---
_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
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
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:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.aav9963
ec_funded: 1
external_id:
isi:
- '000505069600008'
pmid:
- '31840052'
file:
- access_level: open_access
checksum: af99a5dcdc66c6d6102051faf3be48d8
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T13:33:25Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7442'
file_name: 2019_ScienceAdvances_Morales.pdf
file_size: 1869449
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
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intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
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'
...
---
_id: '5678'
abstract:
- lang: eng
text: "The order-k Voronoi tessellation of a locally finite set \U0001D44B⊆ℝ\U0001D45B
decomposes ℝ\U0001D45B into convex domains whose points have the same k nearest
neighbors in X. Assuming X is a stationary Poisson point process, we give explicit
formulas for the expected number and total area of faces of a given dimension
per unit volume of space. We also develop a relaxed version of discrete Morse
theory and generalize by counting only faces, for which the k nearest points in
X are within a given distance threshold."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. Discrete
and Computational Geometry. 2019;62(4):865–878. doi:10.1007/s00454-018-0049-2
apa: Edelsbrunner, H., & Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order
k. Discrete and Computational Geometry. Springer. https://doi.org/10.1007/s00454-018-0049-2
chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of
Order K.” Discrete and Computational Geometry. Springer, 2019. https://doi.org/10.1007/s00454-018-0049-2.
ieee: H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” Discrete
and Computational Geometry, vol. 62, no. 4. Springer, pp. 865–878, 2019.
ista: Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete
and Computational Geometry. 62(4), 865–878.
mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order
K.” Discrete and Computational Geometry, vol. 62, no. 4, Springer, 2019,
pp. 865–878, doi:10.1007/s00454-018-0049-2.
short: H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019)
865–878.
date_created: 2018-12-16T22:59:20Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-07T12:07:12Z
day: '01'
ddc:
- '516'
department:
- _id: HeEd
doi: 10.1007/s00454-018-0049-2
ec_funded: 1
external_id:
arxiv:
- '1709.09380'
isi:
- '000494042900008'
file:
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checksum: f9d00e166efaccb5a76bbcbb4dcea3b4
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date_created: 2019-02-06T10:10:46Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5932'
file_name: 2018_DiscreteCompGeometry_Edelsbrunner.pdf
file_size: 599339
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intvolume: ' 62'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 865–878
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Poisson–Delaunay Mosaics of Order k
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: 62
year: '2019'
...
---
_id: '5828'
abstract:
- lang: eng
text: Hippocampus is needed for both spatial working and reference memories. Here,
using a radial eight-arm maze, we examined how the combined demand on these memories
influenced CA1 place cell assemblies while reference memories were partially updated.
This was contrasted with control tasks requiring only working memory or the update
of reference memory. Reference memory update led to the reward-directed place
field shifts at newly rewarded arms and to the gradual strengthening of firing
in passes between newly rewarded arms but not between those passes that included
a familiar-rewarded arm. At the maze center, transient network synchronization
periods preferentially replayed trajectories of the next chosen arm in reference
memory tasks but the previously visited arm in the working memory task. Hence,
reference memory demand was uniquely associated with a gradual, goal novelty-related
reorganization of place cell assemblies and with trajectory replay that reflected
the animal's decision of which arm to visit next.
article_processing_charge: No
article_type: original
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal
CA1 place cells predict learned behavior in goal-directed spatial tasks on the
radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015
apa: Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly
responses of hippocampal CA1 place cells predict learned behavior in goal-directed
spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015
chicago: Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly
Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed
Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015.
ieee: H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses
of hippocampal CA1 place cells predict learned behavior in goal-directed spatial
tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier,
p. 119–132.e4, 2019.
ista: Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal
CA1 place cells predict learned behavior in goal-directed spatial tasks on the
radial eight-arm maze. Neuron. 101(1), 119–132.e4.
mla: Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict
Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.”
Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015.
short: H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4.
date_created: 2019-01-13T22:59:10Z
date_published: 2019-01-02T00:00:00Z
date_updated: 2023-09-07T12:06:37Z
day: '02'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2018.11.015
ec_funded: 1
external_id:
isi:
- '000454791500014'
intvolume: ' 101'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1016/j.neuron.2018.11.015
month: '01'
oa: 1
oa_version: Published Version
page: 119-132.e4
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: Neuron
publication_identifier:
issn:
- '10974199'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/reading-rats-minds/
record:
- id: '837'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Assembly responses of hippocampal CA1 place cells predict learned behavior
in goal-directed spatial tasks on the radial eight-arm maze
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 101
year: '2019'
...
---
_id: '5856'
abstract:
- lang: eng
text: We give a bound on the ground-state energy of a system of N non-interacting
fermions in a three-dimensional cubic box interacting with an impurity particle
via point interactions. We show that the change in energy compared to the system
in the absence of the impurity is bounded in terms of the gas density and the
scattering length of the interaction, independently of N. Our bound holds as long
as the ratio of the mass of the impurity to the one of the gas particles is larger
than a critical value m∗ ∗≈ 0.36 , which is the same regime for which we recently
showed stability of the system.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Energy contribution of a point-interacting impurity in
a Fermi gas. Annales Henri Poincare. 2019;20(4):1325–1365. doi:10.1007/s00023-018-00757-0
apa: Moser, T., & Seiringer, R. (2019). Energy contribution of a point-interacting
impurity in a Fermi gas. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-00757-0
chicago: Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting
Impurity in a Fermi Gas.” Annales Henri Poincare. Springer, 2019. https://doi.org/10.1007/s00023-018-00757-0.
ieee: T. Moser and R. Seiringer, “Energy contribution of a point-interacting impurity
in a Fermi gas,” Annales Henri Poincare, vol. 20, no. 4. Springer, pp.
1325–1365, 2019.
ista: Moser T, Seiringer R. 2019. Energy contribution of a point-interacting impurity
in a Fermi gas. Annales Henri Poincare. 20(4), 1325–1365.
mla: Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting
Impurity in a Fermi Gas.” Annales Henri Poincare, vol. 20, no. 4, Springer,
2019, pp. 1325–1365, doi:10.1007/s00023-018-00757-0.
short: T. Moser, R. Seiringer, Annales Henri Poincare 20 (2019) 1325–1365.
date_created: 2019-01-20T22:59:17Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-09-07T12:37:42Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s00023-018-00757-0
ec_funded: 1
external_id:
arxiv:
- '1807.00739'
isi:
- '000462444300008'
file:
- access_level: open_access
checksum: 255e42f957a8e2b10aad2499c750a8d6
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:27:17Z
date_updated: 2020-07-14T12:47:12Z
file_id: '5894'
file_name: 2019_Annales_Moser.pdf
file_size: 859846
relation: main_file
file_date_updated: 2020-07-14T12:47:12Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1325–1365
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_identifier:
issn:
- '14240637'
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Energy contribution of a point-interacting impurity in a Fermi gas
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: '6957'
abstract:
- lang: eng
text: "In many shear flows like pipe flow, plane Couette flow, plane Poiseuille
flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough
perturbations, the flow becomes turbulent in spite of the laminar base flow being
linearly stable. The nature of this instability has puzzled the scientific community
for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally
intermittent. In pipe flow the localized turbulent structures are referred to
as puffs and in planar flows like plane Couette and channel flow, patches arise
in the form of localized oblique bands. In this thesis, we study the onset of
turbulence in channel flow in direct numerical simulations from a dynamical system
theory perspective, as well as by performing experiments in a large aspect ratio
channel.\r\n\r\nThe aim of the experimental work is to determine the critical
Reynolds number where turbulence first becomes sustained. Recently, the onset
of turbulence has been described in analogy to absorbing state phase transition
(i.e. directed percolation). In particular, it has been shown that the critical
point can be estimated from the competition between spreading and decay processes.
Here, by performing experiments, we identify the mechanisms underlying turbulence
proliferation in channel flow and find the critical Reynolds number, above which
turbulence becomes sustained. Above the critical point, the continuous growth
at the tip of the stripes outweighs the stochastic shedding of turbulent patches
at the tail and the stripes expand. For growing stripes, the probability to decay
decreases while the probability of stripe splitting increases. Consequently, and
unlike for the puffs in pipe flow, neither of these two processes is time-independent
i.e. memoryless. Coupling between stripe expansion and creation of new stripes
via splitting leads to a significantly lower critical point ($Re_c=670+/-10$)
than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light
on how turbulence first becomes sustained, it provides no insight into the origin
of the stripes themselves. In the numerical part of the thesis we investigate
how turbulent stripes form from invariant solutions of the Navier-Stokes equations.
The origin of these turbulent stripes can be identified by applying concepts from
the dynamical system theory. In doing so, we identify the exact coherent structures
underlying stripes and their bifurcations and how they give rise to the turbulent
attractor in phase space. We first report a family of localized nonlinear traveling
wave solutions of the Navier-Stokes equations in channel flow. These solutions
show structural similarities with turbulent stripes in experiments like obliqueness,
quasi-streamwise streaks and vortices, etc. A parametric study of these traveling
wave solution is performed, with parameters like Reynolds number, stripe tilt
angle and domain size, including the stability of the solutions. These solutions
emerge through saddle-node bifurcations and form a phase space skeleton for the
turbulent stripes observed in the experiments. The lower branches of these TW
solutions at different tilt angles undergo Hopf bifurcation and new solutions
branches of relative periodic orbits emerge. These RPO solutions do not belong
to the same family and therefore the routes to chaos for different angles are
different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature.
\ Consequently,turbulence can not be tracked to lower Reynolds numbers, where
the dynamics may simplify. Before this happens, turbulence becomes short-lived
and laminarizes. In the last part of the thesis, we show that using numerical
simulations we can continue turbulent stripes in channel flow past the 'relaminarization
barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies
and the fluctuations are no longer stochastic and the stripe settles down to a
relative periodic orbit. This relative periodic orbit originates from the aforementioned
traveling wave solutions. Starting from the relative periodic orbit, a small increase
in speed i.e. Reynolds number gives rise to chaos and the attractor dimension
sharply increases in contrast to the classical transition scenario where the instabilities
affect the flow globally and give rise to much more gradual route to turbulence."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
citation:
ama: Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957
apa: Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957
chicago: Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957.
ieee: C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute
of Science and Technology Austria, 2019.
ista: Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute
of Science and Technology Austria.
mla: Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.
short: C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of
Science and Technology Austria, 2019.
date_created: 2019-10-22T12:08:43Z
date_published: 2019-10-24T00:00:00Z
date_updated: 2023-09-07T12:53:25Z
day: '24'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: BjHo
doi: 10.15479/AT:ISTA:6957
file:
- access_level: closed
checksum: 7ba298ba0ce7e1d11691af6b8eaf0a0a
content_type: application/zip
creator: cparanjape
date_created: 2019-10-23T09:54:43Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6962'
file_name: Chaitanya_Paranjape_source_files_tex_figures.zip
file_size: 45828099
relation: source_file
- access_level: open_access
checksum: 642697618314e31ac31392da7909c2d9
content_type: application/pdf
creator: cparanjape
date_created: 2019-10-23T10:37:09Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6963'
file_name: Chaitanya_Paranjape_Thesis.pdf
file_size: 19504197
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
keyword:
- Instabilities
- Turbulence
- Nonlinear dynamics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Onset of turbulence in plane Poiseuille flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6182'
abstract:
- lang: eng
text: "We consider large random matrices with a general slowly decaying correlation
among its entries. We prove universality of the local eigenvalue statistics and
optimal local laws for the resolvent away from the spectral edges, generalizing
the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and
random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019),
293–373] to allow slow correlation decay and arbitrary expectation. The main novel
tool is\r\na systematic diagrammatic control of a multivariate cumulant expansion."
article_number: e8
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Krüger TH, Schröder DJ. Random matrices with slow correlation decay.
Forum of Mathematics, Sigma. 2019;7. doi:10.1017/fms.2019.2
apa: Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Random matrices with
slow correlation decay. Forum of Mathematics, Sigma. Cambridge University
Press. https://doi.org/10.1017/fms.2019.2
chicago: Erdös, László, Torben H Krüger, and Dominik J Schröder. “Random Matrices
with Slow Correlation Decay.” Forum of Mathematics, Sigma. Cambridge University
Press, 2019. https://doi.org/10.1017/fms.2019.2.
ieee: L. Erdös, T. H. Krüger, and D. J. Schröder, “Random matrices with slow correlation
decay,” Forum of Mathematics, Sigma, vol. 7. Cambridge University Press,
2019.
ista: Erdös L, Krüger TH, Schröder DJ. 2019. Random matrices with slow correlation
decay. Forum of Mathematics, Sigma. 7, e8.
mla: Erdös, László, et al. “Random Matrices with Slow Correlation Decay.” Forum
of Mathematics, Sigma, vol. 7, e8, Cambridge University Press, 2019, doi:10.1017/fms.2019.2.
short: L. Erdös, T.H. Krüger, D.J. Schröder, Forum of Mathematics, Sigma 7 (2019).
date_created: 2019-03-28T09:05:23Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2023-09-07T12:54:12Z
day: '26'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2019.2
ec_funded: 1
external_id:
arxiv:
- '1705.10661'
isi:
- '000488847100001'
file:
- access_level: open_access
checksum: 933a472568221c73b2c3ce8c87bf6d15
content_type: application/pdf
creator: dernst
date_created: 2019-09-17T14:24:13Z
date_updated: 2020-07-14T12:47:22Z
file_id: '6883'
file_name: 2019_Forum_Erdoes.pdf
file_size: 1520344
relation: main_file
file_date_updated: 2020-07-14T12:47:22Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- '20505094'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Random matrices with slow correlation decay
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: 7
year: '2019'
...
