theory'
start_date: 2019-07-07
date_created: 2019-11-28T10:19:21Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-06T11:15:41Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/isit.2019.8849240
external_id:
arxiv:
- '1702.08476'
isi:
- '000489100301043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.08476
month: '07'
oa: 1
oa_version: Preprint
publication: 2019 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781538692912'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong chain rules for min-entropy under few bits spoiled
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7122'
abstract:
- lang: eng
text: Data-rich applications in machine-learning and control have motivated an intense
research on large-scale optimization. Novel algorithms have been proposed and
shown to have optimal convergence rates in terms of iteration counts. However,
their practical performance is severely degraded by the cost of exchanging high-dimensional
gradient vectors between computing nodes. Several gradient compression heuristics
have recently been proposed to reduce communications, but few theoretical results
exist that quantify how they impact algorithm convergence. This paper establishes
and strengthens the convergence guarantees for gradient descent under a family
of gradient compression techniques. For convex optimization problems, we derive
admissible step sizes and quantify both the number of iterations and the number
of bits that need to be exchanged to reach a target accuracy. Finally, we validate
the performance of different gradient compression techniques in simulations. The
numerical results highlight the properties of different gradient compression algorithms
and confirm that fast convergence with limited information exchange is possible.
article_number: '8619625'
article_processing_charge: No
author:
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited
convex optimization. In: 2018 IEEE Conference on Decision and Control.
IEEE; 2019. doi:10.1109/cdc.2018.8619625'
apa: 'Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression
for communication-limited convex optimization. In 2018 IEEE Conference on Decision
and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625'
chicago: Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression
for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on
Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625.
ieee: S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited
convex optimization,” in 2018 IEEE Conference on Decision and Control,
Miami Beach, FL, United States, 2019.
ista: 'Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited
convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference
on Decision and Control, 8619625.'
mla: Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex
Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE,
2019, doi:10.1109/cdc.2018.8619625.
short: S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision
and Control, IEEE, 2019.
conference:
end_date: 2018-12-19
location: Miami Beach, FL, United States
name: 'CDC: Conference on Decision and Control'
start_date: 2018-12-17
date_created: 2019-11-26T15:07:49Z
date_published: 2019-01-21T00:00:00Z
date_updated: 2023-09-06T11:14:55Z
day: '21'
department:
- _id: DaAl
doi: 10.1109/cdc.2018.8619625
external_id:
isi:
- '000458114800023'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
publication: 2018 IEEE Conference on Decision and Control
publication_identifier:
isbn:
- '9781538613955'
issn:
- 0743-1546
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient compression for communication-limited convex optimization
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7146'
abstract:
- lang: eng
text: Prevailing models of sex-chromosome evolution were largely inspired by the
stable and highly differentiated XY pairs of model organisms, such as those of
mammals and flies. Recent work has uncovered an incredible diversity of sex-determining
systems, bringing some of the assumptions of these traditional models into question.
One particular question that has arisen is what drives some sex chromosomes to
be maintained over millions of years and differentiate fully, while others are
replaced by new sex-determining chromosomes before differentiation has occurred.
Here, I review recent data on the variability of sex-determining genes and sex
chromosomes in different non-model vertebrates and invertebrates, and discuss
some theoretical models that have been put forward to account for this diversity.
article_processing_charge: No
article_type: original
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover.
Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8
apa: Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome
turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8
chicago: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8.
ieee: B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,”
Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641,
2019.
ista: Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome
turnover. Nature Ecology & Evolution. 3(12), 1632–1641.
mla: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature,
2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8.
short: B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641.
date_created: 2019-12-04T16:05:25Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2023-09-06T11:18:59Z
day: '25'
department:
- _id: BeVi
doi: 10.1038/s41559-019-1050-8
ec_funded: 1
external_id:
isi:
- '000500728800009'
intvolume: ' 3'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1632-1641
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and evolutionary dynamics of animal sex-chromosome turnover
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2019'
...
---
_id: '7143'
abstract:
- lang: eng
text: Roots grow downwards parallel to the gravity vector, to anchor a plant in
soil and acquire water and nutrients, using a gravitropic mechanism dependent
on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al.
demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs
root growth towards higher water content.
article_processing_charge: No
article_type: original
author:
- first_name: Scott A
full_name: Sinclair, Scott A
id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87
last_name: Sinclair
orcid: 0000-0002-4566-0593
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell
Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4'
apa: 'Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest
for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4'
chicago: 'Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for
Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.'
ieee: 'S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,”
Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.'
ista: 'Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture.
Cell Research. 29, 965–966.'
mla: 'Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for
Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.'
short: S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.
date_created: 2019-12-02T12:30:48Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T11:20:58Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41422-019-0254-4
external_id:
isi:
- '000500749600001'
pmid:
- '31745287'
intvolume: ' 29'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41422-019-0254-4
month: '12'
oa: 1
oa_version: Published Version
page: 965-966
pmid: 1
publication: Cell Research
publication_identifier:
eissn:
- 1748-7838
issn:
- 1001-0602
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defying gravity: a plant''s quest for moisture'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '7156'
abstract:
- lang: eng
text: We propose an efficient microwave-photonic modulator as a resource for stationary
entangled microwave-optical fields and develop the theory for deterministic entanglement
generation and quantum state transfer in multi-resonant electro-optic systems.
The device is based on a single crystal whispering gallery mode resonator integrated
into a 3D-microwave cavity. The specific design relies on a new combination of
thin-film technology and conventional machining that is optimized for the lowest
dissipation rates in the microwave, optical, and mechanical domains. We extract
important device properties from finite-element simulations and predict continuous
variable entanglement generation rates on the order of a Mebit/s for optical pump
powers of only a few tens of microwatts. We compare the quantum state transfer
fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation
and direct conversion protocols under realistic conditions. Combining the unique
capabilities of circuit quantum electrodynamics with the resilience of fiber optic
communication could facilitate long-distance solid-state qubit networks, new methods
for quantum signal synthesis, quantum key distribution, and quantum enhanced detection,
as well as more power-efficient classical sensing and modulation.
article_number: '108'
article_processing_charge: No
article_type: original
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement
source for microwave to telecom quantum state transfer. npj Quantum Information.
2019;5. doi:10.1038/s41534-019-0220-5
apa: Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019).
Electro-optic entanglement source for microwave to telecom quantum state transfer.
Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5
chicago: Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes
M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State
Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5.
ieee: A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic
entanglement source for microwave to telecom quantum state transfer,” npj Quantum
Information, vol. 5. Springer Nature, 2019.
ista: Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement
source for microwave to telecom quantum state transfer. npj Quantum Information.
5, 108.
mla: Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave
to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108,
Springer Nature, 2019, doi:10.1038/s41534-019-0220-5.
short: A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information
5 (2019).
date_created: 2019-12-09T08:18:56Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T11:22:39Z
day: '01'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41534-019-0220-5
ec_funded: 1
external_id:
arxiv:
- '1909.01470'
isi:
- '000502996200003'
file:
- access_level: open_access
checksum: 13e0ea1d4f9b5f5710780d9473364f58
content_type: application/pdf
creator: dernst
date_created: 2019-12-09T08:25:06Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7157'
file_name: 2019_NPJ_Rueda.pdf
file_size: 1580132
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
publication: npj Quantum Information
publication_identifier:
issn:
- 2056-6387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electro-optic entanglement source for microwave to telecom quantum state transfer
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: 5
year: '2019'
...
---
_id: '7165'
abstract:
- lang: eng
text: Cell division, movement and differentiation contribute to pattern formation
in developing tissues. This is the case in the vertebrate neural tube, in which
neurons differentiate in a characteristic pattern from a highly dynamic proliferating
pseudostratified epithelium. To investigate how progenitor proliferation and differentiation
affect cell arrangement and growth of the neural tube, we used experimental measurements
to develop a mechanical model of the apical surface of the neuroepithelium that
incorporates the effect of interkinetic nuclear movement and spatially varying
rates of neuronal differentiation. Simulations predict that tissue growth and
the shape of lineage-related clones of cells differ with the rate of differentiation.
Growth is isotropic in regions of high differentiation, but dorsoventrally biased
in regions of low differentiation. This is consistent with experimental observations.
The absence of directional signalling in the simulations indicates that global
mechanical constraints are sufficient to explain the observed differences in anisotropy.
This provides insight into how the tissue growth rate affects cell dynamics and
growth anisotropy and opens up possibilities to study the coupling between mechanics,
pattern formation and growth in the neural tube.
article_number: dev176297
article_processing_charge: No
article_type: original
author:
- first_name: Pilar
full_name: Guerrero, Pilar
last_name: Guerrero
- first_name: Ruben
full_name: Perez-Carrasco, Ruben
last_name: Perez-Carrasco
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: David
full_name: Page, David
last_name: Page
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Karen M.
full_name: Page, Karen M.
last_name: Page
citation:
ama: Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation
influences progenitor arrangement in the vertebrate neuroepithelium. Development.
2019;146(23). doi:10.1242/dev.176297
apa: Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe,
J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement
in the vertebrate neuroepithelium. Development. The Company of Biologists.
https://doi.org/10.1242/dev.176297
chicago: Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna
Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences
Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development.
