---
_id: '1145'
abstract:
- lang: eng
text: Auxin directs plant ontogenesis via differential accumulation within tissues
depending largely on the activity of PIN proteins that mediate auxin efflux from
cells and its directional cell-to-cell transport. Regardless of the developmental
importance of PINs, the structure of these transporters is poorly characterized.
Here, we present experimental data concerning protein topology of plasma membrane-localized
PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters
combined with immunolocalization techniques, we mapped the membrane topology of
PINs and further cross-validated our results using available topology modeling
software. We delineated the topology of PIN1 with two transmembrane (TM) bundles
of five α-helices linked by a large intracellular loop and a C-terminus positioned
outside the cytoplasm. Using constraints derived from our experimental data, we
also provide an updated position of helical regions generating a verisimilitude
model of PIN1. Since the canonical long PINs show a high degree of conservation
in TM domains and auxin transport capacity has been demonstrated for Arabidopsis
representatives of this group, this empirically enhanced topological model of
PIN1 will be an important starting point for further studies on PIN structure–function
relationships. In addition, we have established protocols that can be used to
probe the topology of other plasma membrane proteins in plants. © 2016 The Authors
acknowledgement: This research has been financially supported by the Ministry of Education,
Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N.,
M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]);
Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European
Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G.
Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona
Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E.
Feraru for helpful discussions.
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry
into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010
apa: Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &
Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin
transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010
chicago: Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová,
Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.
ieee: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml,
“Enquiry into the topology of plasma membrane localized PIN auxin transport components,”
Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.
ista: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016.
Enquiry into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 9(11), 1504–1519.
mla: Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell
Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.
short: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml,
Molecular Plant 9 (2016) 1504–1519.
date_created: 2018-12-11T11:50:23Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2021-01-12T06:48:37Z
day: '07'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.molp.2016.08.010
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:22Z
date_updated: 2018-12-12T10:13:22Z
file_id: '5004'
file_name: IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf
file_size: 5005876
relation: main_file
file_date_updated: 2018-12-12T10:13:22Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1504 - 1519
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '6213'
pubrep_id: '746'
quality_controlled: '1'
scopus_import: 1
status: public
title: Enquiry into the topology of plasma membrane localized PIN auxin transport
components
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1147'
abstract:
- lang: eng
text: Apical dominance is one of the fundamental developmental phenomena in plant
biology, which determines the overall architecture of aerial plant parts. Here
we show apex decapitation activated competition for dominance in adjacent upper
and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a
model system to monitor and assess auxin flow, auxin transport channels, and dormancy
and initiation status of axillary buds. Auxin flow was manipulated by lateral
stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid
(TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide
(CHX) treatments, which served to interfere with axillary bud competition. Redirecting
auxin flow to different points influenced which bud formed the outgrowing and
dominant shoot. The obtained results proved that competition between upper and
lower axillary buds as secondary auxin sources is based on the same auxin canalization
principle that operates between the shoot apex and axillary bud. © The Author(s)
2016.
acknowledgement: This research was carried out under the project CEITEC 2020 (LQ1601)
with financial support from the Ministry of Education, Youth and Sports of the Czech
Republic under the National Sustainability Programme II., supported by the project
“CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the
Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).
article_number: '35955'
author:
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Zuzana
full_name: Medved'Ová, Zuzana
last_name: Medved'Ová
- first_name: Petr
full_name: Kalousek, Petr
last_name: Kalousek
- first_name: Natálie
full_name: Matiješčuková, Natálie
last_name: Matiješčuková
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Stanislav
full_name: Procházka, Stanislav
last_name: Procházka
citation:
ama: Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between
axillary buds to restore apical dominance. Scientific Reports. 2016;6.
doi:10.1038/srep35955
apa: Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl,
V., & Procházka, S. (2016). Auxin flow mediated competition between axillary
buds to restore apical dominance. Scientific Reports. Nature Publishing
Group. https://doi.org/10.1038/srep35955
chicago: Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková,
Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition
between Axillary Buds to Restore Apical Dominance.” Scientific Reports.
Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.
ieee: J. Balla et al., “Auxin flow mediated competition between axillary
buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing
Group, 2016.
ista: Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka
S. 2016. Auxin flow mediated competition between axillary buds to restore apical
dominance. Scientific Reports. 6, 35955.
mla: Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds
to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature
Publishing Group, 2016, doi:10.1038/srep35955.