---
_id: '6186'
abstract:
- lang: eng
text: "We prove that the local eigenvalue statistics of real symmetric Wigner-type\r\nmatrices
near the cusp points of the eigenvalue density are universal. Together\r\nwith
the companion paper [arXiv:1809.03971], which proves the same result for\r\nthe
complex Hermitian symmetry class, this completes the last remaining case of\r\nthe
Wigner-Dyson-Mehta universality conjecture after bulk and edge\r\nuniversalities
have been established in the last years. We extend the recent\r\nDyson Brownian
motion analysis at the edge [arXiv:1712.03881] to the cusp\r\nregime using the
optimal local law from [arXiv:1809.03971] and the accurate\r\nlocal shape analysis
of the density from [arXiv:1506.05095, arXiv:1804.07752].\r\nWe also present a
PDE-based method to improve the estimate on eigenvalue\r\nrigidity via the maximum
principle of the heat flow related to the Dyson\r\nBrownian motion."
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Cipolloni G, Erdös L, Krüger TH, Schröder DJ. Cusp universality for random
matrices, II: The real symmetric case. Pure and Applied Analysis . 2019;1(4):615–707.
doi:10.2140/paa.2019.1.615'
apa: 'Cipolloni, G., Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Cusp
universality for random matrices, II: The real symmetric case. Pure and Applied
Analysis . MSP. https://doi.org/10.2140/paa.2019.1.615'
chicago: 'Cipolloni, Giorgio, László Erdös, Torben H Krüger, and Dominik J Schröder.
“Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure
and Applied Analysis . MSP, 2019. https://doi.org/10.2140/paa.2019.1.615.'
ieee: 'G. Cipolloni, L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality
for random matrices, II: The real symmetric case,” Pure and Applied Analysis
, vol. 1, no. 4. MSP, pp. 615–707, 2019.'
ista: 'Cipolloni G, Erdös L, Krüger TH, Schröder DJ. 2019. Cusp universality for
random matrices, II: The real symmetric case. Pure and Applied Analysis . 1(4),
615–707.'
mla: 'Cipolloni, Giorgio, et al. “Cusp Universality for Random Matrices, II: The
Real Symmetric Case.” Pure and Applied Analysis , vol. 1, no. 4, MSP, 2019,
pp. 615–707, doi:10.2140/paa.2019.1.615.'
short: G. Cipolloni, L. Erdös, T.H. Krüger, D.J. Schröder, Pure and Applied Analysis 1
(2019) 615–707.
date_created: 2019-03-28T10:21:17Z
date_published: 2019-10-12T00:00:00Z
date_updated: 2023-09-07T12:54:12Z
day: '12'
department:
- _id: LaEr
doi: 10.2140/paa.2019.1.615
ec_funded: 1
external_id:
arxiv:
- '1811.04055'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.04055
month: '10'
oa: 1
oa_version: Preprint
page: 615–707
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 'Pure and Applied Analysis '
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: MSP
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
status: public
title: 'Cusp universality for random matrices, II: The real symmetric case'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2019'
...
---
_id: '6900'
abstract:
- lang: eng
text: Across diverse biological systems—ranging from neural networks to intracellular
signaling and genetic regulatory networks—the information about changes in the
environment is frequently encoded in the full temporal dynamics of the network
nodes. A pressing data-analysis challenge has thus been to efficiently estimate
the amount of information that these dynamics convey from experimental data. Here
we develop and evaluate decoding-based estimation methods to lower bound the mutual
information about a finite set of inputs, encoded in single-cell high-dimensional
time series data. For biological reaction networks governed by the chemical Master
equation, we derive model-based information approximations and analytical upper
bounds, against which we benchmark our proposed model-free decoding estimators.
In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based
estimators robustly extract a large fraction of the available information from
high-dimensional trajectories with a realistic number of data samples. We apply
these estimators to previously published data on Erk and Ca2+ signaling in mammalian
cells and to yeast stress-response, and find that substantial amount of information
about environmental state can be encoded by non-trivial response statistics even
in stationary signals. We argue that these single-cell, decoding-based information
estimates, rather than the commonly-used tests for significant differences between
selected population response statistics, provide a proper and unbiased measure
for the performance of biological signaling networks.
article_processing_charge: No
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Jakob
full_name: Ruess, Jakob
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying
signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290
apa: Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information
in time-varying signals. PLoS Computational Biology. Public Library of
Science. https://doi.org/10.1371/journal.pcbi.1007290
chicago: Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information
in Time-Varying Signals.” PLoS Computational Biology. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290.
ieee: S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in
time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public
Library of Science, p. e1007290, 2019.
ista: Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying
signals. PLoS computational biology. 15(9), e1007290.
mla: Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.”
PLoS Computational Biology, vol. 15, no. 9, Public Library of Science,
2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
short: S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019)
e1007290.
date_created: 2019-09-22T22:00:37Z
date_published: 2019-09-03T00:00:00Z
date_updated: 2023-09-07T12:55:21Z
day: '03'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007290
external_id:
isi:
- '000489741800021'
pmid:
- '31479447'
file:
- access_level: open_access
checksum: 81bdce1361c9aa8395d6fa635fb6ab47
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T10:53:45Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6925'
file_name: 2019_PLoS_Cepeda-Humerez.pdf
file_size: 3081855
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: e1007290
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLoS computational biology
publication_identifier:
eissn:
- '15537358'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Estimating information in time-varying signals
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: 15
year: '2019'
...
---
_id: '6377'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular
process in eukaryotic cells, but its dynamic and vital nature makes it challenging
to study using classical genetics tools. In contrast, although small molecules
can acutely and reversibly perturb CME, the few chemical CME inhibitors that have
been applied to plants are either ineffective or show undesirable side effects.
Here, we identify the previously described endosidin9 (ES9) as an inhibitor of
clathrin heavy chain (CHC) function in both Arabidopsis and human cells through
affinity-based target isolation, in vitro binding studies and X-ray crystallography.
Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the
undesirable side effects of ES9 while retaining the ability to target CHC. ES9
and ES9-17 have expanded the chemical toolbox used to probe CHC function, and
present chemical scaffolds for further design of more specific and potent CHC
inhibitors across different systems.
article_processing_charge: No
article_type: original
author:
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Isha
full_name: Sharma, Isha
last_name: Sharma
- first_name: Bram
full_name: Denoo, Bram
last_name: Denoo
- first_name: Steven
full_name: De Munck, Steven
last_name: De Munck
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Haydar
full_name: Bulut, Haydar
last_name: Bulut
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: Daniel V.
full_name: Savatin, Daniel V.
last_name: Savatin
- first_name: Wim
full_name: Nerinckx, Wim
last_name: Nerinckx
- first_name: An
full_name: Staes, An
last_name: Staes
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Dominique
full_name: Audenaert, Dominique
last_name: Audenaert
- first_name: Klaas
full_name: Yperman, Klaas
last_name: Yperman
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Volker
full_name: Haucke, Volker
last_name: Haucke
- first_name: Savvas N.
full_name: Savvides, Savvas N.
last_name: Savvides
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical
inhibition of clathrin heavy chain function. Nature Chemical Biology. 2019;15(6):641–649.
doi:10.1038/s41589-019-0262-1
apa: Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova,
E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy
chain function. Nature Chemical Biology. Springer Nature. https://doi.org/10.1038/s41589-019-0262-1
chicago: Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril
Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition
of Clathrin Heavy Chain Function.” Nature Chemical Biology. Springer Nature,
2019. https://doi.org/10.1038/s41589-019-0262-1.
ieee: W. Dejonghe et al., “Disruption of endocytosis through chemical inhibition
of clathrin heavy chain function,” Nature Chemical Biology, vol. 15, no.
6. Springer Nature, pp. 641–649, 2019.
ista: Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle
E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert
D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN,
Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition
of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649.
mla: Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition
of Clathrin Heavy Chain Function.” Nature Chemical Biology, vol. 15, no.
6, Springer Nature, 2019, pp. 641–649, doi:10.1038/s41589-019-0262-1.
short: W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut,
E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A.
Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert,
V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019)
641–649.
date_created: 2019-05-05T21:59:11Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T12:54:35Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41589-019-0262-1
external_id:
isi:
- '000468195600018'
intvolume: ' 15'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 641–649
publication: Nature Chemical Biology
publication_identifier:
eissn:
- '15524469'
issn:
- '15524450'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '7172'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Disruption of endocytosis through chemical inhibition of clathrin heavy chain
function
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '7186'
abstract:
- lang: eng
text: "Tissue morphogenesis in developmental or physiological processes is regulated
by molecular\r\nand mechanical signals. While the molecular signaling cascades
are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape
changes have only recently been\r\nstudied in greater detail. To gain more insight
into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process
(epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation
and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial
cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe
cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the
end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing
within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction
motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely
transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature
and formation of the junctional structure\r\nmediating this process has not been
well described so far. Therefore, our main aim was to\r\ndetermine the nature,
dynamics and potential function of the EVL-YSL junction during this\r\nepithelial
tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive
structure, predominantly made of tight junction (TJ) proteins. The process\r\nof
TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula
Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly,
we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface
of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely
renders the protein\r\nresponsive to flows. These flows are directed towards the
junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching
the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated
through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or
ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive
responses resulting in slower tissue spreading. We could further\r\ndemonstrate
that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring
formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish
epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility
and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale
polarization process mediated through the flow of phase-separated protein\r\nclusters
might have implications for other processes such as immunological synapse\r\nformation,
C. elegans zygote polarization and wound healing."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: EM-Fac
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
citation:
ama: Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation
and flow. 2019. doi:10.15479/AT:ISTA:7186
apa: Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1
phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186
chicago: Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1
Phase Separation and Flow.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7186.
ieee: C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation
and flow,” Institute of Science and Technology Austria, 2019.
ista: Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase
separation and flow. Institute of Science and Technology Austria.
mla: Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1
Phase Separation and Flow. Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7186.
short: C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation
and Flow, Institute of Science and Technology Austria, 2019.
date_created: 2019-12-16T14:26:14Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2023-09-07T12:56:42Z
day: '16'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:7186
file:
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date_updated: 2020-07-14T12:47:52Z
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page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: dissertation_contains
status: public
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relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6681'
abstract:
- lang: eng
text: "The first part of the thesis considers the computational aspects of the homotopy
groups πd(X) of a topological space X. It is well known that there is no algorithm
to decide whether the fundamental group π1(X) of a given finite simplicial complex
X is trivial. On the other hand, there are several algorithms that, given a finite
simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute
the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms
come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract
finitely generated abelian group given by generators and relations, but they work
with very implicit representations of the elements of πd(X). We present an algorithm
that, given a simply connected space X, computes πd(X) and represents its elements
as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed
d, the algorithm runs in time exponential in size(X), the number of simplices
of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct
a family of simply connected spaces X such that for any simplicial map representing
a generator of πd(X), the size of the triangulation of S d on which the map is
defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove
that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋,
k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable
range: Given a finite simplicial complex K of dimension k, decide whether there
exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of
K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephan Y
full_name: Zhechev, Stephan Y
id: 3AA52972-F248-11E8-B48F-1D18A9856A87
last_name: Zhechev
citation:
ama: Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019.
doi:10.15479/AT:ISTA:6681
apa: Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681
chicago: Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.
ieee: S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,”
Institute of Science and Technology Austria, 2019.
ista: Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability.
Institute of Science and Technology Austria.
mla: Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.
short: S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute
of Science and Technology Austria, 2019.
date_created: 2019-07-26T11:14:34Z
date_published: 2019-08-08T00:00:00Z
date_updated: 2023-09-07T13:10:36Z
day: '08'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: UlWa
doi: 10.15479/AT:ISTA:6681
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date_updated: 2020-07-14T12:47:37Z
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file_name: Stephan_Zhechev_thesis.tex
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date_created: 2019-08-07T13:03:34Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6773'
file_name: supplementary_material.zip
file_size: 1087004
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has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '104'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6774'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Algorithmic aspects of homotopy theory and embeddability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '8182'
abstract:
- lang: eng
text: "Suppose that $n\\neq p^k$ and $n\\neq 2p^k$ for all $k$ and all primes $p$.