The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297.
ieee: P. Guerrero et al., “Neuronal differentiation influences progenitor
arrangement in the vertebrate neuroepithelium,” Development, vol. 146,
no. 23. The Company of Biologists, 2019.
ista: Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page
KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate
neuroepithelium. Development. 146(23), dev176297.
mla: Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement
in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297,
The Company of Biologists, 2019, doi:10.1242/dev.176297.
short: P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe,
K.M. Page, Development 146 (2019).
date_created: 2019-12-10T14:39:50Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T11:26:36Z
day: '04'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.176297
ec_funded: 1
external_id:
isi:
- '000507575700004'
pmid:
- '31784457'
file:
- access_level: open_access
checksum: b6533c37dc8fbd803ffeca216e0a8b8a
content_type: application/pdf
creator: dernst
date_created: 2019-12-13T07:34:06Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7177'
file_name: 2019_Development_Guerrero.pdf
file_size: 7797881
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 146'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal differentiation influences progenitor arrangement in the vertebrate
neuroepithelium
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: 146
year: '2019'
...
---
_id: '7159'
abstract:
- lang: eng
text: 'Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a
tremendous amount of generated, measured and recorded time-series data. Extracting
temporal segments that encode patterns with useful information out of these huge
amounts of data is an extremely difficult problem. We propose shape expressions
as a declarative formalism for specifying, querying and extracting sophisticated
temporal patterns from possibly noisy data. Shape expressions are regular expressions
with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters
as atomic predicates and additional constraints on these parameters. We equip
shape expressions with a novel noisy semantics that combines regular expression
matching semantics with statistical regression. We characterize essential properties
of the formalism and propose an efficient approximate shape expression matching
procedure. We demonstrate the wide applicability of this technique on two case
studies. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Xin
full_name: Qin, Xin
last_name: Qin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Cristinel
full_name: Mateis, Cristinel
last_name: Mateis
- first_name: Jyotirmoy
full_name: Deshmukh, Jyotirmoy
last_name: Deshmukh
citation:
ama: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for
specifying and extracting signal features. In: 19th International Conference
on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17'
apa: 'Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019).
Shape expressions for specifying and extracting signal features. In 19th International
Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal:
Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17'
chicago: Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy
Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In
19th International Conference on Runtime Verification, 11757:292–309. Springer
Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.
ieee: D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions
for specifying and extracting signal features,” in 19th International Conference
on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.
ista: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions
for specifying and extracting signal features. 19th International Conference on
Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.'
mla: Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal
Features.” 19th International Conference on Runtime Verification, vol.
11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.
short: D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International
Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.
conference:
end_date: 2019-10-11
location: Porto, Portugal
name: 'RV: Runtime Verification'
start_date: 2019-10-08
date_created: 2019-12-09T08:47:55Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-06T11:24:10Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-030-32079-9_17
external_id:
isi:
- '000570006300017'
intvolume: ' 11757'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 292-309
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication: 19th International Conference on Runtime Verification
publication_identifier:
isbn:
- '9783030320782'
- '9783030320799'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape expressions for specifying and extracting signal features
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11757
year: '2019'
...
---
_id: '7183'
abstract:
- lang: eng
text: 'A probabilistic vector addition system with states (pVASS) is a finite state
Markov process augmented with non-negative integer counters that can be incremented
or decremented during each state transition, blocking any behaviour that would
cause a counter to decrease below zero. The pVASS can be used as abstractions
of probabilistic programs with many decidable properties. The use of pVASS as
abstractions requires the presence of nondeterminism in the model. In this paper,
we develop techniques for checking fast termination of pVASS with nondeterminism.
That is, for every initial configuration of size n, we consider the worst expected
number of transitions needed to reach a configuration with some counter negative
(the expected termination time). We show that the problem whether the asymptotic
expected termination time is linear is decidable in polynomial time for a certain
natural class of pVASS with nondeterminism. Furthermore, we show the following
dichotomy: if the asymptotic expected termination time is not linear, then it
is at least quadratic, i.e., in Ω(n2).'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomás
full_name: Brázdil, Tomás
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Antonín
full_name: Kucera, Antonín
last_name: Kucera
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dominik
full_name: Velan, Dominik
last_name: Velan
citation:
ama: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination
for probabilistic VASS with nondeterminism. In: International Symposium on
Automated Technology for Verification and Analysis. Vol 11781. Springer Nature;
2019:462-478. doi:10.1007/978-3-030-31784-3_27'
apa: 'Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019).
Deciding fast termination for probabilistic VASS with nondeterminism. In International
Symposium on Automated Technology for Verification and Analysis (Vol. 11781,
pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27'
chicago: Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and
Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.”
In International Symposium on Automated Technology for Verification and Analysis,
11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.
ieee: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding
fast termination for probabilistic VASS with nondeterminism,” in International
Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan,
2019, vol. 11781, pp. 462–478.
ista: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast
termination for probabilistic VASS with nondeterminism. International Symposium
on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology
for Verification and Analysis, LNCS, vol. 11781, 462–478.'
mla: Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with
Nondeterminism.” International Symposium on Automated Technology for Verification
and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.
short: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International
Symposium on Automated Technology for Verification and Analysis, Springer Nature,
2019, pp. 462–478.
conference:
end_date: 2019-10-31
location: Taipei, Taiwan
name: 'ATVA: Automated TEchnology for Verification and Analysis'
start_date: 2019-10-28
date_created: 2019-12-15T23:00:44Z
date_published: 2019-10-21T00:00:00Z
date_updated: 2023-09-06T12:40:58Z
day: '21'
department:
- _id: KrCh
doi: 10.1007/978-3-030-31784-3_27
external_id:
arxiv:
- '1907.11010'
isi:
- '000723515700027'
intvolume: ' 11781'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11010
month: '10'
oa: 1
oa_version: Preprint
page: 462-478
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Symposium on Automated Technology for Verification and
Analysis
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030317836'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deciding fast termination for probabilistic VASS with nondeterminism
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11781
year: '2019'
...
---
_id: '7182'
abstract:
- lang: eng
text: During infection pathogens secrete small molecules, termed effectors, to manipulate
and control the interaction with their specific hosts. Both the pathogen and the
plant are under high selective pressure to rapidly adapt and co-evolve in what
is usually referred to as molecular arms race. Components of the host’s immune
system form a network that processes information about molecules with a foreign
origin and damage-associated signals, integrating them with developmental and
abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding
leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction
networks have been extensively characterized. However, little is known on whether
pathogenic effectors form complexes to overcome plant immunity and promote disease.
Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces
effectors that target hubs in the immune network of the host cell. Here we assess
the capability of U. maydis effector candidates to interact with each other, which
may play a crucial role during the infection process. Using a systematic yeast-two-hybrid
approach and based on a preliminary pooled screen, we selected 63 putative effectors
for one-on-one matings with a library of nearly 300 effector candidates. We found
that 126 of these effector candidates interacted either with themselves or other
predicted effectors. Although the functional relevance of the observed interactions
remains elusive, we propose that the observed abundance in complex formation between
effectors adds an additional level of complexity to effector research and should
be taken into consideration when studying effector evolution and function. Based
on this fundamental finding, we suggest various scenarios which could evolutionarily
drive the formation and stabilization of an effector interactome.
article_number: '1437'
article_processing_charge: No
article_type: original
author:
- first_name: André
full_name: Alcântara, André
last_name: Alcântara
- first_name: Jason
full_name: Bosch, Jason
last_name: Bosch
- first_name: Fahimeh
full_name: Nazari, Fahimeh
last_name: Nazari
- first_name: Gesa
full_name: Hoffmann, Gesa
last_name: Hoffmann
- 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: Simon
full_name: Uhse, Simon
last_name: Uhse
- first_name: Martin A.
full_name: Darino, Martin A.
last_name: Darino
- first_name: Toluwase
full_name: Olukayode, Toluwase
last_name: Olukayode
- first_name: Daniel
full_name: Reumann, Daniel
last_name: Reumann
- first_name: Laura
full_name: Baggaley, Laura
last_name: Baggaley
- first_name: Armin
full_name: Djamei, Armin
last_name: Djamei
citation:
ama: Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive
effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437
apa: Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S.,
… Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex
formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437
chicago: Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle
C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals
Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers,
2019. https://doi.org/10.3389/fpls.2019.01437.
ieee: A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex
formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.
ista: Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA,
Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals
extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.
mla: Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex
Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers,
2019, doi:10.3389/fpls.2019.01437.
short: A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A.
Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science
10 (2019).
date_created: 2019-12-15T23:00:43Z
date_published: 2019-11-14T00:00:00Z
date_updated: 2023-09-06T14:33:46Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3389/fpls.2019.01437
external_id:
isi:
- '000499821700001'
pmid:
- '31803201'
file:
- access_level: open_access
checksum: 995aa838aec2064d93550de82b40bbd1
content_type: application/pdf
creator: dernst
date_created: 2019-12-16T07:58:43Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7185'
file_name: 2019_FrontiersPlant_Alcantara.pdf
file_size: 1532505
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systematic Y2H screening reveals extensive effector-complex formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...
---
_id: '7180'
abstract:
- lang: eng
text: Arabidopsis PIN2 protein directs transport of the phytohormone auxin from
the root tip into the root elongation zone. Variation in hormone transport, which
depends on a delicate interplay between PIN2 sorting to and from polar plasma
membrane domains, determines root growth. By employing a constitutively degraded
version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis.