short: J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl,
S. Procházka, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2021-01-12T06:48:38Z
day: '08'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep35955
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:28Z
date_updated: 2018-12-12T10:09:28Z
file_id: '4752'
file_name: IST-2017-745-v1+1_srep35955.pdf
file_size: 1587544
relation: main_file
file_date_updated: 2018-12-12T10:09:28Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6211'
pubrep_id: '745'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin flow mediated competition between axillary buds to restore apical dominance
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1151'
abstract:
- lang: eng
text: Tissue patterning in multicellular organisms is the output of precise spatio–temporal
regulation of gene expression coupled with changes in hormone dynamics. In plants,
the hormone auxin regulates growth and development at every stage of a plant’s
life cycle. Auxin signaling occurs through binding of the auxin molecule to a
TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional
repressor proteins. These are subsequently ubiquitinated and degraded via the
26S proteasome, leading to derepression of auxin response factors (ARFs). How
auxin is able to elicit such a diverse range of developmental responses through
a single signaling module has not yet been resolved. Here we present an alternative
auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through
interactions with process-specific transcription factors. This noncanonical hormonesensing
mechanism exhibits strong preference for the naturally occurring auxin indole
3-acetic acid (IAA) and is important for coordinating growth and patterning in
diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence,
ovule development, and primary branch formation. Disrupting this IAA-sensing ability
induces morphological aberrations with consequences for plant fitness. Therefore,
our findings introduce a novel transcription factor-based mechanism of hormone
perception in plants. © 2016 Simonini et al.
acknowledgement: "We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford,
Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt,
Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds;
Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona
Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are
also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz
Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments
on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1
(Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological
Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1)
to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. "
author:
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Joyita
full_name: Deb, Joyita
last_name: Deb
- first_name: Laila
full_name: Moubayidin, Laila
last_name: Moubayidin
- first_name: Pauline
full_name: Stephenson, Pauline
last_name: Stephenson
- first_name: Manoj
full_name: Valluru, Manoj
last_name: Valluru
- first_name: Alejandra
full_name: Freire Rios, Alejandra
last_name: Freire Rios
- first_name: Karim
full_name: Sorefan, Karim
last_name: Sorefan
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lars
full_name: Östergaard, Lars
last_name: Östergaard
citation:
ama: Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development.
2016;30(20):2286-2296. doi:10.1101/gad.285361.116
apa: Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire
Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116
chicago: Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj
Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars
Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis
in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press,
2016. https://doi.org/10.1101/gad.285361.116.
ieee: S. Simonini et al., “A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30,
no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.
ista: Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan
K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20),
2286–2296.
mla: Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required
for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30,
no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.
short: S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire
Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30
(2016) 2286–2296.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2021-01-12T06:48:39Z
day: '15'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1101/gad.285361.116
external_id:
pmid:
- '27898393'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-25T09:32:55Z
date_updated: 2019-01-25T09:32:55Z
file_id: '5882'
file_name: 2016_GeneDev_Simonini.pdf
file_size: 1419263
relation: main_file
success: 1
file_date_updated: 2019-01-25T09:32:55Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2286 - 2296
pmid: 1
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6207'
quality_controlled: '1'
scopus_import: 1
status: public
title: A noncanonical auxin sensing mechanism is required for organ morphogenesis
in arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2016'
...
---
_id: '1153'
abstract:
- lang: eng
text: Differential cell growth enables flexible organ bending in the presence of
environmental signals such as light or gravity. A prominent example of the developmental
processes based on differential cell growth is the formation of the apical hook
that protects the fragile shoot apical meristem when it breaks through the soil
during germination. Here, we combined in silico and in vivo approaches to identify
a minimal mechanism producing auxin gradient-guided differential growth during
the establishment of the apical hook in the model plant Arabidopsis thaliana.
Computer simulation models based on experimental data demonstrate that asymmetric
expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus
convex (outer) side of the hook suffices to establish an auxin maximum in the
epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism
that translates this maximum into differential growth, and thus curvature, of
the apical hook. Through a combination of experimental and in silico computational
approaches, we have identified the individual contributions of differential cell
elongation and proliferation to defining the apical hook and reveal the role of
auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society
of Plant Biologists. All rights reserved.
acknowledgement: "We thank Martine De Cock and Annick Bleys for help in preparing
the manuscript, Daniel Van Damme for sharing material and stimulating discussion,
and Rudiger Simon for support during revision of the manuscript.\r\nThis work was
supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and
the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural
Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to
P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship
(LT-000209-2014)."
author:
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Marçal
full_name: Gallemí, Marçal
last_name: Gallemí
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Dirk
full_name: Inze, Dirk
last_name: Inze
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Przemysław
full_name: Prusinkiewicz, Przemysław
last_name: Prusinkiewicz
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth
guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477.
doi:10.1105/tpc.15.00569
apa: Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten,
D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical
hook formation in plants. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.15.00569
chicago: Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique
Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz,
and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation
in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.
ieee: P. Žádníková et al., “A model of differential growth guided apical
hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society
of Plant Biologists, pp. 2464–2477, 2016.
ista: Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith
R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential
growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.
mla: Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook
Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of
Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.