We prove that for any Hausdorff compactum $X$ with a free action of the symmetric
group $\\mathfrak S_n$ there exists an $\\mathfrak S_n$-equivariant map $X \\to\r\n{\\mathbb
R}^n$ whose image avoids the diagonal $\\{(x,x\\dots,x)\\in {\\mathbb R}^n|x\\in
{\\mathbb R}\\}$.\r\n Previously, the special cases of this statement for certain
$X$ were usually proved using the equivartiant obstruction theory. Such calculations
are difficult and may become infeasible past the first (primary) obstruction.
We\r\ntake a different approach which allows us to prove the vanishing of all
obstructions simultaneously. The essential step in the proof is classifying the
possible degrees of $\\mathfrak S_n$-equivariant maps from the boundary\r\n$\\partial\\Delta^{n-1}$
of $(n-1)$-simplex to itself. Existence of equivariant maps between spaces is
important for many questions arising from discrete mathematics and geometry, such
as Kneser's conjecture, the Square Peg conjecture, the Splitting Necklace problem,
and the Topological Tverberg conjecture, etc. We demonstrate the utility of our
result applying it to one such question, a specific instance of envy-free division
problem."
article_number: '1910.12628'
article_processing_charge: No
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Sergey
full_name: Kudrya, Sergey
id: ecf01965-d252-11ea-95a5-8ada5f6c6a67
last_name: Kudrya
citation:
ama: Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping
degree. arXiv.
apa: Avvakumov, S., & Kudrya, S. (n.d.). Vanishing of all equivariant obstructions
and the mapping degree. arXiv. arXiv.
chicago: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions
and the Mapping Degree.” ArXiv. arXiv, n.d.
ieee: S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and
the mapping degree,” arXiv. arXiv.
ista: Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping
degree. arXiv, 1910.12628.
mla: Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions
and the Mapping Degree.” ArXiv, 1910.12628, arXiv.
short: S. Avvakumov, S. Kudrya, ArXiv (n.d.).
date_created: 2020-07-30T10:45:08Z
date_published: 2019-10-28T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '28'
department:
- _id: UlWa
external_id:
arxiv:
- '1910.12628'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.12628
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: arXiv
publication_status: submitted
publisher: arXiv
related_material:
record:
- id: '11446'
relation: later_version
status: public
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Vanishing of all equivariant obstructions and the mapping degree
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '8185'
abstract:
- lang: eng
text: "In this paper we study envy-free division problems. The classical approach
to some of such problems, used by David Gale, reduces to considering continuous
maps of a simplex to itself and finding sufficient conditions when this map hits
the center of the simplex. The mere continuity is not sufficient for such a conclusion,
the usual assumption (for example, in the Knaster--Kuratowski--Mazurkiewicz and
the Gale theorem) is a certain boundary condition.\r\n We follow Erel Segal-Halevi,
Fr\\'ed\\'eric Meunier, and Shira Zerbib, and replace the boundary condition by
another assumption, which has the economic meaning of possibility for a player
to prefer an empty part in the segment\r\npartition problem. We solve the problem
positively when $n$, the number of players that divide the segment, is a prime
power, and we provide counterexamples for every $n$ which is not a prime power.
We also provide counterexamples relevant to a wider class of fair or envy-free
partition problems when $n$ is odd and not a prime power."
article_number: '1907.11183'
article_processing_charge: No
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
citation:
ama: Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv.
doi:10.48550/arXiv.1907.11183
apa: Avvakumov, S., & Karasev, R. (n.d.). Envy-free division using mapping degree.
arXiv. https://doi.org/10.48550/arXiv.1907.11183
chicago: Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping
Degree.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1907.11183.
ieee: S. Avvakumov and R. Karasev, “Envy-free division using mapping degree,” arXiv.
.
ista: Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv, 1907.11183.
mla: Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.”
ArXiv, 1907.11183, doi:10.48550/arXiv.1907.11183.
short: S. Avvakumov, R. Karasev, ArXiv (n.d.).
date_created: 2020-07-30T10:45:51Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '25'
department:
- _id: UlWa
doi: 10.48550/arXiv.1907.11183
external_id:
arxiv:
- '1907.11183'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11183
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: arXiv
publication_status: submitted
related_material:
link:
- relation: later_version
url: https://doi.org/10.1112/mtk.12059
record:
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Envy-free division using mapping degree
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7524'
abstract:
- lang: eng
text: "We prove a lower bound for the free energy (per unit volume) of the two-dimensional
Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$
and inverse temperature $\\beta$ differs from the one of the non-interacting system
by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$.
Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ =
\\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless
critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho
\\ll 1$ and if $\\beta \\rho \\gtrsim 1$."
article_processing_charge: No
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
Bose gas. I. Lower bound. arXiv:191003372.
apa: Deuchert, A., Mayer, S., & Seiringer, R. (n.d.). The free energy of the
two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372. ArXiv.
chicago: Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy
of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372.
ArXiv, n.d.
ieee: A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional
dilute Bose gas. I. Lower bound,” arXiv:1910.03372. ArXiv.
ista: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
Bose gas. I. Lower bound. arXiv:1910.03372, .
mla: Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose
Gas. I. Lower Bound.” ArXiv:1910.03372, ArXiv.
short: A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).
date_created: 2020-02-26T08:46:40Z
date_published: 2019-10-08T00:00:00Z
date_updated: 2023-09-07T13:12:41Z
day: '08'
department:
- _id: RoSe
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.03372
month: '10'
oa: 1
oa_version: Preprint
page: '61'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: arXiv:1910.03372
publication_status: draft
publisher: ArXiv
related_material:
record:
- id: '7790'
relation: later_version
status: public
- id: '7514'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The free energy of the two-dimensional dilute Bose gas. I. Lower bound
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6608'
abstract:
- lang: eng
text: We use the canonical bases produced by the tri-partition algorithm in (Edelsbrunner
and Ölsböck, 2018) to open and close holes in a polyhedral complex, K. In a concrete
application, we consider the Delaunay mosaic of a finite set, we let K be an Alpha
complex, and we use the persistence diagram of the distance function to guide
the hole opening and closing operations. The dependences between the holes define
a partial order on the cells in K that characterizes what can and what cannot
be constructed using the operations. The relations in this partial order reveal
structural information about the underlying filtration of complexes beyond what
is expressed by the persistence diagram.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
citation:
ama: Edelsbrunner H, Ölsböck K. Holes and dependences in an ordered complex. Computer
Aided Geometric Design. 2019;73:1-15. doi:10.1016/j.cagd.2019.06.003
apa: Edelsbrunner, H., & Ölsböck, K. (2019). Holes and dependences in an ordered
complex. Computer Aided Geometric Design. Elsevier. https://doi.org/10.1016/j.cagd.2019.06.003
chicago: Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in
an Ordered Complex.” Computer Aided Geometric Design. Elsevier, 2019. https://doi.org/10.1016/j.cagd.2019.06.003.
ieee: H. Edelsbrunner and K. Ölsböck, “Holes and dependences in an ordered complex,”
Computer Aided Geometric Design, vol. 73. Elsevier, pp. 1–15, 2019.
ista: Edelsbrunner H, Ölsböck K. 2019. Holes and dependences in an ordered complex.
Computer Aided Geometric Design. 73, 1–15.
mla: Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an
Ordered Complex.” Computer Aided Geometric Design, vol. 73, Elsevier, 2019,
pp. 1–15, doi:10.1016/j.cagd.2019.06.003.
short: H. Edelsbrunner, K. Ölsböck, Computer Aided Geometric Design 73 (2019) 1–15.
date_created: 2019-07-07T21:59:20Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-09-07T13:15:29Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.cagd.2019.06.003
ec_funded: 1
external_id:
isi:
- '000485207800001'
file:
- access_level: open_access
checksum: 7c99be505dc7533257d42eb1830cef04
content_type: application/pdf
creator: kschuh
date_created: 2019-07-08T15:24:26Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6624'
file_name: Elsevier_2019_Edelsbrunner.pdf
file_size: 2665013
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1-15
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Computer Aided Geometric Design
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '7460'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Holes and dependences in an ordered complex
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...
---
_id: '6677'
abstract:
- lang: eng
text: "The Fiat-Shamir heuristic transforms a public-coin interactive proof into
a non-interactive argument, by replacing the verifier with a cryptographic hash
function that is applied to the protocol’s transcript. Constructing hash functions
for which this transformation is sound is a central and long-standing open question
in cryptography.\r\n\r\nWe show that solving the END−OF−METERED−LINE problem is
no easier than breaking the soundness of the Fiat-Shamir transformation when applied
to the sumcheck protocol. In particular, if the transformed protocol is sound,
then any hard problem in #P gives rise to a hard distribution in the class CLS,
which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized
games for which it is hard to find a Nash equilibrium, by reducing the inversion
of appropriately chosen one-way functions to #SAT.\r\n\r\nOur main technical contribution
is a stateful incrementally verifiable procedure that, given a SAT instance over
n variables, counts the number of satisfying assignments. This is accomplished
via an exponential sequence of small steps, each computable in time poly(n). Incremental
verifiability means that each intermediate state includes a sumcheck-based proof
of its correctness, and the proof can be updated and verified in time poly(n)."
article_processing_charge: No
author:
- first_name: Arka Rai
full_name: Choudhuri, Arka Rai
last_name: Choudhuri
- first_name: Pavel
full_name: Hubáček, Pavel
last_name: Hubáček
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- 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: Alon
full_name: Rosen, Alon
last_name: Rosen
- first_name: Guy N.
full_name: Rothblum, Guy N.
last_name: Rothblum
citation:
ama: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum
GN. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In: Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019.
ACM Press; 2019:1103-1114. doi:10.1145/3313276.3316400'
apa: 'Choudhuri, A. R., Hubáček, P., Kamath Hosdurg, C., Pietrzak, K. Z., Rosen,
A., & Rothblum, G. N. (2019). Finding a Nash equilibrium is no easier than
breaking Fiat-Shamir. In Proceedings of the 51st Annual ACM SIGACT Symposium
on Theory of Computing - STOC 2019 (pp. 1103–1114). Phoenix, AZ, United States:
ACM Press. https://doi.org/10.1145/3313276.3316400'
chicago: Choudhuri, Arka Rai, Pavel Hubáček, Chethan Kamath Hosdurg, Krzysztof Z
Pietrzak, Alon Rosen, and Guy N. Rothblum. “Finding a Nash Equilibrium Is No Easier
than Breaking Fiat-Shamir.” In Proceedings of the 51st Annual ACM SIGACT Symposium
on Theory of Computing - STOC 2019, 1103–14. ACM Press, 2019. https://doi.org/10.1145/3313276.3316400.
ieee: A. R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K. Z. Pietrzak, A. Rosen,
and G. N. Rothblum, “Finding a Nash equilibrium is no easier than breaking Fiat-Shamir,”
in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing
- STOC 2019, Phoenix, AZ, United States, 2019, pp. 1103–1114.
ista: 'Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum
GN. 2019. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019. STOC:
Symposium on Theory of Computing, 1103–1114.'
mla: Choudhuri, Arka Rai, et al. “Finding a Nash Equilibrium Is No Easier than Breaking
Fiat-Shamir.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing - STOC 2019, ACM Press, 2019, pp. 1103–14, doi:10.1145/3313276.3316400.
short: A.R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K.Z. Pietrzak, A. Rosen, G.N.
Rothblum, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of
Computing - STOC 2019, ACM Press, 2019, pp. 1103–1114.
conference:
end_date: 2019-06-26
location: Phoenix, AZ, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2019-06-23
date_created: 2019-07-24T09:20:53Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:15:55Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3313276.3316400
ec_funded: 1
external_id:
isi:
- '000523199100100'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/549
month: '06'
oa: 1
oa_version: Preprint
page: 1103-1114
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing -
STOC 2019
publication_identifier:
isbn:
- '9781450367059'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
record:
- id: '7896'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Finding a Nash equilibrium is no easier than breaking Fiat-Shamir
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '5986'
abstract:
- lang: eng
text: "Given a triangulation of a point set in the plane, a flip deletes an edge
e whose removal leaves a convex quadrilateral, and replaces e by the opposite
diagonal of the quadrilateral. It is well known that any triangulation of a point
set can be reconfigured to any other triangulation by some sequence of flips.