This response does not require de novo protein synthesis, but involves early events
in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2
sorting and intracellular distribution governs formation of a lateral PIN2 gradient
in gravistimulated roots, coinciding with adjustments in auxin signaling and directional
root growth. Strikingly, simulations indicate that PIN2 gradient formation is
no prerequisite for root bending but rather dampens asymmetric auxin flow and
signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting,
thus, appears essential for determining the rate of gravity-induced root curvature
via attenuation of differential cell elongation.
article_number: '5516'
article_processing_charge: No
article_type: original
author:
- first_name: Katarzyna
full_name: Retzer, Katarzyna
last_name: Retzer
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Nataliia
full_name: Konstantinova, Nataliia
last_name: Konstantinova
- first_name: Kateřina
full_name: Malínská, Kateřina
last_name: Malínská
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
citation:
ama: Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits
root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature
Communications. 2019;10. doi:10.1038/s41467-019-13543-1
apa: Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek,
J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism
via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-13543-1
chicago: Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská,
Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling
Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.
ieee: K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism
via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J,
Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting
of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.
mla: Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism
via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications,
vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.
short: K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek,
C. Luschnig, Nature Communications 10 (2019).
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:08:21Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1038/s41467-019-13543-1
external_id:
isi:
- '000500508100001'
pmid:
- '31797871'
file:
- access_level: open_access
checksum: 77e8720a8e0f3091b98159f85be40893
content_type: application/pdf
creator: dernst
date_created: 2019-12-16T07:37:50Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7184'
file_name: 2019_NatureComm_Retzer.pdf
file_size: 5156533
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 264CBBAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02379
name: Modeling epithelial tissue mechanics during cell invasion
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis
PIN2 auxin transporter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...
---
_id: '7181'
abstract:
- lang: eng
text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary
predictions1,2, but the complexity of aligning large datasets requires the use
of approximate solutions3, including the progressive algorithm4. Progressive MSA
methods start by aligning the most similar sequences and subsequently incorporate
the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy
declines substantially as the number of sequences is scaled up5. We introduce
a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard
workstation and substantially improves accuracy on datasets larger than 10,000
sequences. Our regressive algorithm works the other way around to the progressive
algorithm and begins by aligning the most dissimilar sequences. It uses an efficient
divide-and-conquer strategy to run third-party alignment methods in linear time,
regardless of their original complexity. Our approach will enable analyses of
extremely large genomic datasets such as the recently announced Earth BioGenome
Project, which comprises 1.5 million eukaryotic genomes6.
article_processing_charge: No
article_type: original
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: Di Tommaso, Paolo
last_name: Di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470.
doi:10.1038/s41587-019-0333-6
apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf
regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6
chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive
Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.
ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf
regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature,
pp. 1466–1470, 2019.
ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.
mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature,
2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019)
1466–1470.
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:32:52Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41587-019-0333-6
ec_funded: 1
external_id:
isi:
- '000500748900021'
pmid:
- '31792410'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1466-1470
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- '15461696'
issn:
- '10870156'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13059'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2019'
...
---
_id: '7202'
abstract:
- lang: eng
text: The cerebral cortex contains multiple areas with distinctive cytoarchitectonical
patterns, but the cellular mechanisms underlying the emergence of this diversity
remain unclear. Here, we have investigated the neuronal output of individual progenitor
cells in the developing mouse neocortex using a combination of methods that together
circumvent the biases and limitations of individual approaches. Our experimental
results indicate that progenitor cells generate pyramidal cell lineages with a
wide range of sizes and laminar configurations. Mathematical modelling indicates
that these outcomes are compatible with a stochastic model of cortical neurogenesis
in which progenitor cells undergo a series of probabilistic decisions that lead
to the specification of very heterogeneous progenies. Our findings support a mechanism
for cortical neurogenesis whose flexibility would make it capable to generate
the diverse cytoarchitectures that characterize distinct neocortical areas.
article_number: e51381
article_processing_charge: No
article_type: original
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong Kuan
full_name: Wong, Fong Kuan
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou-Pouliou, Eleni
last_name: Serafeimidou-Pouliou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis
underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8.
doi:10.7554/eLife.51381
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou,
E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly
of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni
Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic
Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.”
ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.
ieee: A. Llorca et al., “A stochastic framework of neurogenesis underlies
the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences
Publications, 2019.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E,
Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M,
Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of
neocortical cytoarchitecture. eLife. 8, e51381.
mla: Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the
Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife
Sciences Publications, 2019, doi:10.7554/eLife.51381.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, ELife 8 (2019).
date_created: 2019-12-22T23:00:42Z
date_published: 2019-11-18T00:00:00Z
date_updated: 2023-09-06T14:38:39Z
day: '18'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/eLife.51381
ec_funded: 1
external_id:
isi:
- '000508156800001'
pmid:
- '31736464'
file:
- access_level: open_access
checksum: b460ecc33e1a68265e7adea775021f3a
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T15:19:26Z
date_updated: 2020-07-14T12:47:53Z
file_id: '7503'
file_name: 2019_eLife_Llorca.pdf
file_size: 2960543
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: A stochastic framework of neurogenesis underlies the assembly of neocortical
cytoarchitecture
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: 8
year: '2019'
...
---
_id: '7179'
abstract:
- lang: eng
text: Glutamate is the major excitatory neurotransmitter in the CNS binding to a
variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8)
can act excitatory or inhibitory, depending on associated signal cascades. Expression
and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the
cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4,
mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to
the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3,
and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants.
Using receptor-specific antibodies in cochlear wholemounts, we found expression
of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution
and confocal microscopy in combination with 3-dimensional reconstructions indicated
a postsynaptic localization of mGluR2 that overlaps with postsynaptic density
protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast,
mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary,
we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament
for new therapeutical strategies that could protect the cochlea against noxious
stimuli and excitotoxicity.
article_processing_charge: No
article_type: original
author:
- first_name: Lisa
full_name: Klotz, Lisa
last_name: Klotz
- first_name: Olaf
full_name: Wendler, Olaf
last_name: Wendler
- first_name: Renato
full_name: Frischknecht, Renato
last_name: Frischknecht
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Holger
full_name: Schulze, Holger
last_name: Schulze
- first_name: Ralf
full_name: Enz, Ralf
last_name: Enz
citation:
ama: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization
of group II and III metabotropic glutamate receptors at pre- and postsynaptic
sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746.
doi:10.1096/fj.201901543R
apa: Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., &
Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors
at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal.
FASEB. https://doi.org/10.1096/fj.201901543R
chicago: Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger
Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate
Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.”
FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.
ieee: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz,
“Localization of group II and III metabotropic glutamate receptors at pre- and
postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal,
vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.
ista: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization
of group II and III metabotropic glutamate receptors at pre- and postsynaptic
sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.
mla: Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate
Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.”
FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.
short: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz,
FASEB Journal 33 (2019) 13734–13746.
date_created: 2019-12-15T23:00:42Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:34:36Z
day: '01'
ddc:
- '571'
- '599'
department:
- _id: RySh
doi: 10.1096/fj.201901543R
external_id:
isi:
- '000507466100054'
pmid:
- '31585509'
file:
- access_level: open_access
checksum: 79e3b72481dc32489911121cf3b7d8d0
content_type: application/pdf
creator: shigemot
date_created: 2020-12-06T17:30:09Z
date_updated: 2020-12-06T17:30:09Z
file_id: '8922'
file_name: Klotz et al 2019 EMBO Reports.pdf
file_size: 4766789
relation: main_file
success: 1
file_date_updated: 2020-12-06T17:30:09Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 13734-13746
pmid: 1
publication: FASEB Journal
publication_identifier:
eissn:
- '15306860'
publication_status: published
publisher: FASEB
quality_controlled: '1'
scopus_import: '1'
status: public
title: Localization of group II and III metabotropic glutamate receptors at pre- and
postsynaptic sites of inner hair cell ribbon synapses
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 33
year: '2019'
...
---
_id: '7201'
abstract:
- lang: eng
text: Applying machine learning techniques to the quickly growing data in science
and industry requires highly-scalable algorithms. Large datasets are most commonly
processed "data parallel" distributed across many nodes. Each node's contribution
to the overall gradient is summed using a global allreduce. This allreduce is
the single communication and thus scalability bottleneck for most machine learning
workloads. We observe that frequently, many gradient values are (close to) zero,
leading to sparse of sparsifyable communications. To exploit this insight, we
analyze, design, and implement a set of communication-efficient protocols for
sparse input data, in conjunction with efficient machine learning algorithms which
can leverage these primitives. Our communication protocols generalize standard
collective operations, by allowing processes to contribute arbitrary sparse input
data vectors. Our generic communication library, SparCML1, extends MPI to support
additional features, such as non-blocking (asynchronous) operations and low-precision
data representations. As such, SparCML and its techniques will form the basis
of future highly-scalable machine learning frameworks.
article_number: a11
article_processing_charge: No
author:
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
- first_name: Saleh
full_name: Ashkboos, Saleh
id: 0D0A9058-257B-11EA-A937-9341C3D8BC8A
last_name: Ashkboos
- first_name: Mehdi
full_name: Aghagolzadeh, Mehdi
last_name: Aghagolzadeh
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
citation:
ama: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance
sparse communication for machine learning. In: International Conference for
High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019.
doi:10.1145/3295500.3356222'
apa: 'Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler,
T. (2019). SparCML: High-performance sparse communication for machine learning.
In International Conference for High Performance Computing, Networking, Storage
and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222'
chicago: 'Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh,
and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine
Learning.” In International Conference for High Performance Computing, Networking,
Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.'