short: P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten,
R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016)
2464–2477.
date_created: 2018-12-11T11:50:26Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:48:40Z
day: '01'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1105/tpc.15.00569
ec_funded: 1
intvolume: ' 28'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/
month: '10'
oa: 1
oa_version: Submitted Version
page: 2464 - 2477
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6205'
quality_controlled: '1'
scopus_import: 1
status: public
title: A model of differential growth guided apical hook formation in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1154'
abstract:
- lang: eng
text: "Cellular locomotion is a central hallmark of eukaryotic life. It is governed
by cell-extrinsic molecular factors, which can either emerge in the soluble phase
or as immobilized, often adhesive ligands. To encode for direction, every cue
must be present as a spatial or temporal gradient. Here, we developed a microfluidic
chamber that allows measurement of cell migration in combined response to surface
immobilized and soluble molecular gradients. As a proof of principle we study
the response of dendritic cells to their major guidance cues, chemokines. The
majority of data on chemokine gradient sensing is based on in vitro studies employing
soluble gradients. Despite evidence suggesting that in vivo chemokines are often
immobilized to sugar residues, limited information is available how cells respond
to immobilized chemokines. We tracked migration of dendritic cells towards immobilized
gradients of the chemokine CCL21 and varying superimposed soluble gradients of
CCL19. Differential migratory patterns illustrate the potential of our setup to
quantitatively study the competitive response to both types of gradients. Beyond
chemokines our approach is broadly applicable to alternative systems of chemo-
and haptotaxis such as cells migrating along gradients of adhesion receptor ligands
vs. any soluble cue. \r\n"
acknowledgement: 'This work was supported by the Swiss National Science Foundation
(Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society
(research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF)
to J.S., the European Research Council (grant ERC GA 281556) and a START award from
the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility'
article_number: '36440'
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Veronika
full_name: Bierbaum, Veronika
id: 3FD04378-F248-11E8-B48F-1D18A9856A87
last_name: Bierbaum
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Tino
full_name: Frank, Tino
last_name: Frank
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Savaş
full_name: Tay, Savaş
last_name: Tay
- 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: Matthias
full_name: Mehling, Matthias
id: 3C23B994-F248-11E8-B48F-1D18A9856A87
last_name: Mehling
orcid: 0000-0001-8599-1226
citation:
ama: Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring
cell migration towards substrate bound and soluble chemokine gradients. Scientific
Reports. 2016;6. doi:10.1038/srep36440
apa: Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach,
M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep36440
chicago: Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild,
Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic
Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine
Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.
ieee: J. Schwarz et al., “A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay
S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports. 6,
36440.
mla: Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards
Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol.
6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.
short: J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach,
S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:27Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2021-01-12T06:48:41Z
day: '07'
ddc:
- '579'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
- _id: ToBo
doi: 10.1038/srep36440
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:32Z
date_updated: 2018-12-12T10:09:32Z
file_id: '4756'
file_name: IST-2017-744-v1+1_srep36440.pdf
file_size: 2353456
relation: main_file
file_date_updated: 2018-12-12T10:09:32Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6204'
pubrep_id: '744'
quality_controlled: '1'
scopus_import: 1
status: public
title: A microfluidic device for measuring cell migration towards substrate bound
and soluble chemokine gradients
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1157'
abstract:
- lang: eng
text: We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where
the sample X is an M ×N random matrix whose entries are real independent random
variables with variance 1/N and whereσ is an M × M positive-definite deterministic
matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue
of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class
of populations σ in the sub-critical regime, we show that the distribution of
the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution
under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians
or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.
acknowledgement: "We thank Horng-Tzer Yau for numerous discussions and remarks. We
are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os,
Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the
anonymous referee for carefully reading our manuscript and suggesting several improvements."
author:
- first_name: Ji
full_name: Lee, Ji
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real
sample covariance matrices with general population. Annals of Applied Probability.
2016;26(6):3786-3839. doi:10.1214/16-AAP1193
apa: Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest
eigenvalue of real sample covariance matrices with general population. Annals
of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193
chicago: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest
Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals
of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.
ieee: J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population,” Annals of Applied
Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839,
2016.
ista: Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population. Annals of Applied
Probability. 26(6), 3786–3839.
mla: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue
of Real Sample Covariance Matrices with General Population.” Annals of Applied
Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp.