We explore this question in the setting where each edge of a triangulation has
a label, and a flip transfers the label of the removed edge to the new edge. It
is not true that every labelled triangulation of a point set can be reconfigured
to every other labelled triangulation via a sequence of flips, but we characterize
when this is possible. There is an obvious necessary condition: for each label
l, if edge e has label l in the first triangulation and edge f has label l in
the second triangulation, then there must be some sequence of flips that moves
label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot
formulated the Orbit Conjecture, which states that this necessary condition is
also sufficient, i.e. that all labels can be simultaneously mapped to their destination
if and only if each label individually can be mapped to its destination. We prove
this conjecture. Furthermore, we give a polynomial-time algorithm (with \U0001D442(\U0001D45B8)
being a crude bound on the run-time) to find a sequence of flips to reconfigure
one labelled triangulation to another, if such a sequence exists, and we prove
an upper bound of \U0001D442(\U0001D45B7) on the length of the flip sequence.
Our proof uses the topological result that the sets of pairwise non-crossing edges
on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional
ball (this follows from a result of Orden and Santos; we give a different proof
based on a shelling argument). The dual cell complex of this simplicial ball,
called the flip complex, has the usual flip graph as its 1-skeleton. We use properties
of the 2-skeleton of the flip complex to prove the Orbit Conjecture."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anna
full_name: Lubiw, Anna
last_name: Lubiw
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping
edge-labelled triangulations. Discrete & Computational Geometry. 2019;61(4):880-898.
doi:10.1007/s00454-018-0035-8
apa: Lubiw, A., Masárová, Z., & Wagner, U. (2019). A proof of the orbit conjecture
for flipping edge-labelled triangulations. Discrete & Computational Geometry.
Springer Nature. https://doi.org/10.1007/s00454-018-0035-8
chicago: Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture
for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry.
Springer Nature, 2019. https://doi.org/10.1007/s00454-018-0035-8.
ieee: A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for
flipping edge-labelled triangulations,” Discrete & Computational Geometry,
vol. 61, no. 4. Springer Nature, pp. 880–898, 2019.
ista: Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping
edge-labelled triangulations. Discrete & Computational Geometry. 61(4), 880–898.
mla: Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled
Triangulations.” Discrete & Computational Geometry, vol. 61, no. 4,
Springer Nature, 2019, pp. 880–98, doi:10.1007/s00454-018-0035-8.
short: A. Lubiw, Z. Masárová, U. Wagner, Discrete & Computational Geometry 61
(2019) 880–898.
date_created: 2019-02-14T11:54:08Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:17:36Z
day: '01'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.1007/s00454-018-0035-8
external_id:
arxiv:
- '1710.02741'
isi:
- '000466130000009'
file:
- access_level: open_access
checksum: e1bff88f1d77001b53b78c485ce048d7
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T11:57:22Z
date_updated: 2020-07-14T12:47:14Z
file_id: '5988'
file_name: 2018_DiscreteGeometry_Lubiw.pdf
file_size: 556276
relation: main_file
file_date_updated: 2020-07-14T12:47:14Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 880-898
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '683'
relation: earlier_version
status: public
- id: '7944'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A proof of the orbit conjecture for flipping edge-labelled triangulations
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: 61
year: '2019'
...
---
_id: '5886'
abstract:
- lang: eng
text: Problems involving quantum impurities, in which one or a few particles are
interacting with a macroscopic environment, represent a pervasive paradigm, spanning
across atomic, molecular, and condensed-matter physics. In this paper we introduce
new variational approaches to quantum impurities and apply them to the Fröhlich
polaron–a quasiparticle formed out of an electron (or other point-like impurity)
in a polar medium, and to the angulon–a quasiparticle formed out of a rotating
molecule in a bosonic bath. We benchmark these approaches against established
theories, evaluating their accuracy as a function of the impurity-bath coupling.
article_processing_charge: No
author:
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: 'Li X, Bighin G, Yakaboylu E, Lemeshko M. Variational approaches to quantum
impurities: from the Fröhlich polaron to the angulon. Molecular Physics.
2019. doi:10.1080/00268976.2019.1567852'
apa: 'Li, X., Bighin, G., Yakaboylu, E., & Lemeshko, M. (2019). Variational
approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular
Physics. Taylor and Francis. https://doi.org/10.1080/00268976.2019.1567852'
chicago: 'Li, Xiang, Giacomo Bighin, Enderalp Yakaboylu, and Mikhail Lemeshko. “Variational
Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular
Physics. Taylor and Francis, 2019. https://doi.org/10.1080/00268976.2019.1567852.'
ieee: 'X. Li, G. Bighin, E. Yakaboylu, and M. Lemeshko, “Variational approaches
to quantum impurities: from the Fröhlich polaron to the angulon,” Molecular
Physics. Taylor and Francis, 2019.'
ista: 'Li X, Bighin G, Yakaboylu E, Lemeshko M. 2019. Variational approaches to
quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics.'
mla: 'Li, Xiang, et al. “Variational Approaches to Quantum Impurities: From the
Fröhlich Polaron to the Angulon.” Molecular Physics, Taylor and Francis,
2019, doi:10.1080/00268976.2019.1567852.'
short: X. Li, G. Bighin, E. Yakaboylu, M. Lemeshko, Molecular Physics (2019).
date_created: 2019-01-27T22:59:10Z
date_published: 2019-01-18T00:00:00Z
date_updated: 2023-09-07T13:16:42Z
day: '18'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1080/00268976.2019.1567852
ec_funded: 1
external_id:
isi:
- '000474641400008'
file:
- access_level: open_access
checksum: 178964744b636a6f036372f4f090a657
content_type: application/pdf
creator: dernst
date_created: 2019-01-29T08:32:57Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5896'
file_name: 2019_MolecularPhysics_Li.pdf
file_size: 1309966
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Molecular Physics
publication_identifier:
issn:
- '00268976'
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
related_material:
record:
- id: '8958'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Variational approaches to quantum impurities: from the Fröhlich polaron to
the angulon'
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
year: '2019'
...
---
_id: '6556'
abstract:
- lang: eng
text: 'Motivated by fixed-parameter tractable (FPT) problems in computational topology,
we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined
to be the minimum treewidth of the face pairing graph of any triangulation T of
M. In this setting the relationship between the topology of a 3-manifold and its
treewidth is of particular interest. First, as a corollary of work of Jaco and
Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth
tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination
with our earlier work with Wagner, this yields that for non-Haken manifolds the
Heegaard genus and the treewidth are within a constant factor. Second, we characterize
all 3-manifolds of treewidth one: These are precisely the lens spaces and a single
other Seifert fibered space. Furthermore, we show that all remaining orientable
Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth
two. In particular, for every spherical 3-manifold we exhibit a triangulation
of treewidth at most two. Our results further validate the parameter of treewidth
(and other related parameters such as cutwidth or congestion) to be useful for
topological computing, and also shed more light on the scope of existing FPT-algorithms
in the field.'
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Jonathan
full_name: Spreer, Jonathan
last_name: Spreer
citation:
ama: 'Huszár K, Spreer J. 3-manifold triangulations with small treewidth. In: 35th
International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2019:44:1-44:20. doi:10.4230/LIPIcs.SoCG.2019.44'
apa: 'Huszár, K., & Spreer, J. (2019). 3-manifold triangulations with small
treewidth. In 35th International Symposium on Computational Geometry (Vol.
129, p. 44:1-44:20). Portland, Oregon, United States: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2019.44'
chicago: Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small
Treewidth.” In 35th International Symposium on Computational Geometry,
129:44:1-44:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPIcs.SoCG.2019.44.
ieee: K. Huszár and J. Spreer, “3-manifold triangulations with small treewidth,”
in 35th International Symposium on Computational Geometry, Portland, Oregon,
United States, 2019, vol. 129, p. 44:1-44:20.
ista: 'Huszár K, Spreer J. 2019. 3-manifold triangulations with small treewidth.
35th International Symposium on Computational Geometry. SoCG: Symposium on Computational
Geometry, LIPIcs, vol. 129, 44:1-44:20.'
mla: Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small
Treewidth.” 35th International Symposium on Computational Geometry, vol.
129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20, doi:10.4230/LIPIcs.SoCG.2019.44.
short: K. Huszár, J. Spreer, in:, 35th International Symposium on Computational
Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20.
conference:
end_date: 2019-06-21
location: Portland, Oregon, United States
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2019-06-11T20:09:57Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:18:26Z
day: '01'
ddc:
- '516'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2019.44
external_id:
arxiv:
- '1812.05528'
file:
- access_level: open_access
checksum: 29d18c435368468aa85823dabb157e43
content_type: application/pdf
creator: kschuh
date_created: 2019-06-12T06:45:33Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6557'
file_name: 2019_LIPIcs-Huszar.pdf
file_size: 905885
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 129'
keyword:
- computational 3-manifold topology
- fixed-parameter tractability
- layered triangulations
- structural graph theory
- treewidth
- cutwidth
- Heegaard genus
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 44:1-44:20
publication: 35th International Symposium on Computational Geometry
publication_identifier:
isbn:
- 978-3-95977-104-7
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '8032'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: 3-manifold triangulations with small treewidth
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '7093'
abstract:
- lang: eng
text: "In graph theory, as well as in 3-manifold topology, there exist several width-type
parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold
is. These parameters, such as pathwidth or treewidth for graphs, or the concept
of thin position for 3-manifolds, play an important role when studying algorithmic
problems; in particular, there is a variety of problems in computational 3-manifold
topology - some of them known to be computationally hard in general - that become
solvable in polynomial time as soon as the dual graph of the input triangulation
has bounded treewidth.\r\nIn view of these algorithmic results, it is natural
to ask whether every 3-manifold admits a triangulation of bounded treewidth. We
show that this is not the case, i.e., that there exists an infinite family of
closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth
(the latter implies the former, but we present two separate proofs).\r\nWe derive
these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann,
Schultens and Saito by exhibiting explicit connections between the topology of
a 3-manifold M on the one hand and width-type parameters of the dual graphs of
triangulations of M on the other hand, answering a question that had been raised
repeatedly by researchers in computational 3-manifold topology. In particular,
we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has
a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M
is at most 18(k+1) (resp. 4(3k+1))."
article_processing_charge: No
article_type: original
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Jonathan
full_name: Spreer, Jonathan
last_name: Spreer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds.
Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5
apa: Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated
3-manifolds. Journal of Computational Geometry. Computational Geometry
Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5
chicago: Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of
Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational
Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5.
ieee: K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,”
Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry
Laborartoy, pp. 70–98, 2019.
ista: Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds.
Journal of Computational Geometry. 10(2), 70–98.
mla: Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal
of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy,
2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5.
short: K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019)
70–98.
date_created: 2019-11-23T12:14:09Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-07T13:18:26Z
day: '01'
ddc:
- '514'
department:
- _id: UlWa
doi: 10.20382/JOGC.V10I2A5
external_id:
arxiv:
- '1712.00434'
file:
- access_level: open_access
checksum: c872d590d38d538404782bca20c4c3f5
content_type: application/pdf
creator: khuszar
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date_updated: 2020-07-14T12:47:49Z
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file_size: 857590
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file_date_updated: 2020-07-14T12:47:49Z
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issue: '2'
language:
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month: '11'
oa: 1
oa_version: Published Version
page: 70–98
publication: Journal of Computational Geometry
publication_identifier:
issn:
- 1920-180X
publication_status: published
publisher: Computational Geometry Laborartoy
quality_controlled: '1'
related_material:
record:
- id: '285'
relation: earlier_version
status: public
- id: '8032'
relation: part_of_dissertation
status: public
status: public
title: On the treewidth of triangulated 3-manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...
---
_id: '7197'
abstract:
- lang: eng
text: During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like
structure at the center of the cell. This Z-ring not only organizes the division
machinery, but treadmilling of FtsZ filaments was also found to play a key role
in distributing proteins at the division site. What regulates the architecture,
dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated
proteins are known to play an important role. Here, using an in vitro reconstitution
approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling
and filament organization into large-scale patterns. Using high-resolution fluorescence
microscopy and quantitative image analysis, we found that ZapA cooperatively increases
the spatial order of the filament network, but binds only transiently to FtsZ
filaments and has no effect on filament length and treadmilling velocity. Together,
our data provides a model for how FtsZ-associated proteins can increase the precision
and stability of the bacterial cell division machinery in a switch-like manner.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
article_number: '5744'
article_processing_charge: No
article_type: original
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: Daniel J. G.
full_name: Pearce, Daniel J. G.
last_name: Pearce
- 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: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J,
Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks
of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4
apa: Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur,
N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling
filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4
chicago: Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce,
Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling
Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature
Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4.
ieee: P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur,
J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal
networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol.