ieee: 'C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler,
“SparCML: High-performance sparse communication for machine learning,” in International
Conference for High Performance Computing, Networking, Storage and Analysis, SC,
Denver, CO, Unites States, 2019.'
ista: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML:
High-performance sparse communication for machine learning. International Conference
for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference
for High Performance Computing, Networking, Storage and Analysis, a11.'
mla: 'Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for
Machine Learning.” International Conference for High Performance Computing,
Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.'
short: C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:,
International Conference for High Performance Computing, Networking, Storage and
Analysis, SC, ACM, 2019.
conference:
end_date: 2019-11-19
location: Denver, CO, Unites States
name: 'SC: Conference for High Performance Computing, Networking, Storage and Analysis'
start_date: 2019-11-17
date_created: 2019-12-22T23:00:42Z
date_published: 2019-11-17T00:00:00Z
date_updated: 2023-09-06T14:37:55Z
day: '17'
department:
- _id: DaAl
doi: 10.1145/3295500.3356222
ec_funded: 1
external_id:
arxiv:
- '1802.08021'
isi:
- '000545976800011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.08021
month: '11'
oa: 1
oa_version: Preprint
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: International Conference for High Performance Computing, Networking,
Storage and Analysis, SC
publication_identifier:
eissn:
- '21674337'
isbn:
- '9781450362290'
issn:
- '21674329'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SparCML: High-performance sparse communication for machine learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '13067'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong
barriers to gene flow, while the role of postzygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Postzygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside
contact zones of three populations in Sweden. Females' clutch size ranged from
0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterised female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant postzygotic barriers contributing
to ecotype divergence and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo
abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019.
doi:10.5061/DRYAD.TB2RBNZWK'
apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
(2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between
Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK'
chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow
between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.'
ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data
from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?” Dryad, 2019.'
ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from:
Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?,
Dryad, 10.5061/DRYAD.TB2RBNZWK.'
mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic
Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.'
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).
date_created: 2023-05-23T16:36:27Z
date_published: 2019-12-02T00:00:00Z
date_updated: 2023-09-06T14:48:57Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.TB2RBNZWK
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.tb2rbnzwk
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7205'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7214'
abstract:
- lang: eng
text: "Background: Many cancer genomes are extensively rearranged with highly aberrant
chromosomal karyotypes. Structural and copy number variations in cancer genomes
can be determined via abnormal mapping of sequenced reads to the reference genome.
Recently it became possible to reconcile both of these types of large-scale variations
into a karyotype graph representation of the rearranged cancer genomes. Such a
representation, however, does not directly describe the linear and/or circular
structure of the underlying rearranged cancer chromosomes, thus limiting possible
analysis of cancer genomes somatic evolutionary process as well as functional
genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults:
Here we address the aforementioned limitation by introducing a novel methodological
framework for recovering rearranged cancer chromosomes from karyotype graphs.
For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP)
of finding a collection of linear and/or circular rearranged cancer chromosomes
that are determined by the graph. We derive and prove computational complexities
for several variations of the EDP. We then demonstrate that Eulerian decomposition
of the cancer karyotype graphs is not always unique and present the Consistent
Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the
cancer karyotype graph, and describe a novel algorithm CCR capable of solving
CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate
that it is capable of consistently recovering large cancer contigs even when underlying
cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged
cancer contigs from karyotype graphs thereby addressing existing limitation in
inferring chromosomal structures of rearranged cancer genomes and advancing our
understanding of both patient/cancer-specific as well as the overall genetic instability
in cancer."
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Sergey
full_name: Aganezov, Sergey
last_name: Aganezov
- first_name: Ilya
full_name: Zban, Ilya
last_name: Zban
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- first_name: Nikita
full_name: Alexeev, Nikita
last_name: Alexeev
- first_name: Michael C.
full_name: Schatz, Michael C.
last_name: Schatz
citation:
ama: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged
cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20.
doi:10.1186/s12859-019-3208-4
apa: Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019).
Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics.
BMC. https://doi.org/10.1186/s12859-019-3208-4
chicago: Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael
C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC
Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.
ieee: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering
rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics,
vol. 20. BMC, 2019.
ista: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged
cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.
mla: Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype
Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.
short: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics
20 (2019).
date_created: 2019-12-29T23:00:46Z
date_published: 2019-12-17T00:00:00Z
date_updated: 2023-09-06T14:51:06Z
day: '17'
ddc:
- '570'
department:
- _id: DaAl
doi: 10.1186/s12859-019-3208-4
external_id:
isi:
- '000511618800007'
file:
- access_level: open_access
checksum: 7a30357efdcf8f66587ed495c0927724
content_type: application/pdf
creator: dernst
date_created: 2020-01-02T16:10:58Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7221'
file_name: 2019_BMCBioinfo_Aganezov.pdf
file_size: 1917374
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: BMC Bioinformatics
publication_identifier:
eissn:
- '14712105'
publication_status: published
publisher: BMC
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recovering rearranged cancer chromosomes from karyotype graphs
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: '2019'
...
---
_id: '7225'
abstract:
- lang: eng
text: "This is a literature teaching resource review for biologically inspired microfluidics
courses\r\nor exploring the diverse applications of microfluidics. The structure
is around key papers and model\r\norganisms. While courses gradually change over
time, a focus remains on understanding how\r\nmicrofluidics has developed as well
as what it can and cannot do for researchers. As a primary\r\nstarting point,
we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof
applications are discussed using model prokaryotic and eukaryotic organisms from
the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei),
yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms
(Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis
thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical
methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic
games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics
can still be used effectively for specific applications."
article_number: '109'
article_processing_charge: Yes
article_type: review
author:
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
citation:
ama: Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering.
2019;6(4). doi:10.3390/bioengineering6040109
apa: Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review.
Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109
chicago: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.”
Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.
ieee: J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering,
vol. 6, no. 4. MDPI, 2019.
ista: Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering.
6(4), 109.
mla: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering,
vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.
short: J. Merrin, Bioengineering 6 (2019).
date_created: 2020-01-05T23:00:45Z
date_published: 2019-12-03T00:00:00Z
date_updated: 2023-09-06T14:52:49Z
day: '03'
ddc:
- '620'
department:
- _id: NanoFab
doi: 10.3390/bioengineering6040109
external_id:
isi:
- '000505590000024'
pmid:
- '31816954'
file:
- access_level: open_access
checksum: 80f1499e2a4caccdf3aa54b137fd99a0
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:49:59Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7243'
file_name: 2019_Bioengineering_Merrin.pdf
file_size: 2660780
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bioengineering
publication_identifier:
eissn:
- '23065354'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frontiers in microfluidics, a teaching resource review
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: 6
year: '2019'
...
---
_id: '7228'
abstract:
- lang: eng
text: "Traditional concurrent programming involves manipulating shared mutable state.
Alternatives to this programming style are communicating sequential processes
(CSP) and actor models, which share data via explicit communication. These models
have been known for almost half a century, and have recently had started to gain
significant traction among modern programming languages. The common abstraction
for communication between several processes is the channel. Although channels
are similar to producer-consumer data structures, they have different semantics
and support additional operations, such as the select expression. Despite their
growing popularity, most known implementations of channels use lock-based data
structures and can be rather inefficient.\r\n\r\nIn this paper, we present the
first efficient lock-free algorithm for implementing a communication channel for
CSP programming. We provide implementations and experimental results in the Kotlin
and Go programming languages. Our new algorithm outperforms existing implementations
on many workloads, while providing non-blocking progress guarantee. Our design
can serve as an example of how to construct general communication data structures
for CSP and actor models. "
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: 'Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming
via communicating sequential processes. In: 25th Anniversary of Euro-Par.
Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23'
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels
for programming via communicating sequential processes. In 25th Anniversary
of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-29400-7_23'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO
Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary
of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming
via communicating sequential processes,” in 25th Anniversary of Euro-Par,
Göttingen, Germany, 2019, vol. 11725, pp. 317–333.
ista: 'Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming
via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par:
European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.'
mla: Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating
Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer
Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.
short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par,
Springer Nature, 2019, pp. 317–333.
conference:
end_date: 2019-08-30
location: Göttingen, Germany
name: 'Euro-Par: European Conference on Parallel Processing'
start_date: 2019-08-26
date_created: 2020-01-05T23:00:46Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:53:59Z
day: '13'
department:
- _id: DaAl
doi: 10.1007/978-3-030-29400-7_23
external_id:
isi:
- '000851061400023'
intvolume: ' 11725'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 317-333
publication: 25th Anniversary of Euro-Par
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9399-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable FIFO channels for programming via communicating sequential processes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11725
year: '2019'
...