3786–839, doi:10.1214/16-AAP1193.
short: J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.
date_created: 2018-12-11T11:50:27Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2021-01-12T06:48:43Z
day: '15'
department:
- _id: LaEr
doi: 10.1214/16-AAP1193
ec_funded: 1
intvolume: ' 26'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1409.4979
month: '12'
oa: 1
oa_version: Preprint
page: 3786 - 3839
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6201'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tracy-widom distribution for the largest eigenvalue of real sample covariance
matrices with general population
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '11574'
abstract:
- lang: eng
text: We present new results from the widest narrow-band survey search for Lyα emitters
at z = 5.7, just after reionization. We survey a total of 7 deg2 spread over the
COSMOS, UDS and SA22 fields. We find over 11 000 line emitters, out of which 514
are robust Lyα candidates at z = 5.7 within a volume of 6.3 × 106 Mpc3. Our Lyα
emitters span a wide range in Lyα luminosities, from faint to bright (LLyα ∼ 1042.5–44
erg s−1) and rest-frame equivalent widths (EW0 ∼ 25–1000 Å) in a single, homogeneous
data set. By combining all our fields, we find that the faint end slope of the
z = 5.7 Lyα luminosity function is very steep, with α=−2.3+0.4−0.3. We also present
an updated z = 6.6 Lyα luminosity function, based on comparable volumes and obtained
with the same methods, which we directly compare with that at z = 5.7. We find
a significant decline of the number density of faint Lyα emitters from z = 5.7
to 6.6 (by 0.5 ± 0.1 dex), but no evolution at the bright end/no evolution in
L*. Faint Lyα emitters at z = 6.6 show much more extended haloes than those at
z = 5.7, suggesting that neutral Hydrogen plays an important role, increasing
the scattering and leading to observations missing faint Lyα emission within the
epoch of reionization. Altogether, our results suggest that we are observing patchy
reionization which happens first around the brightest Lyα emitters, allowing the
number densities of those sources to remain unaffected by the increase of neutral
Hydrogen fraction from z ∼ 5 to 7.
acknowledgement: 'We thank the anonymous referee for useful and constructive comments
and suggestions which greatly improved the quality and clarity of our work. The
authors acknowledge financial support from the Netherlands Organisation for Scientific
research (NWO) through a Veni fellowship. SS and DS acknowledge funding from FCT
through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010).
SS also acknowledges support from FCT through the research grants UID/FIS/04434/2013
and PTDC/FIS-AST/2194/2012. JM acknowledges a Huygens PhD fellowship from Leiden
University. Based on observations with the Subaru Telescope (Program IDs: S05B-027,
S06A-025, S06B-010, S07A-013, S07B-008, S08B-008, S09A-017, S14A-086). Based on
observations made with ESO Telescopes at the La Silla Paranal Observatory under
programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam,
a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT)
which is operated by the National Research Council (NRC) of Canada, the Institut
National des Science de l’Univers of the Centre National de la Recherche Scientifique
(CNRS) of France, and the University of Hawaii. This work is based in part on data
products produced at TERAPIX available at the Canadian Astronomy Data Centre as
part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project
of NRC and CNRS. Based on data products from observations made with ESO Telescopes
at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data
products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of
the UltraVISTA consortium. We are grateful to the CFHTLS, COSMOS-UltraVISTA, UKIDSS,
SXDF and COSMOS survey teams. Without these legacy surveys, this research would
have been impossible. The authors wish to recognize and acknowledge the very significant
cultural role and reverence that the summit of Mauna Kea has always had within the
indigenous Hawaiian community. We are most fortunate to have the opportunity to
conduct and explore observations from this mountain. Finally, the authors acknowledge
the unique value of the publicly available programming language PYTHON, including
the NUMPY, PYFITS, MATPLOTLIB, SCIPY and ASTROPY (Astropy Collaboration et al.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sérgio
full_name: Santos, Sérgio
last_name: Santos
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
citation:
ama: 'Santos S, Sobral D, Matthee JJ. The Lyα luminosity function at z= 5.7–6.6
and the steep drop of the faint end: Implications for reionization. Monthly
Notices of the Royal Astronomical Society. 2016;463(2):1678-1691. doi:10.1093/mnras/stw2076'
apa: 'Santos, S., Sobral, D., & Matthee, J. J. (2016). The Lyα luminosity function
at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization.
Monthly Notices of the Royal Astronomical Society. Oxford University Press.
https://doi.org/10.1093/mnras/stw2076'
chicago: 'Santos, Sérgio, David Sobral, and Jorryt J Matthee. “The Lyα Luminosity
Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.”