10. Springer Nature, 2019.
ista: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J,
Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal
networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.
mla: Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments
in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications,
vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4.
short: P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur,
J. Brugués, M. Loose, Nature Communications 10 (2019).
date_created: 2019-12-20T12:22:57Z
date_published: 2019-12-17T00:00:00Z
date_updated: 2023-09-07T13:18:51Z
day: '17'
ddc:
- '570'
department:
- _id: MaLo
- _id: BjHo
doi: 10.1038/s41467-019-13702-4
ec_funded: 1
external_id:
isi:
- '000503009300001'
file:
- access_level: open_access
checksum: a1b44b427ba341383197790d0e8789fa
content_type: application/pdf
creator: dernst
date_created: 2019-12-23T07:34:56Z
date_updated: 2020-07-14T12:47:53Z
file_id: '7208'
file_name: 2019_NatureComm_Caldas.pdf
file_size: 8488733
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8358'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cooperative ordering of treadmilling filaments in cytoskeletal networks of
FtsZ and its crosslinker ZapA
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: '7210'
abstract:
- lang: eng
text: The rate of biological evolution depends on the fixation probability and on
the fixation time of new mutants. Intensive research has focused on identifying
population structures that augment the fixation probability of advantageous mutants.
But these amplifiers of natural selection typically increase fixation time. Here
we study population structures that achieve a tradeoff between fixation probability
and time. First, we show that no amplifiers can have an asymptotically lower absorption
time than the well-mixed population. Then we design population structures that
substantially augment the fixation probability with just a minor increase in fixation
time. Finally, we show that those structures enable higher effective rate of evolution
than the well-mixed population provided that the rate of generating advantageous
mutants is relatively low. Our work sheds light on how population structure affects
the rate of evolution. Moreover, our structures could be useful for lab-based,
medical, or industrial applications of evolutionary optimization.
article_number: '138'
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines
the tradeoff between fixation probability and fixation time. Communications
Biology. 2019;2. doi:10.1038/s42003-019-0373-y
apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2019). Population
structure determines the tradeoff between fixation probability and fixation time.
Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0373-y
chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin
A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability
and Fixation Time.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0373-y.
ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure
determines the tradeoff between fixation probability and fixation time,” Communications
Biology, vol. 2. Springer Nature, 2019.
ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure
determines the tradeoff between fixation probability and fixation time. Communications
Biology. 2, 138.
mla: Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between
Fixation Probability and Fixation Time.” Communications Biology, vol. 2,
138, Springer Nature, 2019, doi:10.1038/s42003-019-0373-y.
short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology
2 (2019).
date_created: 2019-12-23T13:36:50Z
date_published: 2019-04-23T00:00:00Z
date_updated: 2023-09-07T13:19:22Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s42003-019-0373-y
ec_funded: 1
external_id:
isi:
- '000465425700006'
pmid:
- '31044163'
file:
- access_level: open_access
checksum: d1a69bfe73767e4246f0a38e4e1554dd
content_type: application/pdf
creator: dernst
date_created: 2019-12-23T13:39:30Z
date_updated: 2020-07-14T12:47:53Z
file_id: '7211'
file_name: 2019_CommBio_Tkadlec.pdf
file_size: 1670274
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '7196'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Population structure determines the tradeoff between fixation probability and
fixation time
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: 2
year: '2019'
...
---
_id: '10190'
abstract:
- lang: eng
text: 'The verification of concurrent programs remains an open challenge, as thread
interaction has to be accounted for, which leads to state-space explosion. Stateless
model checking battles this problem by exploring traces rather than states of
the program. As there are exponentially many traces, dynamic partial-order reduction
(DPOR) techniques are used to partition the trace space into equivalence classes,
and explore a few representatives from each class. The standard equivalence that
underlies most DPOR techniques is the happens-before equivalence, however recent
works have spawned a vivid interest towards coarser equivalences. The efficiency
of such approaches is a product of two parameters: (i) the size of the partitioning
induced by the equivalence, and (ii) the time spent by the exploration algorithm
in each class of the partitioning. In this work, we present a new equivalence,
called value-happens-before and show that it has two appealing features. First,
value-happens-before is always at least as coarse as the happens-before equivalence,
and can be even exponentially coarser. Second, the value-happens-before partitioning
is efficiently explorable when the number of threads is bounded. We present an
algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning
using polynomial time per class. Finally, we perform an experimental evaluation
of VCDPOR on various benchmarks, and compare it against other state-of-the-art
approaches. Our results show that value-happens-before typically induces a significant
reduction in the size of the underlying partitioning, which leads to a considerable
reduction in the running time for exploring the whole partitioning.'
acknowledgement: "The authors would also like to thank anonymous referees for their
valuable comments and helpful suggestions. This work is supported by the Austrian
Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE),
by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian
Science Fund (FWF) Schrodinger grant J-4220.\r\n"
article_number: '124'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order
reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550'
apa: 'Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic
partial order reduction. In Proceedings of the 34th ACM International Conference
on Object-Oriented Programming, Systems, Languages, and Applications (Vol.
3). Athens, Greece: ACM. https://doi.org/10.1145/3360550'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric
Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International
Conference on Object-Oriented Programming, Systems, Languages, and Applications,
Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550.
ieee: K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial
order reduction,” in Proceedings of the 34th ACM International Conference on
Object-Oriented Programming, Systems, Languages, and Applications, Athens,
Greece, 2019, vol. 3.
ista: 'Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial
order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming,
Systems, Languages and Applications vol. 3, 124.'
mla: Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.”
Proceedings of the 34th ACM International Conference on Object-Oriented Programming,
Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550.
short: K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM
International Conference on Object-Oriented Programming, Systems, Languages, and
Applications, ACM, 2019.
conference:
end_date: 2019-10-25
location: Athens, Greece
name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications'
start_date: 2019-10-23
date_created: 2021-10-27T14:57:06Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-07T13:30:27Z
day: '10'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3360550
external_id:
arxiv:
- '1909.00989'
file:
- access_level: open_access
checksum: 2149979c46964c4d117af06ccb6c0834
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-12T11:41:56Z
date_updated: 2021-11-12T11:41:56Z
file_id: '10278'
file_name: 2019_ACM_Chatterjee.pdf
file_size: 570829
relation: main_file
success: 1
file_date_updated: 2021-11-12T11:41:56Z
has_accepted_license: '1'
intvolume: ' 3'
keyword:
- safety
- risk
- reliability and quality
- software
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3360550
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '10199'
relation: dissertation_contains
status: public
status: public
title: Value-centric dynamic partial order 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: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2019'
...
---
_id: '6673'
abstract:
- lang: eng
text: Several classic problems in graph processing and computational geometry are
solved via incremental algorithms, which split computation into a series of small
tasks acting on shared state, which gets updated progressively. While the sequential
variant of such algorithms usually specifies a fixed (but sometimes random) order
in which the tasks should be performed, a standard approach to parallelizing such
algorithms is to relax this constraint to allow for out-of-order parallel execution.
This is the case for parallel implementations of Dijkstra's single-source shortest-paths
(SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software
frameworks parallelize incremental computation in this way, it is still not well
understood whether this relaxed ordering approach can still provide any complexity
guarantees. In this paper, we address this problem, and analyze the efficiency
guarantees provided by a range of incremental algorithms when parallelized via
relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation
and sorting by insertion, schedulers with a maximum relaxation factor of k in
terms of the maximum priority inversion allowed will introduce a maximum amount
of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed.
For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax
is the maximum distance between two nodes, and wmin is the minimum such distance.
In practical settings where n >> k, this suggests that the overheads of relaxation
will be outweighed by the improved scalability of the relaxed scheduler. On the
negative side, we provide lower bounds showing that certain algorithms will inherently
incur a non-trivial amount of wasted work due to scheduler relaxation, even for
relatively benign relaxed schedulers.
article_processing_charge: No
author:
- 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: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
citation:
ama: 'Alistarh D-A, Nadiradze G, Koval N. Efficiency guarantees for parallel incremental
algorithms under relaxed schedulers. In: 31st ACM Symposium on Parallelism
in Algorithms and Architectures. ACM Press; 2019:145-154. doi:10.1145/3323165.3323201'
apa: 'Alistarh, D.-A., Nadiradze, G., & Koval, N. (2019). Efficiency guarantees
for parallel incremental algorithms under relaxed schedulers. In 31st ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 145–154). Phoenix, AZ,
United States: ACM Press. https://doi.org/10.1145/3323165.3323201'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees
for Parallel Incremental Algorithms under Relaxed Schedulers.” In 31st ACM
Symposium on Parallelism in Algorithms and Architectures, 145–54. ACM Press,
2019. https://doi.org/10.1145/3323165.3323201.
ieee: D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel
incremental algorithms under relaxed schedulers,” in 31st ACM Symposium on
Parallelism in Algorithms and Architectures, Phoenix, AZ, United States, 2019,
pp. 145–154.
ista: 'Alistarh D-A, Nadiradze G, Koval N. 2019. Efficiency guarantees for parallel
incremental algorithms under relaxed schedulers. 31st ACM Symposium on Parallelism
in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms
and Architectures, 145–154.'
mla: Alistarh, Dan-Adrian, et al. “Efficiency Guarantees for Parallel Incremental
Algorithms under Relaxed Schedulers.” 31st ACM Symposium on Parallelism in
Algorithms and Architectures, ACM Press, 2019, pp. 145–54, doi:10.1145/3323165.3323201.
short: D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism
in Algorithms and Architectures, ACM Press, 2019, pp. 145–154.
conference:
end_date: 2019-06-24
location: Phoenix, AZ, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2019-06-22
date_created: 2019-07-24T08:59:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T13:31:39Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3323165.3323201
ec_funded: 1
external_id:
arxiv:
- '2003.09363'
isi:
- '000507618500018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2003.09363
month: '06'
oa: 1
oa_version: Preprint
page: 145-154
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 31st ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450361842'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Efficiency guarantees for parallel incremental algorithms under relaxed schedulers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7398'
abstract:
- lang: eng
text: 'Transporters of the solute carrier 6 (SLC6) family translocate their cognate
substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters
of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4).
Here, we posited that the transport cycle of individual SLC6 transporters reflects
the physiological requirements they operate under. We tested this hypothesis by
analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine
transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate
glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions
in real time by electrophysiological recordings. Contrary to monoamine transporters,
both GlyTs were found to have a high transport capacity driven by rapid return
of the empty transporter after release of Cl− on the intracellular side. Rapid
cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate
ions and substrate such that their forward transport mode was maintained even
under conditions of elevated intracellular Na+ or Cl−. The most important differences
in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement
and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1
were governed by transition of the substrate-bound transporter from outward- to
inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+
binding (or a related conformational change). Kinetic modeling showed that the
kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels
required for NMDA receptor activation.'
article_processing_charge: No
article_type: original
author:
- first_name: Fatma Asli
full_name: Erdem, Fatma Asli
last_name: Erdem
- first_name: Marija
full_name: Ilic, Marija
last_name: Ilic
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Jakub
full_name: Gołacki, Jakub
last_name: Gołacki
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
- first_name: Michael
full_name: Freissmuth, Michael
last_name: Freissmuth
- first_name: Walter
full_name: Sandtner, Walter
last_name: Sandtner
citation:
ama: Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics
of glycine transporter 1 and glycine transporter 2. The Journal of General
Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318
apa: Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth,
M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine
transporter 1 and glycine transporter 2. The Journal of General Physiology.
Rockefeller University Press. https://doi.org/10.1085/jgp.201912318
chicago: Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert
Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport
Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of
General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318.
ieee: F. A. Erdem et al., “A comparison of the transport kinetics of glycine
transporter 1 and glycine transporter 2,” The Journal of General Physiology,
vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.
ista: Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner
W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine
transporter 2. The Journal of General Physiology. 151(8), 1035–1050.
mla: Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine
Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology,
vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.
short: F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth,
W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.
date_created: 2020-01-29T16:06:29Z
date_published: 2019-07-03T00:00:00Z
date_updated: 2023-09-07T14:52:23Z
day: '03'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1085/jgp.201912318
external_id:
isi:
- '000478792500008'
pmid:
- '31270129'
file:
- access_level: open_access
checksum: 5706b4ccd74ee3e50bf7ecb2a203df71
content_type: application/pdf
creator: dernst
date_created: 2020-02-05T07:20:32Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7450'
file_name: 2019_JGP_Erdem.pdf
file_size: 2641297
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1035-1050
pmid: 1
publication: The Journal of General Physiology
publication_identifier:
eissn:
- 1540-7748
issn:
- 0022-1295
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of the transport kinetics of glycine transporter 1 and glycine
transporter 2
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 151
year: '2019'
...
---
_id: '7395'
abstract:
- lang: eng
text: The mitochondrial electron transport chain complexes are organized into supercomplexes
(SCs) of defined stoichiometry, which have been proposed to regulate electron
flux via substrate channeling. We demonstrate that CoQ trapping in the isolated
SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure,
resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may
be rate limiting because of unequal access of CoQ to the active sites of CIII2.
CI shows a transition between “closed” and “open” conformations, accompanied by
the striking rotation of a key transmembrane helix. Furthermore, the state of
CI affects the conformational flexibility within CIII2, demonstrating crosstalk
between the enzymes. CoQ was identified at only three of the four binding sites
in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally
relevant manner. Together, these observations indicate a more nuanced functional
role for the SCs.
article_processing_charge: No
article_type: original
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Gianluca
full_name: Degliesposti, Gianluca
last_name: Degliesposti
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- 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: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of
respiratory supercomplex I+III2 reveal functional and conformational crosstalk.
Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022
apa: Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov,
L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional
and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022
chicago: Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and
Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional
and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022.
ieee: J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov,
“Structures of respiratory supercomplex I+III2 reveal functional and conformational
crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6,
2019.
ista: Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures
of respiratory supercomplex I+III2 reveal functional and conformational crosstalk.
Molecular Cell. 75(6), 1131–1146.e6.
mla: Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal
Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no.
6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.
short: J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular
Cell 75 (2019) 1131–1146.e6.
date_created: 2020-01-29T16:02:33Z
date_published: 2019-09-19T00:00:00Z
date_updated: 2023-09-07T14:53:06Z
day: '19'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.molcel.2019.07.022
ec_funded: 1
external_id:
isi:
- '000486614200006'
pmid:
- '31492636'
file:
- access_level: open_access
checksum: 5202f53a237d6650ece038fbf13bdcea
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:37:28Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7447'
file_name: 2019_MolecularCell_Letts.pdf
file_size: 9654895
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1131-1146.e6
pmid: 1
project:
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structures of respiratory supercomplex I+III2 reveal functional and conformational
crosstalk
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: 75
year: '2019'
...
---
_id: '7405'
abstract:
- lang: eng
text: Biophysical modeling of neuronal networks helps to integrate and interpret
rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE
tool (www.netpyne.org) provides both programmatic and graphical interfaces to
develop data-driven multiscale network models in NEURON. NetPyNE clearly separates
model parameters from implementation code. Users provide specifications at a high
level via a standardized declarative language, for example connectivity rules,
to create millions of cell-to-cell connections. NetPyNE then enables users to
generate the NEURON network, run efficiently parallelized simulations, optimize
and explore network parameters through automated batch runs, and use built-in
functions for visualization and analysis – connectivity matrices, voltage traces,
spike raster plots, local field potentials, and information theoretic measures.
NetPyNE also facilitates model sharing by exporting and importing standardized
formats (NeuroML and SONATA). NetPyNE is already being used to teach computational
neuroscience students and by modelers to investigate brain regions and phenomena.
article_number: e44494
article_processing_charge: No
article_type: original
author:
- first_name: Salvador
full_name: Dura-Bernal, Salvador
last_name: Dura-Bernal
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Padraig
full_name: Gleeson, Padraig
last_name: Gleeson
- first_name: Matteo
full_name: Cantarelli, Matteo
last_name: Cantarelli
- first_name: Adrian
full_name: Quintana, Adrian
last_name: Quintana
- first_name: Facundo
full_name: Rodriguez, Facundo
last_name: Rodriguez
- first_name: David J
full_name: Kedziora, David J
last_name: Kedziora
- first_name: George L
full_name: Chadderdon, George L
last_name: Chadderdon
- first_name: Cliff C
full_name: Kerr, Cliff C
last_name: Kerr
- first_name: Samuel A
full_name: Neymotin, Samuel A
last_name: Neymotin
- first_name: Robert A
full_name: McDougal, Robert A
last_name: McDougal
- first_name: Michael
full_name: Hines, Michael
last_name: Hines
- first_name: Gordon MG
full_name: Shepherd, Gordon MG
last_name: Shepherd
- first_name: William W
full_name: Lytton, William W
last_name: Lytton
citation:
ama: Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale
modeling of brain circuits. eLife. 2019;8. doi:10.7554/elife.44494
apa: Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez,
F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling
of brain circuits. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.44494
chicago: Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli,
Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool
for Data-Driven Multiscale Modeling of Brain Circuits.” ELife. eLife Sciences
Publications, 2019. https://doi.org/10.7554/elife.44494.
ieee: S. Dura-Bernal et al., “NetPyNE, a tool for data-driven multiscale
modeling of brain circuits,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F,
Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd
GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain
circuits. eLife. 8, e44494.
mla: Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling
of Brain Circuits.” ELife, vol. 8, e44494, eLife Sciences Publications,
2019, doi:10.7554/elife.44494.
short: S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez,
D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines,
G.M. Shepherd, W.W. Lytton, ELife 8 (2019).
date_created: 2020-01-30T09:08:01Z
date_published: 2019-05-31T00:00:00Z
date_updated: 2023-09-07T14:27:52Z
day: '31'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.7554/elife.44494
external_id:
isi:
- '000468968400001'
pmid:
- '31025934'
file:
- access_level: open_access
checksum: 7014189c11c10a12feeeae37f054871d
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T08:41:47Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7444'
file_name: 2019_eLife_DuraBernal.pdf
file_size: 6182359
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: NetPyNE, a tool for data-driven multiscale modeling of brain circuits
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: '7400'
abstract:
- lang: eng
text: 'Suppressed recombination allows divergence between homologous sex chromosomes
and the functionality of their genes. Here, we reveal patterns of the earliest
stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua
on the basis of cytological analysis, de novo genome assembly and annotation,
genetic mapping, exome resequencing of natural populations, and transcriptome
analysis. The genome assembly contained 34,105 expressed genes, of which 10,076
were assigned to linkage groups. Genetic mapping and exome resequencing of individuals
across the species range both identified the largest linkage group, LG1, as the
sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic,
we estimate that about one-third of the Y chromosome, containing 568 transcripts
and spanning 22.3 cM in the corresponding female map, has ceased recombining.
Nevertheless, we found limited evidence for Y-chromosome degeneration in terms
of gene loss and pseudogenization, and most X- and Y-linked genes appear to have
diverged in the period subsequent to speciation between M. annua and its sister
species M. huetii, which shares the same sex-determining region. Taken together,
our results suggest that the M. annua Y chromosome has at least two evolutionary
strata: a small old stratum shared with M. huetii, and a more recent larger stratum
that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns
of gene expression within the nonrecombining region are consistent with the idea
that sexually antagonistic selection may have played a role in favoring suppressed
recombination.'
article_processing_charge: No
article_type: original
author:
- first_name: Paris
full_name: Veltsos, Paris
last_name: Veltsos
- first_name: Kate E.
full_name: Ridout, Kate E.
last_name: Ridout
- 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: Santiago C.
full_name: González-Martínez, Santiago C.
last_name: González-Martínez
- first_name: Aline
full_name: Muyle, Aline
last_name: Muyle
- first_name: Olivier
full_name: Emery, Olivier
last_name: Emery
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Vojtech
full_name: Hudzieczek, Vojtech
last_name: Hudzieczek
- first_name: Roman
full_name: Hobza, Roman
last_name: Hobza
- first_name: Boris
full_name: Vyskot, Boris
last_name: Vyskot
- first_name: Gabriel A. B.
full_name: Marais, Gabriel A. B.
last_name: Marais
- first_name: Dmitry A.
full_name: Filatov, Dmitry A.
last_name: Filatov
- first_name: John R.
full_name: Pannell, John R.
last_name: Pannell
citation:
ama: Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835.
doi:10.1534/genetics.119.302045
apa: Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle,
A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.119.302045
chicago: Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez,
Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution
in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society
of America, 2019. https://doi.org/10.1534/genetics.119.302045.
ieee: P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious
plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of
America, pp. 815–835, 2019.
ista: Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas
P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019.
Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua.
Genetics. 212(3), 815–835.
mla: Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious
Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of
America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045.
short: P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O.
Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov,
J.R. Pannell, Genetics 212 (2019) 815–835.
date_created: 2020-01-29T16:15:44Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-07T14:49:29Z
day: '01'
department:
- _id: BeVi
doi: 10.1534/genetics.119.302045
ec_funded: 1
external_id:
isi:
- '000474809300015'
pmid:
- '31113811'
intvolume: ' 212'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.119.302045
month: '07'
oa: 1
oa_version: Published Version
page: 815-835
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 212
year: '2019'
...
---
_id: '7404'
abstract:
- lang: eng
text: The formation of neuronal dendrite branches is fundamental for the wiring
and function of the nervous system. Indeed, dendrite branching enhances the coverage
of the neuron's receptive field and modulates the initial processing of incoming
stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process
of de novo branch formation, branch extension and retraction. The first step towards
branch formation is the generation of a dynamic filopodium-like branchlet. The
mechanisms underlying the initiation of dendrite branchlets are therefore crucial
to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular
localization of actin during the process of branching of Drosophila larva sensory
neurons, combined with genetic analysis and electron tomography, we have identified
the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved
in the initiation of dendrite branchlet formation, under the control of the activator
WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component
marks the site of branchlet initiation in vivo. These data position the activation
of Arp2/3 as an early hub for the initiation of branchlet formation.
article_number: dev171397
article_processing_charge: No
article_type: original
author:
- first_name: Tomke
full_name: Stürner, Tomke
last_name: Stürner
- first_name: Anastasia
full_name: Tatarnikova, Anastasia
last_name: Tatarnikova
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Barbara
full_name: Schaffran, Barbara
last_name: Schaffran
- first_name: Hermann
full_name: Cuntz, Hermann
last_name: Cuntz
- first_name: Yun
full_name: Zhang, Yun
last_name: Zhang
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Sven
full_name: Bogdan, Sven
last_name: Bogdan
- first_name: Vic
full_name: Small, Vic
last_name: Small
- first_name: Gaia
full_name: Tavosanis, Gaia
last_name: Tavosanis
citation:
ama: Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3
complex initiates neuronal dendrite branching in vivo. Development. 2019;146(7).
doi:10.1242/dev.171397
apa: Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang,
Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates
neuronal dendrite branching in vivo. Development. The Company of Biologists.
https://doi.org/10.1242/dev.171397
chicago: Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann
Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis.
“Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching
in Vivo.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.171397.
ieee: T. Stürner et al., “Transient localization of the Arp2/3 complex initiates
neuronal dendrite branching in vivo,” Development, vol. 146, no. 7. The
Company of Biologists, 2019.
ista: Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova
M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3
complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.
mla: Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates
Neuronal Dendrite Branching in Vivo.” Development, vol. 146, no. 7, dev171397,
The Company of Biologists, 2019, doi:10.1242/dev.171397.
short: T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang,
M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).
date_created: 2020-01-29T16:27:10Z
date_published: 2019-04-04T00:00:00Z
date_updated: 2023-09-07T14:47:00Z
day: '04'
department:
- _id: MiSi
doi: 10.1242/dev.171397
external_id:
isi:
- '000464583200006'
pmid:
- '30910826'
intvolume: ' 146'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.171397
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
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: Transient localization of the Arp2/3 complex initiates neuronal dendrite branching
in vivo
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 146
year: '2019'
...
---
_id: '7402'
abstract:
- lang: eng
text: Graph planning gives rise to fundamental algorithmic questions such as shortest
path, traveling salesman problem, etc. A classical problem in discrete planning
is to consider a weighted graph and construct a path that maximizes the sum of
weights for a given time horizon T. However, in many scenarios, the time horizon
is not fixed, but the stopping time is chosen according to some distribution such
that the expected stopping time is T. If the stopping time distribution is not
known, then to ensure robustness, the distribution is chosen by an adversary,
to represent the worst-case scenario. A stationary plan for every vertex always
chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution,
stationary plans are not sufficient for optimality. Quite surprisingly we show
that when an adversary chooses the stopping-time distribution with expected stopping
time T, then stationary plans are sufficient. While computing optimal stationary
plans for fixed horizon is NP-complete, we show that computing optimal stationary
plans under adversarial stopping-time distribution can be achieved in polynomial
time. Consequently, our polynomial-time algorithm for adversarial stopping time
also computes an optimal plan among all possible plans.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th
Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706'
apa: 'Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite
horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science
(pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected
Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science,
1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706.
ieee: K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,”
in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver,
BC, Canada, 2019, pp. 1–13.
ista: 'Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon.
34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on
Logic in Computer Science, 1–13.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite
Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science,
IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706.
short: K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in
Computer Science, IEEE, 2019, pp. 1–13.
conference:
end_date: 2019-06-27
location: Vancouver, BC, Canada
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2019-06-24
date_created: 2020-01-29T16:18:33Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T14:48:11Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/lics.2019.8785706
external_id:
arxiv:
- '1802.03642'
isi:
- '000805002800001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.03642
month: '06'
oa: 1
oa_version: Preprint
page: 1-13
publication: 34th Annual ACM/IEEE Symposium on Logic in Computer Science
publication_identifier:
isbn:
- '9781728136080'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '11402'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Graph planning with expected finite horizon
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7451'
abstract:
- lang: eng
text: We prove that the observable telegraph signal accompanying the bistability
in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings
model is the finite-size precursor of what in the thermodynamic limit is a genuine
first-order phase transition. We construct a finite-size scaling of the system
parameters to a well-defined thermodynamic limit, in which the system remains
the same microscopic system, but the telegraph signal becomes macroscopic both
in its timescale and intensity. The existence of such a finite-size scaling completes
and justifies the classification of the photon-blockade-breakdown effect as a
first-order dissipative quantum phase transition.
article_number: '150'
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Vukics, A.
last_name: Vukics
- first_name: A.
full_name: Dombi, A.
last_name: Dombi
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: P.
full_name: Domokos, P.
last_name: Domokos
citation:
ama: Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade
breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150
apa: Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling
of the photon-blockade breakdown dissipative quantum phase transition. Quantum.
Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften.
https://doi.org/10.22331/q-2019-06-03-150
chicago: Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling
of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum.
Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften,
2019. https://doi.org/10.22331/q-2019-06-03-150.
ieee: A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the
photon-blockade breakdown dissipative quantum phase transition,” Quantum,
vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften,
2019.
ista: Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade
breakdown dissipative quantum phase transition. Quantum. 3, 150.
mla: Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative
Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des
Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150.
short: A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).
date_created: 2020-02-05T09:57:57Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-09-07T14:57:39Z
day: '03'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.22331/q-2019-06-03-150
external_id:
arxiv:
- '1809.09737'
isi:
- '000469987500004'
file:
- access_level: open_access
checksum: 26b9ba8f0155d183f1ee55295934a17f
content_type: application/pdf
creator: dernst
date_created: 2020-02-11T09:25:23Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7483'
file_name: 2019_Quantum_Vukics.pdf
file_size: 5805248
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Quantum
publication_identifier:
issn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
status: public
title: Finite-size scaling of the photon-blockade breakdown dissipative quantum phase
transition
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: 3
year: '2019'
...
---
_id: '7468'
abstract:
- lang: eng
text: We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference
in structured energy minimization problems. The method optimizes a Lagrangean
relaxation of the original energy minimization problem using a multi plane block-coordinate
Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean
decomposition. We show empirically that our method outperforms state-of-the-art
Lagrangean decomposition based algorithms on some challenging Markov Random Field,
multi-label discrete tomography and graph matching problems.
article_number: 11138-11147
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm.
In: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. Vol 2019-June. IEEE; 2019. doi:10.1109/CVPR.2019.01140'
apa: 'Swoboda, P., & Kolmogorov, V. (2019). Map inference via block-coordinate
Frank-Wolfe algorithm. In Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition (Vol. 2019–June). Long Beach, CA,
United States: IEEE. https://doi.org/10.1109/CVPR.2019.01140'
chicago: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
Frank-Wolfe Algorithm.” In Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, Vol. 2019–June. IEEE, 2019. https://doi.org/10.1109/CVPR.2019.01140.
ieee: P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe
algorithm,” in Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition, Long Beach, CA, United States, 2019, vol.
2019–June.
ista: 'Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe
algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition
vol. 2019–June, 11138–11147.'
mla: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
Frank-Wolfe Algorithm.” Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, vol. 2019–June, 11138–11147, IEEE,
2019, doi:10.1109/CVPR.2019.01140.
short: P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, IEEE, 2019.
conference:
end_date: 2019-06-20
location: Long Beach, CA, United States
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2019-06-15
date_created: 2020-02-09T23:00:52Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T14:54:24Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/CVPR.2019.01140
ec_funded: 1
external_id:
arxiv:
- '1806.05049'
isi:
- '000542649304076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05049
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- '9781728132938'
issn:
- '10636919'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Map inference via block-coordinate Frank-Wolfe algorithm
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-June
year: '2019'
...
---
_id: '7415'
article_processing_charge: No
article_type: original
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Morandell J, Nicolas A, Schwarz LA, Novarino G. S.16.05 Illuminating the role
of the e3 ubiquitin ligase cullin3 in brain development and autism. European
Neuropsychopharmacology. 2019;29(Supplement 6):S11-S12. doi:10.1016/j.euroneuro.2019.09.040
apa: Morandell, J., Nicolas, A., Schwarz, L. A., & Novarino, G. (2019). S.16.05
Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development
and autism. European Neuropsychopharmacology. Elsevier. https://doi.org/10.1016/j.euroneuro.2019.09.040
chicago: Morandell, Jasmin, Armel Nicolas, Lena A Schwarz, and Gaia Novarino. “S.16.05
Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development
and Autism.” European Neuropsychopharmacology. Elsevier, 2019. https://doi.org/10.1016/j.euroneuro.2019.09.040.
ieee: J. Morandell, A. Nicolas, L. A. Schwarz, and G. Novarino, “S.16.05 Illuminating
the role of the e3 ubiquitin ligase cullin3 in brain development and autism,”
European Neuropsychopharmacology, vol. 29, no. Supplement 6. Elsevier,
pp. S11–S12, 2019.
ista: Morandell J, Nicolas A, Schwarz LA, Novarino G. 2019. S.16.05 Illuminating
the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European
Neuropsychopharmacology. 29(Supplement 6), S11–S12.
mla: Morandell, Jasmin, et al. “S.16.05 Illuminating the Role of the E3 Ubiquitin
Ligase Cullin3 in Brain Development and Autism.” European Neuropsychopharmacology,
vol. 29, no. Supplement 6, Elsevier, 2019, pp. S11–12, doi:10.1016/j.euroneuro.2019.09.040.
short: J. Morandell, A. Nicolas, L.A. Schwarz, G. Novarino, European Neuropsychopharmacology
29 (2019) S11–S12.
date_created: 2020-01-30T10:07:41Z
date_published: 2019-12-13T00:00:00Z
date_updated: 2023-09-07T14:56:17Z
day: '13'
department:
- _id: GaNo
- _id: LifeSc
doi: 10.1016/j.euroneuro.2019.09.040
external_id:
isi:
- '000502657500021'
intvolume: ' 29'
isi: 1
issue: Supplement 6
language:
- iso: eng
month: '12'
oa_version: None
page: S11-S12
publication: European Neuropsychopharmacology
publication_identifier:
issn:
- 0924-977X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development
and autism
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '7414'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Knaus L, Tarlungeanu D-C, Novarino G. S.16.03 A homozygous missense mutation
in SLC7A5 leads to autism spectrum disorder and microcephaly. European Neuropsychopharmacology.
2019;29(Supplement 6):S11. doi:10.1016/j.euroneuro.2019.09.039
apa: Knaus, L., Tarlungeanu, D.-C., & Novarino, G. (2019). S.16.03 A homozygous
missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly.
European Neuropsychopharmacology. Elsevier. https://doi.org/10.1016/j.euroneuro.2019.09.039
chicago: Knaus, Lisa, Dora-Clara Tarlungeanu, and Gaia Novarino. “S.16.03 A Homozygous
Missense Mutation in SLC7A5 Leads to Autism Spectrum Disorder and Microcephaly.”
European Neuropsychopharmacology. Elsevier, 2019. https://doi.org/10.1016/j.euroneuro.2019.09.039.
ieee: L. Knaus, D.-C. Tarlungeanu, and G. Novarino, “S.16.03 A homozygous missense
mutation in SLC7A5 leads to autism spectrum disorder and microcephaly,” European
Neuropsychopharmacology, vol. 29, no. Supplement 6. Elsevier, p. S11, 2019.
ista: Knaus L, Tarlungeanu D-C, Novarino G. 2019. S.16.03 A homozygous missense
mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. European
Neuropsychopharmacology. 29(Supplement 6), S11.
mla: Knaus, Lisa, et al. “S.16.03 A Homozygous Missense Mutation in SLC7A5 Leads
to Autism Spectrum Disorder and Microcephaly.” European Neuropsychopharmacology,
vol. 29, no. Supplement 6, Elsevier, 2019, p. S11, doi:10.1016/j.euroneuro.2019.09.039.
short: L. Knaus, D.-C. Tarlungeanu, G. Novarino, European Neuropsychopharmacology
29 (2019) S11.
date_created: 2020-01-30T10:06:15Z
date_published: 2019-12-13T00:00:00Z
date_updated: 2023-09-07T14:55:23Z
day: '13'
department:
- _id: GaNo
doi: 10.1016/j.euroneuro.2019.09.039
external_id:
isi:
- '000502657500020'
intvolume: ' 29'
isi: 1
issue: Supplement 6
language:
- iso: eng
month: '12'
oa_version: None
page: S11
publication: European Neuropsychopharmacology
publication_identifier:
issn:
- 0924-977X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder
and microcephaly
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2019'
...
---
_id: '7394'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Yasin
full_name: Dagdas, Yasin
last_name: Dagdas
citation:
ama: 'Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics?
Current Opinion in Plant Biology. 2019;52(12):A1-A2. doi:10.1016/j.pbi.2019.11.002'
apa: 'Benková, E., & Dagdas, Y. (2019). Editorial overview: Cell biology in
the era of omics? Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.11.002'
chicago: 'Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the
Era of Omics?” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.11.002.'
ieee: 'E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of
omics?,” Current Opinion in Plant Biology, vol. 52, no. 12. Elsevier, pp.
A1–A2, 2019.'
ista: 'Benková E, Dagdas Y. 2019. Editorial overview: Cell biology in the era of
omics? Current Opinion in Plant Biology. 52(12), A1–A2.'
mla: 'Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era
of Omics?” Current Opinion in Plant Biology, vol. 52, no. 12, Elsevier,
2019, pp. A1–2, doi:10.1016/j.pbi.2019.11.002.'
short: E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2.
date_created: 2020-01-29T16:00:07Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-07T14:56:55Z
day: '01'
department:
- _id: EvBe
doi: 10.1016/j.pbi.2019.11.002
external_id:
isi:
- '000502890600001'
pmid:
- '31787165'
intvolume: ' 52'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: A1-A2
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Editorial overview: Cell biology in the era of omics?'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 52
year: '2019'
...
---
_id: '7479'
abstract:
- lang: eng
text: "Multi-exit architectures, in which a stack of processing layers is interleaved
with early output layers, allow the processing of a test example to stop early
and thus save computation time and/or energy. In this work, we propose a new
training procedure for multi-exit architectures based on the principle of knowledge
distillation. The method encourage searly exits to mimic later, more accurate
exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and
\ ImageNet show that distillation-based training significantly improves the
accuracy of early exits while maintaining state-of-the-art accuracy for late
\ ones. The method is particularly beneficial when training data is limited
\ and it allows a straightforward extension to semi-supervised learning,i.e.
making use of unlabeled data at training time. Moreover, it takes only afew lines
to implement and incurs almost no computational overhead at training time, and
none at all at test time."
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Phuong M, Lampert C. Distillation-based training for multi-exit architectures.
In: IEEE International Conference on Computer Vision. Vol 2019-October.
IEEE; 2019:1355-1364. doi:10.1109/ICCV.2019.00144'
apa: 'Phuong, M., & Lampert, C. (2019). Distillation-based training for multi-exit
architectures. In IEEE International Conference on Computer Vision (Vol.
2019–October, pp. 1355–1364). Seoul, Korea: IEEE. https://doi.org/10.1109/ICCV.2019.00144'
chicago: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit
Architectures.” In IEEE International Conference on Computer Vision, 2019–October:1355–64.
IEEE, 2019. https://doi.org/10.1109/ICCV.2019.00144.
ieee: M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,”
in IEEE International Conference on Computer Vision, Seoul, Korea, 2019,
vol. 2019–October, pp. 1355–1364.
ista: 'Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures.
IEEE International Conference on Computer Vision. ICCV: International Conference
on Computer Vision vol. 2019–October, 1355–1364.'
mla: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit
Architectures.” IEEE International Conference on Computer Vision, vol.
2019–October, IEEE, 2019, pp. 1355–64, doi:10.1109/ICCV.2019.00144.
short: M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision,
IEEE, 2019, pp. 1355–1364.
conference:
end_date: 2019-11-02
location: Seoul, Korea
name: 'ICCV: International Conference on Computer Vision'
start_date: 2019-10-27
date_created: 2020-02-11T09:06:57Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:11:12Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1109/ICCV.2019.00144
ec_funded: 1
external_id:
isi:
- '000531438101047'
file:
- access_level: open_access
checksum: 7b77fb5c2d27c4c37a7612ba46a66117
content_type: application/pdf
creator: bphuong
date_created: 2020-02-11T09:06:39Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7480'
file_name: main.pdf
file_size: 735768
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 1355-1364
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: IEEE International Conference on Computer Vision
publication_identifier:
isbn:
- '9781728148038'
issn:
- '15505499'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '9418'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Distillation-based training for multi-exit architectures
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-October
year: '2019'
...
---
_id: '7542'
abstract:
- lang: eng
text: We present a novel class of convolutional neural networks (CNNs) for set functions,i.e.,
data indexed with the powerset of a finite set. The convolutions are derivedas
linear, shift-equivariant functions for various notions of shifts on set functions.The
framework is fundamentally different from graph convolutions based on theLaplacian,
as it provides not one but several basic shifts, one for each element inthe ground
set. Prototypical experiments with several set function classificationtasks on
synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate
the potential of our new powerset CNNs.
article_processing_charge: No
author:
- first_name: Chris
full_name: Wendler, Chris
last_name: Wendler
- 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: Markus
full_name: Püschel, Markus
last_name: Püschel
citation:
ama: 'Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks.