---
_id: '7216'
abstract:
- lang: eng
text: 'We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system
to label a stream of noisy observations of transit vehicle trajectories with the
transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently
to large transit networks, our system first retrieves a small set of candidate
routes from a geometrically indexed data structure, then applies a fine-grained
scoring step to choose the best match. Given that real-time data remains unavailable
for the majority of the world’s transit agencies, these inferences can help feed
a real-time map of a transit system’s trips, infer transit trip delays in real
time, or measure and correct noisy transit tracking data. This system can run
on vehicle observations from a variety of sources that don’t attach route information
to vehicle observations, such as public imagery streams or user-contributed transit
vehicle sightings.We abstract away the specifics of the sensing system and demonstrate
the effectiveness of our system on a "semisynthetic" dataset of all New York City
buses, where we simulate sensed trajectories by starting with fully labeled vehicle
trajectories reported via the GTFS-Realtime protocol, removing the transit route
IDs, and perturbing locations with synthetic noise. Using just the geometric shapes
of the trajectories, we demonstrate that our system converges on the correct route
ID within a few minutes, even after a vehicle switches from serving one trip to
the next.'
article_number: '8917514'
article_processing_charge: No
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: James
full_name: Cook, James
last_name: Cook
- first_name: Alex
full_name: Fabrikant, Alex
last_name: Fabrikant
- first_name: Marco
full_name: Gruteser, Marco
last_name: Gruteser
citation:
ama: 'Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching
of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent
Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514'
apa: 'Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL:
Real-time matching of transit vehicle trajectories to transit routes at scale.
In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New
Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514'
chicago: 'Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL:
Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.”
In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019.
https://doi.org/10.1109/ITSC.2019.8917514.'
ieee: 'G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time
matching of transit vehicle trajectories to transit routes at scale,” in 2019
IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand,
2019.'
ista: 'Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching
of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent
Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference,
8917514.'
mla: 'Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle
Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation
Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.'
short: G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent
Transportation Systems Conference, IEEE, 2019.
conference:
end_date: 2019-10-30
location: Auckland, New Zealand
name: 'ITSC: Intelligent Transportation Systems Conference'
start_date: 2019-10-27
date_created: 2019-12-29T23:00:47Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2023-09-06T14:50:28Z
day: '28'
department:
- _id: HeEd
doi: 10.1109/ITSC.2019.8917514
external_id:
isi:
- '000521238102050'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
publication: 2019 IEEE Intelligent Transportation Systems Conference
publication_identifier:
isbn:
- '9781538670248'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'LiveTraVeL: Real-time matching of transit vehicle trajectories to transit
routes at scale'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7231'
abstract:
- lang: eng
text: Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation
for nonlinear systems with polynomial dynamics, which leverages a combination
of barrier certificates. PBT has advantages over traditional time-step based methods
in dealing with those nonlinear dynamical systems in which there is a large difference
in speed between trajectories, producing an overapproximation that is time independent.
However, the existing approach for PBT is not efficient due to the application
of interval methods for enclosure-box computation, and it can only deal with continuous
dynamical systems without uncertainty. In this paper, we extend the approach with
the ability to handle both continuous and hybrid dynamical systems with uncertainty
that can reside in parameters and/or noise. We also improve the efficiency of
the method significantly, by avoiding the use of interval-based methods for the
enclosure-box computation without loosing soundness. We have developed a C++ prototype
implementing the proposed approach and we evaluate it on several benchmarks. The
experiments show that our approach is more efficient and precise than other methods
in the literature.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes
for nonlinear hybrid systems with uncertainty. In: 17th International Conference
on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature;
2019:123-141. doi:10.1007/978-3-030-29662-9_8'
apa: 'Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise
robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th
International Conference on Formal Modeling and Analysis of Timed Systems
(Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8'
chicago: Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise
Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th
International Conference on Formal Modeling and Analysis of Timed Systems,
11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.
ieee: H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty,” in 17th International
Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The
Netherlands, 2019, vol. 11750, pp. 123–141.
ista: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty. 17th International Conference
on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and
Analysis of Timed Systems, LNCS, vol. 11750, 123–141.'
mla: Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems
with Uncertainty.” 17th International Conference on Formal Modeling and Analysis
of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.
short: H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference
on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:47Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:55:15Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_8
external_id:
arxiv:
- '1907.11514'
isi:
- '000611677700008'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11514
month: '08'
oa: 1
oa_version: Preprint
page: 123-141
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7340'
abstract:
- lang: eng
text: Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation
of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone
ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal
domain (IRE1LD) that favours the latter's monomeric inactive state and loss of
ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations
is presently lacking. We report that enforced loading of endogenous BiP onto endogenous
IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that
de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated
BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry
profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent
with active destabilisation of the IRE1LD dimer. Together, these observations
support a competition model whereby waning ER stress passively partitions ERdj4
and BiP to IRE1LD to initiate active repression of UPR signalling.
acknowledgement: We thank the CIMR flow cytometry core facility team (Reiner Schulte,
Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington
lab for access to the Octet machine, Steffen Preissler for advice on data interpretation,
Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.
article_number: e50793
article_processing_charge: No
article_type: original
author:
- first_name: Niko Paresh
full_name: Amin-Wetzel, Niko Paresh
id: E95D3014-9D8C-11E9-9C80-D2F8E5697425
last_name: Amin-Wetzel
- first_name: Lisa
full_name: Neidhardt, Lisa
last_name: Neidhardt
- first_name: Yahui
full_name: Yan, Yahui
last_name: Yan
- first_name: Matthias P.
full_name: Mayer, Matthias P.
last_name: Mayer
- first_name: David
full_name: Ron, David
last_name: Ron
citation:
ama: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in
IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression
of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793
apa: Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019).
Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.50793
chicago: Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer,
and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation
of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences
Publications, 2019. https://doi.org/10.7554/eLife.50793.
ieee: N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured
regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer
and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions
in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and
repression of the UPR. eLife. 8, e50793.
mla: Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated
Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife,
vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.
short: N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).
date_created: 2020-01-19T23:00:39Z
date_published: 2019-12-24T00:00:00Z
date_updated: 2023-09-06T14:58:02Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.50793
external_id:
isi:
- '000512303700001'
pmid:
- '31873072'
file:
- access_level: open_access
checksum: 29fcbcd8c1fc7f11a596ed7f14ea1c82
content_type: application/pdf
creator: dernst
date_created: 2020-11-19T11:37:41Z
date_updated: 2020-11-19T11:37:41Z
file_id: '8777'
file_name: 2019_eLife_AminWetzel.pdf
file_size: 4817384
relation: main_file
success: 1
file_date_updated: 2020-11-19T11:37:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR
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: 8
year: '2019'
...
---
_id: '7422'
abstract:
- lang: eng
text: Biochemical reactions often occur at low copy numbers but at once in crowded
and diverse environments. Space and stochasticity therefore play an essential
role in biochemical networks. Spatial-stochastic simulations have become a prominent
tool for understanding how stochasticity at the microscopic level influences the
macroscopic behavior of such systems. While particle-based models guarantee the
level of detail necessary to accurately describe the microscopic dynamics at very
low copy numbers, the algorithms used to simulate them typically imply trade-offs
between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s
Function Reaction Dynamics) is an exact algorithm that evades such trade-offs
by partitioning the N-particle system into M ≤ N analytically tractable one- and
two-particle systems; the analytical solutions (Green’s functions) then are used
to implement an event-driven particle-based scheme that allows particles to make
large jumps in time and space while retaining access to their state variables
at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that
implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based
simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on
2D planes representing membranes, and on 1D elongated cylinders representative
of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion
used to model active transport. We find that, for low particle densities, eGFRD2
is up to 6 orders of magnitude faster than conventional Brownian dynamics. We
exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1
gradient formation, which involves 3D diffusion, active transport on microtubules,
and autophosphorylation on the membrane, confirming recent experimental and theoretical
results on this system to hold under genuinely stochastic conditions.
article_number: '054108'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Joris
full_name: Paijmans, Joris
last_name: Paijmans
- first_name: Laurens
full_name: Bossen, Laurens
last_name: Bossen
- first_name: Thomas
full_name: Miedema, Thomas
last_name: Miedema
- first_name: Martijn
full_name: Wehrens, Martijn
last_name: Wehrens
- first_name: Nils B.
full_name: Becker, Nils B.
last_name: Becker
- first_name: Kazunari
full_name: Kaizu, Kazunari
last_name: Kaizu
- first_name: Koichi
full_name: Takahashi, Koichi
last_name: Takahashi
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: Pieter Rein
full_name: ten Wolde, Pieter Rein
last_name: ten Wolde
citation:
ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The
Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker,
N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn
Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom,
and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal
of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu
K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal
of Chemical Physics. 150(5), 054108.
mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of
Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker,
K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics
150 (2019).
date_created: 2020-01-30T10:34:36Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-09-06T14:59:28Z
day: '07'
department:
- _id: GaTk
doi: 10.1063/1.5064867
external_id:
arxiv:
- '1708.09364'
isi:
- '000458109300009'
intvolume: ' 150'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.09364
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: eGFRD in all dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2019'
...
---
_id: '7230'
abstract:
- lang: eng
text: Simple drawings of graphs are those in which each pair of edges share at most
one point, either a common endpoint or a proper crossing. In this paper we study
the problem of extending a simple drawing D(G) of a graph G by inserting a set
of edges from the complement of G into D(G) such that the result is a simple drawing.
In the context of rectilinear drawings, the problem is trivial. For pseudolinear
drawings, the existence of such an extension follows from Levi’s enlargement lemma.
In contrast, we prove that deciding if a given set of edges can be inserted into
a simple drawing is NP-complete. Moreover, we show that the maximization version
of the problem is APX-hard. We also present a polynomial-time algorithm for deciding
whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for
the graph G.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Martin
full_name: Derka, Martin
last_name: Derka
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
citation:
ama: 'Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th
International Symposium on Graph Drawing and Network Visualization. Vol 11904.
Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18'
apa: 'Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple
drawings. In 27th International Symposium on Graph Drawing and Network Visualization
(Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18'
chicago: Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple
Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization,
11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.
ieee: A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,”
in 27th International Symposium on Graph Drawing and Network Visualization,
Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.
ista: 'Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th
International Symposium on Graph Drawing and Network Visualization. GD: Graph
Drawing and Network Visualization, LNCS, vol. 11904, 230–243.'
mla: Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International
Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer
Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.
short: A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium
on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.
conference:
end_date: 2019-09-20
location: Prague, Czech Republic
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2019-09-17
date_created: 2020-01-05T23:00:47Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2023-09-06T14:56:00Z
day: '28'
department:
- _id: UlWa
doi: 10.1007/978-3-030-35802-0_18
ec_funded: 1
external_id:
arxiv:
- '1908.08129'
isi:
- '000612918800018'
intvolume: ' 11904'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.08129
month: '11'
oa: 1
oa_version: Preprint
page: 230-243
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 27th International Symposium on Graph Drawing and Network Visualization
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0303-5801-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending simple drawings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11904
year: '2019'
...
---
_id: '7232'
abstract:
- lang: eng
text: 'We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism
which extends STL by capturing the discrete/ continuous time duality found in
many cyber-physical systems (CPS), as well as mixed-signal electronic designs.
In STL−MX, properties of components with continuous dynamics are expressed in
STL, while specifications of components with discrete dynamics are written in
LTL. To combine the two layers, we evaluate formulas on two traces, discrete-
and continuous-time, and introduce two interface operators that map signals, properties
and their satisfaction signals across the two time domains. We show that STL-mx
has the expressive power of STL supplemented with an implicit T-periodic clock
signal. We develop and implement an algorithm for monitoring STL-mx formulas and
illustrate the approach using a mixed-signal example. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th
International Conference on Formal Modeling and Analysis of Timed Systems.
Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4'
apa: 'Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal
logic. In 17th International Conference on Formal Modeling and Analysis of
Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer
Nature. https://doi.org/10.1007/978-3-030-29662-9_4'
chicago: Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal
Logic.” In 17th International Conference on Formal Modeling and Analysis of
Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.
ieee: T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,”
in 17th International Conference on Formal Modeling and Analysis of Timed Systems,
Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.
ista: 'Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th
International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS:
Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.'
mla: Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International
Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer
Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.
short: T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on
Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Anaysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:48Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:57:17Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_4
external_id:
isi:
- '000611677700004'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 59-75
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixed-time signal temporal logic
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7420'
abstract:
- lang: eng
text: β1-integrins mediate cell–matrix interactions and their trafficking is important
in the dynamic regulation of cell adhesion, migration and malignant processes,
including cancer cell invasion. Here, we employ an RNAi screen to characterize
regulators of integrin traffic and identify the association of Golgi-localized
gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role
in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2
limits active β1-integrin levels in focal adhesions and decreases cancer cell
migration and invasion, which is in agreement with its ability to regulate the
dynamics of active integrins. By using the proximity-dependent biotin identification
(BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10,
as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular
accumulation of active β1-integrin, and reduces integrin activity in focal adhesions
and cell migration similarly to GGA2 depletion, indicating that both facilitate
active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are
important specificity determinants for integrin activity-dependent traffic.
article_number: jcs233387
article_processing_charge: No
article_type: original
author:
- first_name: Pranshu
full_name: Sahgal, Pranshu
last_name: Sahgal
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Jaroslav
full_name: Icha, Jaroslav
last_name: Icha
- first_name: Ilkka
full_name: Paatero, Ilkka
last_name: Paatero
- first_name: Hellyeh
full_name: Hamidi, Hellyeh
last_name: Hamidi
- first_name: Antti
full_name: Arjonen, Antti
last_name: Arjonen
- first_name: Mika
full_name: Pietilä, Mika
last_name: Pietilä
- first_name: Anne
full_name: Rokka, Anne
last_name: Rokka
- first_name: Johanna
full_name: Ivaska, Johanna
last_name: Ivaska
citation:
ama: Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent
β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387
apa: Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A.,
… Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387
chicago: Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh
Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and
RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science.
The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.
ieee: P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin
recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists,
2019.
ista: Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka
A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. 132(11), jcs233387.
mla: Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin
Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company
of Biologists, 2019, doi:10.1242/jcs.233387.
short: P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä,
A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).
date_created: 2020-01-30T10:31:42Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-06T15:01:00Z
day: '07'
department:
- _id: MiSi
doi: 10.1242/jcs.233387
external_id:
isi:
- '000473327900017'
pmid:
- '31076515'
intvolume: ' 132'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.233387
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: GGA2 and RAB13 promote activity-dependent β1-integrin recycling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 132
year: '2019'
...
---
_id: '7423'
abstract:
- lang: eng
text: 'We compare finite rank perturbations of the following three ensembles of
complex rectangular random matrices: First, a generalised Wishart ensemble with
one random and two fixed correlation matrices introduced by Borodin and Péché,
second, the product of two independent random matrices where one has correlated
entries, and third, the case when the two random matrices become also coupled
through a fixed matrix. The singular value statistics of all three ensembles is
shown to be determinantal and we derive double contour integral representations
for their respective kernels. Three different kernels are found in the limit of
infinite matrix dimension at the origin of the spectrum. They depend on finite
rank perturbations of the correlation and coupling matrices and are shown to be
integrable. The first kernel (I) is found for two independent matrices from the
second, and two weakly coupled matrices from the third ensemble. It generalises
the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel
(III) is obtained for the generalised Wishart ensemble and for two strongly coupled
matrices. It further generalises the perturbed Bessel kernel of Desrosiers and
Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices,
provides an interpolation between the kernels (I) and (III), generalising previous
findings of part of the authors.'
article_processing_charge: No
article_type: original
author:
- first_name: Gernot
full_name: Akemann, Gernot
last_name: Akemann
- first_name: Tomasz
full_name: Checinski, Tomasz
last_name: Checinski
- first_name: Dangzheng
full_name: Liu, Dangzheng
id: 2F947E34-F248-11E8-B48F-1D18A9856A87
last_name: Liu
- first_name: Eugene
full_name: Strahov, Eugene
last_name: Strahov
citation:
ama: 'Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products
of coupled random matrices: From one correlated to two Wishart ensembles. Annales
de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479.
doi:10.1214/18-aihp888'
apa: 'Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank
perturbations in products of coupled random matrices: From one correlated to two
Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888'
chicago: 'Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov.
“Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated
to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités
et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.'
ieee: 'G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles,”
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol.
55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.'
ista: 'Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles.
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.'
mla: 'Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled
Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de
l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute
of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.'
short: G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri
Poincaré, Probabilités et Statistiques 55 (2019) 441–479.
date_created: 2020-01-30T10:36:50Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-06T14:58:39Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-aihp888
external_id:
arxiv:
- '1704.05224'
isi:
- '000456070200013'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.05224
month: '02'
oa: 1
oa_version: Preprint
page: 441-479
publication: Annales de l'Institut Henri Poincaré, Probabilités et Statistiques
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: 'Finite rank perturbations in products of coupled random matrices: From one
correlated to two Wishart ensembles'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2019'
...
---
_id: '7421'
abstract:
- lang: eng
text: X and Y chromosomes can diverge when rearrangements block recombination between
them. Here we present the first genomic view of a reciprocal translocation that
causes two physically unconnected pairs of chromosomes to be coinherited as sex
chromosomes. In a population of the common frog (Rana temporaria), both pairs
of X and Y chromosomes show extensive sequence differentiation, but not degeneration
of the Y chromosomes. A new method based on gene trees shows both chromosomes
are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical
topologies, showing they have been coinherited since the reciprocal translocation
occurred. Reciprocal translocations can thus reshape sex linkage on a much greater
scale compared with inversions, the type of rearrangement that is much better
known in sex chromosome evolution, and they can greatly amplify the power of sexually
antagonistic selection to drive genomic rearrangement. Two more populations show
evidence of other rearrangements, suggesting that this species has unprecedented
structural polymorphism in its sex chromosomes.
article_processing_charge: No
article_type: original
author:
- 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: Nicolas
full_name: Rodrigues, Nicolas
last_name: Rodrigues
- first_name: Nicolas
full_name: Perrin, Nicolas
last_name: Perrin
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
citation:
ama: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology.
2019;28(8):1877-1889. doi:10.1111/mec.14990
apa: Toups, M. A., Rodrigues, N., Perrin, N., & Kirkpatrick, M. (2019). A reciprocal
translocation radically reshapes sex‐linked inheritance in the common frog. Molecular
Ecology. Wiley. https://doi.org/10.1111/mec.14990
chicago: Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick.
“A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common
Frog.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14990.
ieee: M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog,” Molecular Ecology,
vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.
ista: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology.
28(8), 1877–1889.
mla: Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked
Inheritance in the Common Frog.” Molecular Ecology, vol. 28, no. 8, Wiley,
2019, pp. 1877–89, doi:10.1111/mec.14990.
short: M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28
(2019) 1877–1889.
date_created: 2020-01-30T10:33:05Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-09-06T15:00:13Z
day: '01'
department:
- _id: BeVi
doi: 10.1111/mec.14990
external_id:
isi:
- '000468200800004'
pmid:
- '30576024'
intvolume: ' 28'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: 1877-1889
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: A reciprocal translocation radically reshapes sex‐linked inheritance in the
common frog
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2019'
...