Monthly Notices of the Royal Astronomical Society. Oxford University Press,
2016. https://doi.org/10.1093/mnras/stw2076.'
ieee: 'S. Santos, D. Sobral, and J. J. Matthee, “The Lyα luminosity function at
z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization,”
Monthly Notices of the Royal Astronomical Society, vol. 463, no. 2. Oxford
University Press, pp. 1678–1691, 2016.'
ista: 'Santos S, Sobral D, Matthee JJ. 2016. The Lyα luminosity function at z= 5.7–6.6
and the steep drop of the faint end: Implications for reionization. Monthly Notices
of the Royal Astronomical Society. 463(2), 1678–1691.'
mla: 'Santos, Sérgio, et al. “The Lyα Luminosity Function at Z= 5.7–6.6 and the
Steep Drop of the Faint End: Implications for Reionization.” Monthly Notices
of the Royal Astronomical Society, vol. 463, no. 2, Oxford University Press,
2016, pp. 1678–91, doi:10.1093/mnras/stw2076.'
short: S. Santos, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical
Society 463 (2016) 1678–1691.
date_created: 2022-07-13T10:08:20Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2022-08-19T08:09:54Z
day: '01'
doi: 10.1093/mnras/stw2076
extern: '1'
external_id:
arxiv:
- '1606.07435'
intvolume: ' 463'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: high-redshift'
- 'galaxies: luminosity function'
- mass function
- 'cosmology: observations'
- dark ages
- reionization
- first stars
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.07435
month: '12'
oa: 1
oa_version: Preprint
page: 1678-1691
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint
end: Implications for reionization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 463
year: '2016'
...
---
_id: '11575'
abstract:
- lang: eng
text: We investigate correlations between different physical properties of star-forming
galaxies in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE)
cosmological hydrodynamical simulation suite over the redshift range 0 ≤ z ≤ 4.5.
A principal component analysis reveals that neutral gas fraction (fgas,neutral),
stellar mass (Mstellar) and star formation rate (SFR) account for most of the
variance seen in the population, with galaxies tracing a two-dimensional, nearly
flat, surface in the three-dimensional space of fgas, neutral–Mstellar–SFR with
little scatter. The location of this plane varies little with redshift, whereas
galaxies themselves move along the plane as their fgas, neutral and SFR drop with
redshift. The positions of galaxies along the plane are highly correlated with
gas metallicity. The metallicity can therefore be robustly predicted from fgas,
neutral, or from the Mstellar and SFR. We argue that the appearance of this ‘Fundamental
Plane of star formation’ is a consequence of self-regulation, with the plane's
curvature set by the dependence of the SFR on gas density and metallicity. We
analyse a large compilation of observations spanning the redshift range 0 ≲ z
≲ 3, and find that such a plane is also present in the data. The properties of
the observed Fundamental Plane of star formation are in good agreement with EAGLE's
predictions.
acknowledgement: We thank Luca Cortese, Matt Bothwell, Paola Santini and Tim Davis
for providing observational data sets, and Aaron Robotham, Luca Cortese and Barbara
Catinella for useful discussions. CdPL is funded by a Discovery Early Career Researcher
Award (DE150100618). CdPL also thanks the MERAC Foundation for a Postdoctoral Research
Award. This work used the DiRAC Data Centric system at Durham University, operated
by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility
(www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital
grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant
ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure.
Support was also received via the Interuniversity Attraction Poles Programme initiated
by the Belgian Science Policy Office ([AP P7/08 CHARM]), the National Science Foundation
under grant no. NSF PHY11-25915, and the UK Science and Technology Facilities Council
(grant numbers ST/F001166/1 and ST/I000976/1) via rolling and consolidating grants
awarded to the ICC. The research was supported in part by the European Research
Council under the European Union‘s Seventh Framework Programme (FP7/2007-2013)/ERC
grant agreement 278594-GasAroundGalaxies.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Claudia del P.
full_name: Lagos, Claudia del P.
last_name: Lagos
- first_name: Tom
full_name: Theuns, Tom
last_name: Theuns
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
- first_name: Michelle
full_name: Furlong, Michelle
last_name: Furlong
- first_name: Richard G.
full_name: Bower, Richard G.
last_name: Bower
- first_name: Matthieu
full_name: Schaller, Matthieu
last_name: Schaller
- first_name: Robert A.
full_name: Crain, Robert A.
last_name: Crain
- first_name: James W.
full_name: Trayford, James W.
last_name: Trayford
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
citation:
ama: Lagos C del P, Theuns T, Schaye J, et al. The Fundamental Plane of star formation
in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices
of the Royal Astronomical Society. 2016;459(3):2632-2650. doi:10.1093/mnras/stw717
apa: Lagos, C. del P., Theuns, T., Schaye, J., Furlong, M., Bower, R. G., Schaller,
M., … Matthee, J. J. (2016). The Fundamental Plane of star formation in galaxies
revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal
Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw717
chicago: Lagos, Claudia del P., Tom Theuns, Joop Schaye, Michelle Furlong, Richard
G. Bower, Matthieu Schaller, Robert A. Crain, James W. Trayford, and Jorryt J
Matthee. “The Fundamental Plane of Star Formation in Galaxies Revealed by the
EAGLE Hydrodynamical Simulations.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw717.