In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.'
apa: 'Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional
neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural
Information Processing Systems, Vancouver, Canada: Neural Information Processing
Systems Foundation.'
chicago: Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional
Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation,
2019.
ieee: 'C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural
networks,” presented at the NIPS: Conference on Neural Information Processing
Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.'
ista: 'Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks.
NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.'
mla: Wendler, Chris, et al. Powerset Convolutional Neural Networks. Vol.
32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.
short: C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing
Systems Foundation, 2019, pp. 927–938.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NIPS: Conference on Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2020-02-28T10:03:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-08T11:13:52Z
day: '01'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '1909.02253'
isi:
- '000534424300084'
intvolume: ' 32'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks
month: '12'
oa: 1
oa_version: Published Version
page: 927-938
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Powerset convolutional neural networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2019'
...
---
_id: '7513'
abstract:
- lang: eng
text: 'Social insects (i.e., ants, termites and the social bees and wasps) protect
their colonies from disease using a combination of individual immunity and collectively
performed defenses, termed social immunity. The first line of social immune defense
is sanitary care, which is performed by colony members to protect their pathogen-exposed
nestmates from developing an infection. If sanitary care fails and an infection
becomes established, a second line of social immune defense is deployed to stop
disease transmission within the colony and to protect the valuable queens, which
together with the males are the reproductive individuals of the colony. Insect
colonies are separated into these reproductive individuals and the sterile worker
force, forming a superorganismal reproductive unit reminiscent of the differentiated
germline and soma in a multicellular organism. Ultimately, the social immune response
preserves the germline of the superorganism insect colony and increases overall
fitness of the colony in case of disease. '
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
citation:
ama: 'Cremer S, Kutzer M. Social immunity. In: Choe J, ed. Encyclopedia of Animal
Behavior. 2nd ed. Elsevier; 2019:747-755. doi:10.1016/B978-0-12-809633-8.90721-0'
apa: Cremer, S., & Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), Encyclopedia
of Animal Behavior (2nd ed., pp. 747–755). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.90721-0
chicago: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In Encyclopedia
of Animal Behavior, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.90721-0.
ieee: S. Cremer and M. Kutzer, “Social immunity,” in Encyclopedia of Animal Behavior,
2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.
ista: 'Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior.
, 747–755.'
mla: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” Encyclopedia of Animal
Behavior, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:10.1016/B978-0-12-809633-8.90721-0.
short: S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior,
2nd ed., Elsevier, 2019, pp. 747–755.
date_created: 2020-02-23T23:00:36Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-09-08T11:12:04Z
day: '06'
department:
- _id: SyCr
doi: 10.1016/B978-0-12-809633-8.90721-0
edition: '2'
editor:
- first_name: Jae
full_name: Choe, Jae
last_name: Choe
external_id:
isi:
- '000248989500026'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 747-755
publication: Encyclopedia of Animal Behavior
publication_identifier:
eisbn:
- '9780128132524'
isbn:
- '9780128132517'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social immunity
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '9261'
abstract:
- lang: eng
text: 'Bending-active structures are able to efficiently produce complex curved
shapes starting from flat panels. The desired deformation of the panels derives
from the proper selection of their elastic properties. Optimized panels, called
FlexMaps, are designed such that, once they are bent and assembled, the resulting
static equilibrium configuration matches a desired input 3D shape. The FlexMaps
elastic properties are controlled by locally varying spiraling geometric mesostructures,
which are optimized in size and shape to match the global curvature (i.e., bending
requests) of the target shape. The design pipeline starts from a quad mesh representing
the input 3D shape, which defines the edge size and the total amount of spirals:
every quad will embed one spiral. Then, an optimization algorithm tunes the geometry
of the spirals by using a simplified pre-computed rod model. This rod model is
derived from a non-linear regression algorithm which approximates the non-linear
behavior of solid FEM spiral models subject to hundreds of load combinations.
This innovative pipeline has been applied to the project of a lightweight plywood
pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc
that fits a bounding box of 3.90x3.96x3.25 meters.'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Laccone, Francesco
last_name: Laccone
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Jesus
full_name: Perez Rodriguez, Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Federico
full_name: Ponchio, Federico
last_name: Ponchio
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted
arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 -
60th Anniversary Symposium of the International Association for Shell and Spatial
Structures; Structural Membranes 2019 - 9th International Conference on Textile
Composites and Inflatable Structures, FORM and FORCE. International Center
for Numerical Methods in Engineering; 2019:509-515.'
apa: 'Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel,
B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured
flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of
the International Association for Shell and Spatial Structures; Structural Membranes
2019 - 9th International Conference on Textile Composites and Inflatable Structures,
FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical
Methods in Engineering.'
chicago: 'Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni,
Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted
Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 -
60th Anniversary Symposium of the International Association for Shell and Spatial
Structures; Structural Membranes 2019 - 9th International Conference on Textile
Composites and Inflatable Structures, FORM and FORCE, 509–15. International
Center for Numerical Methods in Engineering, 2019.'
ieee: 'F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured
flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium
of the International Association for Shell and Spatial Structures; Structural
Membranes 2019 - 9th International Conference on Textile Composites and Inflatable
Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.'
ista: 'Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B,
Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat
flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th
International Conference on Textile Composites and Inflatable Structures, FORM
and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.'
mla: 'Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured
Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of
the International Association for Shell and Spatial Structures; Structural Membranes
2019 - 9th International Conference on Textile Composites and Inflatable Structures,
FORM and FORCE, International Center for Numerical Methods in Engineering,
2019, pp. 509–15.'
short: F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel,
P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th
International Conference on Textile Composites and Inflatable Structures, FORM
and FORCE, International Center for Numerical Methods in Engineering, 2019, pp.
509–515.
conference:
end_date: 2019-10-10
location: Barcelona, Spain
name: 'IASS: International Association for Shell and Spatial Structures'
start_date: 2019-10-07
date_created: 2021-03-21T23:01:21Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-08T11:21:54Z
day: '10'
department:
- _id: BeBi
external_id:
isi:
- '000563497600059'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 509-515
publication: IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International
Conference on Textile Composites and Inflatable Structures, FORM and FORCE
publication_identifier:
isbn:
- '9788412110104'
issn:
- 2518-6582
publication_status: published
publisher: International Center for Numerical Methods in Engineering
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7640'
abstract:
- lang: eng
text: We propose a new model for detecting visual relationships, such as "person
riding motorcycle" or "bottle on table". This task is an important step towards
comprehensive structured mage understanding, going beyond detecting individual
objects. Our main novelty is a Box Attention mechanism that allows to model pairwise
interactions between objects using standard object detection pipelines. The resulting
model is conceptually clean, expressive and relies on well-justified training
and prediction procedures. Moreover, unlike previously proposed approaches, our
model does not introduce any additional complex components or hyperparameters
on top of those already required by the underlying detection model. We conduct
an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating
strong quantitative and qualitative results.
article_number: 1749-1753
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Alina
full_name: Kuznetsova, Alina
last_name: Kuznetsova
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Vittorio
full_name: Ferrari, Vittorio
last_name: Ferrari
citation:
ama: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships
using box attention. In: Proceedings of the 2019 International Conference on
Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217'
apa: 'Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting
visual relationships using box attention. In Proceedings of the 2019 International
Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217'
chicago: Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio
Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings
of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019.
https://doi.org/10.1109/ICCVW.2019.00217.
ieee: A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual
relationships using box attention,” in Proceedings of the 2019 International
Conference on Computer Vision Workshop, Seoul, South Korea, 2019.
ista: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual
relationships using box attention. Proceedings of the 2019 International Conference
on Computer Vision Workshop. ICCVW: International Conference on Computer Vision
Workshop, 1749–1753.'
mla: Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.”
Proceedings of the 2019 International Conference on Computer Vision Workshop,
1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217.
short: A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of
the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.
conference:
end_date: 2019-10-28
location: Seoul, South Korea
name: 'ICCVW: International Conference on Computer Vision Workshop'
start_date: 2019-10-27
date_created: 2020-04-05T22:00:51Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:18:37Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/ICCVW.2019.00217
ec_funded: 1
external_id:
arxiv:
- '1807.02136'
isi:
- '000554591601098'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.02136
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the 2019 International Conference on Computer Vision Workshop
publication_identifier:
isbn:
- '9781728150239'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detecting visual relationships using box attention
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7639'
abstract:
- lang: eng
text: Deep neural networks (DNNs) have become increasingly important due to their
excellent empirical performance on a wide range of problems. However, regularization
is generally achieved by indirect means, largely due to the complex set of functions
defined by a network and the difficulty in measuring function complexity. There
exists no method in the literature for additive regularization based on a norm
of the function, as is classically considered in statistical learning theory.
In this work, we study the tractability of function norms for deep neural networks
with ReLU activations. We provide, to the best of our knowledge, the first proof
in the literature of the NP-hardness of computing function norms of DNNs of 3
or more layers. We also highlight a fundamental difference between shallow and
deep networks. In the light on these results, we propose a new regularization
strategy based on approximate function norms, and show its efficiency on a segmentation
task with a DNN.
article_number: 748-752
article_processing_charge: No
author:
- first_name: Amal
full_name: Rannen-Triki, Amal
last_name: Rannen-Triki
- first_name: Maxim
full_name: Berman, Maxim
last_name: Berman
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Matthew B.
full_name: Blaschko, Matthew B.
last_name: Blaschko
citation:
ama: 'Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural
networks. In: Proceedings of the 2019 International Conference on Computer
Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00097'
apa: 'Rannen-Triki, A., Berman, M., Kolmogorov, V., & Blaschko, M. B. (2019).
Function norms for neural networks. In Proceedings of the 2019 International
Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00097'
chicago: Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko.
“Function Norms for Neural Networks.” In Proceedings of the 2019 International
Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00097.
ieee: A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms
for neural networks,” in Proceedings of the 2019 International Conference on
Computer Vision Workshop, Seoul, South Korea, 2019.
ista: 'Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms
for neural networks. Proceedings of the 2019 International Conference on Computer
Vision Workshop. ICCVW: International Conference on Computer Vision Workshop,
748–752.'
mla: Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” Proceedings
of the 2019 International Conference on Computer Vision Workshop, 748–752,
IEEE, 2019, doi:10.1109/ICCVW.2019.00097.
short: A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings
of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.
conference:
end_date: 2019-10-28
location: Seoul, South Korea
name: 'ICCVW: International Conference on Computer Vision Workshop'
start_date: 2019-10-27
date_created: 2020-04-05T22:00:50Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:19:12Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/ICCVW.2019.00097
external_id:
isi:
- '000554591600090'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
publication: Proceedings of the 2019 International Conference on Computer Vision Workshop
publication_identifier:
isbn:
- '9781728150239'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Function norms for neural networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '8281'
abstract:
- lang: eng
text: We review the history of population genetics, starting with its origins a
century ago from the synthesis between Mendel and Darwin's ideas, through to the
recent development of sophisticated schemes of inference from sequence data, based
on the coalescent. We explain the close relation between the coalescent and a
diffusion process, which we illustrate by their application to understand spatial
structure. We summarise the powerful methods available for analysis of multiple
loci, when linkage equilibrium can be assumed, and then discuss approaches to
the more challenging case, where associations between alleles require that we
follow genotype, rather than allele, frequencies. Though we can hardly cover the
whole of population genetics, we give an overview of the current state of the
subject, and future challenges to it.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding
D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed.
Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4'
apa: Barton, N. H., & Etheridge, A. (2019). Mathematical models in population
genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical
genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4
chicago: Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population
Genetics.” In Handbook of Statistical Genomics, edited by David Balding,
Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.
ieee: N. H. Barton and A. Etheridge, “Mathematical models in population genetics,”
in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and
J. Marioni, Eds. Wiley, 2019, pp. 115–144.
ista: 'Barton NH, Etheridge A. 2019.Mathematical models in population genetics.
In: Handbook of statistical genomics. , 115–144.'
mla: Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population
Genetics.” Handbook of Statistical Genomics, edited by David Balding et
al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.
short: N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.),
Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.
date_created: 2020-08-21T04:25:39Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-09-08T11:24:15Z
day: '29'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/9781119487845.ch4
edition: '4'
editor:
- first_name: David
full_name: Balding, David
last_name: Balding
- first_name: Ida
full_name: Moltke, Ida
last_name: Moltke
- first_name: John
full_name: Marioni, John
last_name: Marioni
external_id:
isi:
- '000261343000003'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 115-144
publication: Handbook of statistical genomics
publication_identifier:
isbn:
- '9781119429142'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Mathematical models in population genetics
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...