---
_id: '7411'
abstract:
- lang: eng
text: "Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving
a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently
and publicly verifiable. The proof can be computed in T sequential steps, but
not much less, even by a malicious party having large parallelism. A PoSW thus
serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW
were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical
construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn
this work we construct a new simple PoSW in the random permutation model which
is almost as simple and efficient as [CP18] but conceptually very different. Whereas
the structure underlying [CP18] is a hash tree, our construction is based on skip
lists and has the interesting property that computing the PoSW is a reversible
computation.\r\nThe fact that the construction is reversible can potentially be
used for new applications like constructing proofs of replication. We also show
how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW
to get a PoSW where one additionally can verify correctness of the output much
more efficiently than recomputing it (though recent constructions of “verifiable
delay functions” subsume most of the applications this construction was aiming
at)."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible
proofs of sequential work. In: Advances in Cryptology – EUROCRYPT 2019.
Vol 11477. Springer International Publishing; 2019:277-291. doi:10.1007/978-3-030-17656-3_10'
apa: 'Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter,
M. (2019). Reversible proofs of sequential work. In Advances in Cryptology
– EUROCRYPT 2019 (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International
Publishing. https://doi.org/10.1007/978-3-030-17656-3_10'
chicago: Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak,
and Michael Walter. “Reversible Proofs of Sequential Work.” In Advances in
Cryptology – EUROCRYPT 2019, 11477:277–91. Springer International Publishing,
2019. https://doi.org/10.1007/978-3-030-17656-3_10.
ieee: H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter,
“Reversible proofs of sequential work,” in Advances in Cryptology – EUROCRYPT
2019, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.
ista: Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible
proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International
Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol.
11477, 277–291.
mla: Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” Advances
in Cryptology – EUROCRYPT 2019, vol. 11477, Springer International Publishing,
2019, pp. 277–91, doi:10.1007/978-3-030-17656-3_10.
short: H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:,
Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019,
pp. 277–291.
conference:
end_date: 2019-05-23
location: Darmstadt, Germany
name: International Conference on the Theory and Applications of Cryptographic Techniques
start_date: 2019-05-19
date_created: 2020-01-30T09:26:14Z
date_published: 2019-04-24T00:00:00Z
date_updated: 2023-09-06T15:26:06Z
day: '24'
department:
- _id: KrPi
doi: 10.1007/978-3-030-17656-3_10
ec_funded: 1
external_id:
isi:
- '000483516200010'
intvolume: ' 11477'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/252
month: '04'
oa: 1
oa_version: Submitted Version
page: 277-291
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Advances in Cryptology – EUROCRYPT 2019
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030176556'
- '9783030176563'
issn:
- 0302-9743
publication_status: published
publisher: Springer International Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible proofs of sequential work
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11477
year: '2019'
...
---
_id: '7406'
abstract:
- lang: eng
text: "Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission
machinery, and isolation of SVs from their host neuron is necessary to reveal
their most fundamental biochemical and functional properties in in vitro assays.
Isolated SVs from neurons that have been genetically engineered, e.g. to introduce
genetically encoded indicators, are not readily available but would permit new
insights into SV structure and function. Furthermore, it is unclear if cultured
neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew
method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional
SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe
show that ∼108 plated cortical neurons allow isolation of suitable SV amounts
for functional analysis and imaging. We found that SVs isolated from cultured
neurons have neurotransmitter uptake comparable to that of SVs isolated from intact
cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized
an exogenous SV-targeted marker protein and demonstrated the high efficiency of
SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from
genetically engineered neurons currently generally requires the availability of
transgenic animals, which is constrained by technical (e.g. cost and time) and
biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese
results demonstrate the modification and isolation of functional SVs using cultured
neurons and viral transduction. The ability to readily obtain SVs from genetically
engineered neurons will permit linking in situ studies to in vitro experiments
in a variety of genetic contexts."
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Miroslava
full_name: Spanova, Miroslava
id: 44A924DC-F248-11E8-B48F-1D18A9856A87
last_name: Spanova
- 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: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Harald H.
full_name: Sitte, Harald H.
last_name: Sitte
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from
genetically engineered cultured neurons. Journal of Neuroscience Methods.
2019;312:114-121. doi:10.1016/j.jneumeth.2018.11.018
apa: Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte,
H. H., & Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically
engineered cultured neurons. Journal of Neuroscience Methods. Elsevier.
https://doi.org/10.1016/j.jneumeth.2018.11.018
chicago: Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie
Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of
Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of
Neuroscience Methods. Elsevier, 2019. https://doi.org/10.1016/j.jneumeth.2018.11.018.
ieee: C. Mckenzie et al., “Isolation of synaptic vesicles from genetically
engineered cultured neurons,” Journal of Neuroscience Methods, vol. 312.
Elsevier, pp. 114–121, 2019.
ista: Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak
HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured
neurons. Journal of Neuroscience Methods. 312, 114–121.
mla: Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically
Engineered Cultured Neurons.” Journal of Neuroscience Methods, vol. 312,
Elsevier, 2019, pp. 114–21, doi:10.1016/j.jneumeth.2018.11.018.
short: C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte,
H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.
date_created: 2020-01-30T09:12:19Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-09-06T15:27:29Z
day: '15'
department:
- _id: HaJa
- _id: Bio
doi: 10.1016/j.jneumeth.2018.11.018
ec_funded: 1
external_id:
isi:
- '000456220900013'
pmid:
- '30496761'
intvolume: ' 312'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 114-121
pmid: 1
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Journal of Neuroscience Methods
publication_identifier:
issn:
- 0165-0270
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isolation of synaptic vesicles from genetically engineered cultured neurons
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 312
year: '2019'
...
---
_id: '7437'
abstract:
- lang: eng
text: 'Most of today''s distributed machine learning systems assume reliable networks:
whenever two machines exchange information (e.g., gradients or models), the network
should guarantee the delivery of the message. At the same time, recent work exhibits
the impressive tolerance of machine learning algorithms to errors or noise arising
from relaxed communication or synchronization. In this paper, we connect these
two trends, and consider the following question: Can we design machine learning
systems that are tolerant to network unreliability during training? With this
motivation, we focus on a theoretical problem of independent interest-given a
standard distributed parameter server architecture, if every communication between
the worker and the server has a non-zero probability p of being dropped, does
there exist an algorithm that still converges, and at what speed? The technical
contribution of this paper is a novel theoretical analysis proving that distributed
learning over unreliable network can achieve comparable convergence rate to centralized
or distributed learning over reliable networks. Further, we prove that the influence
of the packet drop rate diminishes with the growth of the number of parameter
servers. We map this theoretical result onto a real-world scenario, training deep
neural networks over an unreliable network layer, and conduct network simulation
to validate the system improvement by allowing the networks to be unreliable.'
article_processing_charge: No
author:
- first_name: Chen
full_name: Yu, Chen
last_name: Yu
- first_name: Hanlin
full_name: Tang, Hanlin
last_name: Tang
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
- first_name: Simon
full_name: Kassing, Simon
last_name: Kassing
- first_name: Ankit
full_name: Singla, Ankit
last_name: Singla
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
- first_name: Ji
full_name: Liu, Ji
last_name: Liu
citation:
ama: 'Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks.
In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June.
IMLS; 2019:12481-12512.'
apa: 'Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., …
Liu, J. (2019). Distributed learning over unreliable networks. In 36th International
Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512).
Long Beach, CA, United States: IMLS.'
chicago: Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian
Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.”
In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512.
IMLS, 2019.
ieee: C. Yu et al., “Distributed learning over unreliable networks,” in 36th
International Conference on Machine Learning, ICML 2019, Long Beach, CA, United
States, 2019, vol. 2019–June, pp. 12481–12512.
ista: 'Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu
J. 2019. Distributed learning over unreliable networks. 36th International Conference
on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning
vol. 2019–June, 12481–12512.'
mla: Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International
Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp.
12481–512.
short: C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang,
J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS,
2019, pp. 12481–12512.
conference:
end_date: 2019-06-15
location: Long Beach, CA, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2019-06-10
date_created: 2020-02-02T23:01:06Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-06T15:21:48Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1810.07766'
isi:
- '000684034307036'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.07766
month: '06'
oa: 1
oa_version: Preprint
page: 12481-12512
publication: 36th International Conference on Machine Learning, ICML 2019
publication_identifier:
isbn:
- '9781510886988'
publication_status: published
publisher: IMLS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed learning over unreliable networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-June
year: '2019'
...
---
_id: '7412'
abstract:
- lang: eng
text: We develop a framework for the rigorous analysis of focused stochastic local
search algorithms. These algorithms search a state space by repeatedly selecting
some constraint that is violated in the current state and moving to a random nearby
state that addresses the violation, while (we hope) not introducing many new violations.
An important class of focused local search algorithms with provable performance
guarantees has recently arisen from algorithmizations of the Lovász local lemma
(LLL), a nonconstructive tool for proving the existence of satisfying states by
introducing a background measure on the state space. While powerful, the state
transitions of algorithms in this class must be, in a precise sense, perfectly
compatible with the background measure. In many applications this is a very restrictive
requirement, and one needs to step outside the class. Here we introduce the notion
of measure distortion and develop a framework for analyzing arbitrary focused
stochastic local search algorithms, recovering LLL algorithmizations as the special
case of no distortion. Our framework takes as input an arbitrary algorithm of
such type and an arbitrary probability measure and shows how to use the measure
as a yardstick of algorithmic progress, even for algorithms designed independently
of the measure.
article_processing_charge: No
article_type: original
author:
- first_name: Dimitris
full_name: Achlioptas, Dimitris
last_name: Achlioptas
- first_name: Fotis
full_name: Iliopoulos, Fotis
last_name: Iliopoulos
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical
algorithms. SIAM Journal on Computing. 2019;48(5):1583-1602. doi:10.1137/16m109332x
apa: Achlioptas, D., Iliopoulos, F., & Kolmogorov, V. (2019). A local lemma
for focused stochastical algorithms. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16m109332x
chicago: Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local
Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing.