ieee: C. del P. Lagos et al., “The Fundamental Plane of star formation in
galaxies revealed by the EAGLE hydrodynamical simulations,” Monthly Notices
of the Royal Astronomical Society, vol. 459, no. 3. Oxford University Press,
pp. 2632–2650, 2016.
ista: Lagos C del P, Theuns T, Schaye J, Furlong M, Bower RG, Schaller M, Crain
RA, Trayford JW, Matthee JJ. 2016. The Fundamental Plane of star formation in
galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of
the Royal Astronomical Society. 459(3), 2632–2650.
mla: Lagos, Claudia del P., et al. “The Fundamental Plane of Star Formation in Galaxies
Revealed by the EAGLE Hydrodynamical Simulations.” Monthly Notices of the Royal
Astronomical Society, vol. 459, no. 3, Oxford University Press, 2016, pp.
2632–50, doi:10.1093/mnras/stw717.
short: C. del P. Lagos, T. Theuns, J. Schaye, M. Furlong, R.G. Bower, M. Schaller,
R.A. Crain, J.W. Trayford, J.J. Matthee, Monthly Notices of the Royal Astronomical
Society 459 (2016) 2632–2650.
date_created: 2022-07-13T10:21:24Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2022-08-19T08:12:07Z
day: '01'
doi: 10.1093/mnras/stw717
extern: '1'
external_id:
arxiv:
- '1510.08067'
intvolume: ' 459'
issue: '3'
keyword:
- Space and Planetary Science
- 'Astronomy and Astrophysics stars: formation'
- 'ISM: evolution'
- 'galaxies: evolution'
- 'galaxies: formation'
- 'galaxies: ISM'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08067
month: '07'
oa: 1
oa_version: Preprint
page: 2632-2650
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical
simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 459
year: '2016'
...
---
_id: '11576'
abstract:
- lang: eng
text: We use new near-infrared spectroscopic observations to investigate the nature
and evolution of the most luminous Hα emitters at z ∼ 0.8–2.23, which evolve strongly
in number density over this period, and compare them to more typical Hα emitters.
We study 59 luminous Hα emitters with LHα > L∗Hα, roughly equally split per redshift
slice at z ∼ 0.8, 1.47 and 2.23 from the HiZELS and CF-HiZELS surveys. We find
that, overall, 30 ± 8 per cent are active galactic nuclei [AGNs; 80 ± 30 per cent
of these AGNs are broad-line AGNs, BL-AGNs], and we find little to no evolution
in the AGN fraction with redshift, within the errors. However, the AGN fraction
increases strongly with Hα luminosity and correlates best with LHα/L∗Hα(z). While
LHα ≤ L∗Hα(z) Hα emitters are largely dominated by star-forming galaxies (>80
per cent), the most luminous Hα emitters (LHα>10L∗Hα(z)) at any cosmic time
are essentially all BL-AGN. Using our AGN-decontaminated sample of luminous star-forming
galaxies, and integrating down to a fixed Hα luminosity, we find a factor of ∼1300
evolution in the star formation rate density from z = 0 to 2.23. This is much
stronger than the evolution from typical Hα star-forming galaxies and in line
with the evolution seen for constant luminosity cuts used to select ‘ultraluminous’
infrared galaxies and/or sub-millimetre galaxies. By taking into account the evolution
in the typical Hα luminosity, we show that the most strongly star-forming Hα-selected
galaxies at any epoch (LHα>L∗Hα(z)) contribute the same fractional amount of
≈15 per cent to the total star formation rate density, at least up to z = 2.23.
acknowledgement: "The authors would like to thank the anonymous reviewer for the many
helpful comments and suggestions which greatly improved the clarity and quality
of this work. DS and SAK acknowledge financial support from the Netherlands Organisation
for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding
from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010)
and from FCT grant PEst-OE/FIS/UI2751/2014. Part of this project was undertaken
during the inaugural Leiden/ESA Astrophysics Program for Summer Students (LEAPS).
IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator
programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. CH acknowledges
support from STFC. Based on observations made with ESO Telescopes at the La Silla
Paranal Observatory under programme ID 087.A-0337 and ID 089.A-0965. Also based
on data from the Telescopio Nazionale Galileo, with time awarded through OPTICON
programmes 2011A/026 and 2012A020 and the William Herschel Telescope under programme
W12BN007. The William Herschel Telescope is operated on the island of La Palma by
the Isaac Newton Group in the Spanish\r\nObservatorio del Roque de los Muchachos
of the Instituto de Astrofisica de Canarias. The authors wish to thank all the help
given by the telescope staff from all the observatories used in this study: ESO
staff in La Silla, and the TNG and WHT staff in La Palma. This publication makes
use of data products from the Two Micron All-Sky Survey, which is a joint project
of the University of Massachusetts and the Infrared Processing and Analysis Center/California
Institute of Technology, funded by the National Aeronautics and Space Administration
and the National Science Foundation."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Saul A.