SIAM, 2019. https://doi.org/10.1137/16m109332x.
ieee: D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused
stochastical algorithms,” SIAM Journal on Computing, vol. 48, no. 5. SIAM,
pp. 1583–1602, 2019.
ista: Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused
stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.
mla: Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.”
SIAM Journal on Computing, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:10.1137/16m109332x.
short: D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48
(2019) 1583–1602.
date_created: 2020-01-30T09:27:32Z
date_published: 2019-10-31T00:00:00Z
date_updated: 2023-09-06T15:25:29Z
day: '31'
department:
- _id: VlKo
doi: 10.1137/16m109332x
ec_funded: 1
external_id:
arxiv:
- '1809.01537'
isi:
- '000493900200005'
intvolume: ' 48'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.01537
month: '10'
oa: 1
oa_version: Preprint
page: 1583-1602
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: A local lemma for focused stochastical algorithms
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2019'
...
---
_id: '7418'
abstract:
- lang: eng
text: Multiple importance sampling (MIS) has become an indispensable tool in Monte
Carlo rendering, widely accepted as a near-optimal solution for combining different
sampling techniques. But an MIS combination, using the common balance or power
heuristics, often results in an overly defensive estimator, leading to high variance.
We show that by generalizing the MIS framework, variance can be substantially
reduced. Specifically, we optimize one of the combined sampling techniques so
as to decrease the overall variance of the resulting MIS estimator. We apply the
approach to the computation of direct illumination due to an HDR environment map
and to the computation of global illumination using a path guiding algorithm.
The implementation can be as simple as subtracting a constant value from the tabulated
sampling density done entirely in a preprocessing step. This produces a consistent
noise reduction in all our tests with no negative influence on run time, no artifacts
or bias, and no failure cases.
article_number: '151'
article_processing_charge: No
article_type: original
author:
- first_name: Ondřej
full_name: Karlík, Ondřej
last_name: Karlík
- first_name: Martin
full_name: Šik, Martin
last_name: Šik
- first_name: Petr
full_name: Vévoda, Petr
last_name: Vévoda
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
citation:
ama: 'Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing
sampling techniques in multiple importance sampling. ACM Transactions on Graphics.
2019;38(6). doi:10.1145/3355089.3356565'
apa: 'Karlík, O., Šik, M., Vévoda, P., Skrivan, T., & Křivánek, J. (2019). MIS
compensation: Optimizing sampling techniques in multiple importance sampling.
ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356565'
chicago: 'Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek.
“MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.”
ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356565.'
ieee: 'O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation:
Optimizing sampling techniques in multiple importance sampling,” ACM Transactions
on Graphics, vol. 38, no. 6. ACM, 2019.'
ista: 'Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation:
Optimizing sampling techniques in multiple importance sampling. ACM Transactions
on Graphics. 38(6), 151.'
mla: 'Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in
Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no.
6, 151, ACM, 2019, doi:10.1145/3355089.3356565.'
short: O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on
Graphics 38 (2019).
date_created: 2020-01-30T10:19:43Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T15:22:23Z
day: '01'
department:
- _id: ChWo
doi: 10.1145/3355089.3356565
external_id:
isi:
- '000498397300001'
intvolume: ' 38'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MIS compensation: Optimizing sampling techniques in multiple importance sampling'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2019'
...
---
_id: '7413'
abstract:
- lang: eng
text: We consider Bose gases consisting of N particles trapped in a box with volume
one and interacting through a repulsive potential with scattering length of order
N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy
excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s
predictions.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Christian
full_name: Brennecke, Christian
last_name: Brennecke
- first_name: Serena
full_name: Cenatiempo, Serena
last_name: Cenatiempo
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii
limit. Acta Mathematica. 2019;222(2):219-335. doi:10.4310/acta.2019.v222.n2.a1
apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2019). Bogoliubov
theory in the Gross–Pitaevskii limit. Acta Mathematica. International Press
of Boston. https://doi.org/10.4310/acta.2019.v222.n2.a1
chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein.
“Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica. International
Press of Boston, 2019. https://doi.org/10.4310/acta.2019.v222.n2.a1.
ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory
in the Gross–Pitaevskii limit,” Acta Mathematica, vol. 222, no. 2. International
Press of Boston, pp. 219–335, 2019.
ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in
the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.
mla: Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.”
Acta Mathematica, vol. 222, no. 2, International Press of Boston, 2019,
pp. 219–335, doi:10.4310/acta.2019.v222.n2.a1.
short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222
(2019) 219–335.
date_created: 2020-01-30T09:30:41Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-06T15:24:31Z
day: '07'
department:
- _id: RoSe
doi: 10.4310/acta.2019.v222.n2.a1
external_id:
arxiv:
- '1801.01389'
isi:
- '000495865300001'
intvolume: ' 222'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.01389
month: '06'
oa: 1
oa_version: Preprint
page: 219-335
publication: Acta Mathematica
publication_identifier:
eissn:
- 1871-2509
issn:
- 0001-5962
publication_status: published
publisher: International Press of Boston
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bogoliubov theory in the Gross–Pitaevskii limit
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 222
year: '2019'
...
---
_id: '7393'
abstract:
- lang: eng
text: The study of parallel ecological divergence provides important clues to the
operation of natural selection. Parallel divergence often occurs in heterogeneous
environments with different kinds of environmental gradients in different locations,
but the genomic basis underlying this process is unknown. We investigated the
genomics of rapid parallel adaptation in the marine snail Littorina saxatilis
in response to two independent environmental axes (crab-predation versus wave-action
and low-shore versus high-shore). Using pooled whole-genome resequencing, we show
that sharing of genomic regions of high differentiation between environments is
generally low but increases at smaller spatial scales. We identify different shared
genomic regions of divergence for each environmental axis and show that most of
these regions overlap with candidate chromosomal inversions. Several inversion
regions are divergent and polymorphic across many localities. We argue that chromosomal
inversions could store shared variation that fuels rapid parallel adaptation to
heterogeneous environments, possibly as balanced polymorphism shared by adaptive
gene flow.
article_number: eaav9963
article_processing_charge: No
article_type: original
author:
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel
ecological divergence: Beyond a single environmental contrast. Science Advances.
2019;5(12). doi:10.1126/sciadv.aav9963'
apa: 'Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram,
A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.aav9963'
chicago: 'Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina
Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel
Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances.
AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.'
ieee: 'H. E. Morales et al., “Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast,” Science Advances,
vol. 5, no. 12. AAAS, 2019.'
ista: 'Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin
RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single
environmental contrast. Science Advances. 5(12), eaav9963.'
mla: 'Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence:
Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no.
12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.'
short: H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram,
R.K. Butlin, Science Advances 5 (2019).
date_created: 2020-01-29T15:58:27Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T15:35:56Z
day: '04'
ddc:
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department:
- _id: NiBa
doi: 10.1126/sciadv.aav9963
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creator: dernst
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intvolume: ' 5'
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month: '12'
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oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomic architecture of parallel ecological divergence: Beyond a single environmental
contrast'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '7397'
abstract:
- lang: eng
text: Polymer additives can substantially reduce the drag of turbulent flows and
the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal,
i.e. inde-pendent of the type of polymer and solvent used. Until recently, the
consensus was that,in this limit, flows are in a marginal state where only a minimal
level of turbulence activ-ity persists. Observations in direct numerical simulations
using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence
is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg
number (Wi), turbulence expresses long periods of hibernation if the domainsize
is small. However, with increasing pipe length, the temporal hibernation continuouslyalters
to spatio-temporal intermittency and here the flow consists of turbulent puffs
sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully
relaminarises,in agreement with recent experiments. At even larger Wi, a different
instability is en-countered causing a drag increase towards MDR. Our findings
hence link earlier minimalflow unit simulations with recent experiments and confirm
that the addition of polymersinitially suppresses Newtonian turbulence and leads
to a reverse transition. The MDRstate on the other hand results from a separate
instability and the underlying dynamicscorresponds to the recently proposed state
of elasto-inertial-turbulence (EIT).
article_processing_charge: No
article_type: original
author:
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at
low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid
Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486
apa: Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic
pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal
of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486
chicago: Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic
Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal
of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.
ieee: J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic
pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal
of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.
ista: Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow
at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid
Mechanics. 874, 699–719.
mla: Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds
Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics,
vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.
short: J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874
(2019) 699–719.
date_created: 2020-01-29T16:05:19Z
date_published: 2019-09-10T00:00:00Z
date_updated: 2023-09-06T15:36:36Z
day: '10'
department:
- _id: BjHo
doi: 10.1017/jfm.2019.486
external_id:
arxiv:
- '1808.04080'
isi:
- '000475349900001'
intvolume: ' 874'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04080
month: '09'
oa: 1
oa_version: Preprint
page: 699-719
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: CUP
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag
reduction limit
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 874
year: '2019'
...