full_name: Kohn, Saul A.
last_name: Kohn
- first_name: Philip N.
full_name: Best, Philip N.
last_name: Best
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: Chris M.
full_name: Harrison, Chris M.
last_name: Harrison
- first_name: John
full_name: Stott, John
last_name: Stott
- first_name: João
full_name: Calhau, João
last_name: Calhau
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
citation:
ama: 'Sobral D, Kohn SA, Best PN, et al. The most luminous H α emitters at z ∼ 0.8–2.23
from HiZELS: Evolution of AGN and star-forming galaxies. Monthly Notices of
the Royal Astronomical Society. 2016;457(2):1739-1752. doi:10.1093/mnras/stw022'
apa: 'Sobral, D., Kohn, S. A., Best, P. N., Smail, I., Harrison, C. M., Stott, J.,
… Matthee, J. J. (2016). The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS:
Evolution of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical
Society. Oxford University Press. https://doi.org/10.1093/mnras/stw022'
chicago: 'Sobral, David, Saul A. Kohn, Philip N. Best, Ian Smail, Chris M. Harrison,
John Stott, João Calhau, and Jorryt J Matthee. “The Most Luminous H α Emitters
at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and Star-Forming Galaxies.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2016.
https://doi.org/10.1093/mnras/stw022.'
ieee: 'D. Sobral et al., “The most luminous H α emitters at z ∼ 0.8–2.23
from HiZELS: Evolution of AGN and star-forming galaxies,” Monthly Notices of
the Royal Astronomical Society, vol. 457, no. 2. Oxford University Press,
pp. 1739–1752, 2016.'
ista: 'Sobral D, Kohn SA, Best PN, Smail I, Harrison CM, Stott J, Calhau J, Matthee
JJ. 2016. The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution
of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical Society.
457(2), 1739–1752.'
mla: 'Sobral, David, et al. “The Most Luminous H α Emitters at z ∼ 0.8–2.23 from
HiZELS: Evolution of AGN and Star-Forming Galaxies.” Monthly Notices of the
Royal Astronomical Society, vol. 457, no. 2, Oxford University Press, 2016,
pp. 1739–52, doi:10.1093/mnras/stw022.'
short: D. Sobral, S.A. Kohn, P.N. Best, I. Smail, C.M. Harrison, J. Stott, J. Calhau,
J.J. Matthee, Monthly Notices of the Royal Astronomical Society 457 (2016) 1739–1752.
date_created: 2022-07-13T12:50:36Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2022-08-19T08:15:21Z
day: '01'
doi: 10.1093/mnras/stw022
extern: '1'
external_id:
arxiv:
- '1601.02266'
intvolume: ' 457'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'cosmology: observations'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.02266
month: '04'
oa: 1
oa_version: Preprint
page: 1739-1752
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN
and star-forming galaxies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 457
year: '2016'
...
---
_id: '11578'
abstract:
- lang: eng
text: We present the first results from our CAlibrating LYMan α with Hα (CALYMHA)
pilot survey at the Isaac Newton Telescope. We measure Lyα emission for 488 Hα
selected galaxies at z = 2.23 from High-z Emission Line Survey in the COSMOS and
UDS fields with a specially designed narrow-band filter (λc = 3918 Å, Δλ = 52
Å). We find 17 dual Hα-Lyα emitters [fLyα > 5 × 10−17 erg s−1 cm−2, of which five
are X-ray active galactic nuclei (AGN)]. For star-forming galaxies, we find a
range of Lyα escape fractions (fesc, measured with 3 arcsec apertures) from 2
to 30 per cent. These galaxies have masses from 3 × 108 M⊙ to 1011 M⊙ and dust
attenuations E(B − V) = 0–0.5. Using stacking, we measure a median escape fraction
of 1.6 ± 0.5 per cent (4.0 ± 1.0 per cent without correcting Hα for dust), but
show that this depends on galaxy properties. The stacked fesc tends to decrease
with increasing star formation rate and dust attenuation. However, at the highest
masses and dust attenuations, we detect individual galaxies with fesc much higher
than the typical values from stacking, indicating significant scatter in the values
of fesc. Relations between fesc and UV slope are bimodal, with high fesc for either
the bluest or reddest galaxies. We speculate that this bimodality and large scatter
in the values of fesc is due to additional physical mechanisms such as outflows
facilitating fesc for dusty/massive systems. Lyα is significantly more extended
than Hα and the UV. fesc continues to increase up to at least 20 kpc (3σ, 40 kpc
[2σ]) for typical star-forming galaxies and thus the aperture is the most important
predictor of fesc.
acknowledgement: "We thank the anonymous referee for constructive comments and suggestions
which have improved the quality of this work. JM acknowledges the support of a Huygens
PhD fellowship from Leiden University. DS and JM acknowledge financial support from
the Netherlands Organization for Scientific research (NWO) through a Veni fellowship,
and DS from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010)
and from FCT grant PEst-OE/FIS/UI2751/2014. IO acknowledges support from the European
Research Council (ERC) in the form of Advanced Investigator Programme, COSMICISM,
321302. HR acknowledges support from the ERC Advanced Investigator programme NewClusters
321271. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator
programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. APA acknowledges
support from the Fundac¸ao para a Ciencia e para a Tecnologia (FCT) through the
Fellowship SFRH/BD/52706/2014.\r\nBased on observations made with the Isaac Newton
Telescope (proposals 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118)
operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio
del Roque de los Muchachos of the Instituto de Astrof´ısica de Canarias. We acknowledge
the tremendous work that has been done by both COSMOS and UKIDSS UDS/SXDF teams
in assembling such large, state-ofthe-art multi-wavelength data sets over such wide
areas, as those have been crucial for the results presented in this paper. The sample
of HAEs is publicly available from Sobral et al. (2013).\r\nWe have benefited greatly
from the publically available programming language PYTHON, including the NUMPY,
MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert
& Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the
imaging tools SEXTRACTOR, SWARP and SCAMP (Bertin & Arnouts 1996; Bertin 2006, 2010)
and the TOPCAT analysis program (Taylor 2005)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: David
full_name: Sobral, David
last_name: Sobral
- first_name: Iván
full_name: Oteo, Iván
last_name: Oteo
- first_name: Philip
full_name: Best, Philip
last_name: Best
- first_name: Ian
full_name: Smail, Ian
last_name: Smail
- first_name: Huub
full_name: Röttgering, Huub
last_name: Röttgering
- first_name: Ana
full_name: Paulino-Afonso, Ana
last_name: Paulino-Afonso
citation:
ama: 'Matthee JJ, Sobral D, Oteo I, et al. The CALYMHA survey: Lyα escape fraction
and its dependence on galaxy properties at z = 2.23. Monthly Notices of the
Royal Astronomical Society. 2016;458(1):449-467. doi:10.1093/mnras/stw322'
apa: 'Matthee, J. J., Sobral, D., Oteo, I., Best, P., Smail, I., Röttgering, H.,
& Paulino-Afonso, A. (2016). The CALYMHA survey: Lyα escape fraction and its
dependence on galaxy properties at z = 2.23. Monthly Notices of the Royal Astronomical
Society. Oxford University Press. https://doi.org/10.1093/mnras/stw322'
chicago: 'Matthee, Jorryt J, David Sobral, Iván Oteo, Philip Best, Ian Smail, Huub
Röttgering, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Escape Fraction and
Its Dependence on Galaxy Properties at z = 2.23.” Monthly Notices of the Royal
Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw322.'
ieee: 'J. J. Matthee et al., “The CALYMHA survey: Lyα escape fraction and
its dependence on galaxy properties at z = 2.23,” Monthly Notices of the Royal
Astronomical Society, vol. 458, no. 1. Oxford University Press, pp. 449–467,
2016.'
ista: 'Matthee JJ, Sobral D, Oteo I, Best P, Smail I, Röttgering H, Paulino-Afonso
A. 2016. The CALYMHA survey: Lyα escape fraction and its dependence on galaxy
properties at z = 2.23. Monthly Notices of the Royal Astronomical Society. 458(1),
449–467.'
mla: 'Matthee, Jorryt J., et al. “The CALYMHA Survey: Lyα Escape Fraction and Its
Dependence on Galaxy Properties at z = 2.23.” Monthly Notices of the Royal
Astronomical Society, vol. 458, no. 1, Oxford University Press, 2016, pp.
449–67, doi:10.1093/mnras/stw322.'
short: J.J. Matthee, D. Sobral, I. Oteo, P. Best, I. Smail, H. Röttgering, A. Paulino-Afonso,
Monthly Notices of the Royal Astronomical Society 458 (2016) 449–467.
date_created: 2022-07-14T08:51:37Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2022-08-19T08:17:19Z
day: '01'
doi: 10.1093/mnras/stw322
extern: '1'
external_id:
arxiv:
- '1602.02756'
intvolume: ' 458'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'galaxies: ISM'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02756
month: '05'
oa: 1
oa_version: Preprint
page: 449-467
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The CALYMHA survey: Lyα escape fraction and its dependence on galaxy properties
at z = 2.23'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 458
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1164'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, … , Ck with common center c, and edges are drawn radially: every edge
intersects every circle centered at c at most once. G is radial planar if it has
a radial embedding, that is, a crossing-free radial drawing. If the vertices of
G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. A pair of edges e and f in a graph is independent if e and
f do not share a vertex. We show that a graph G is radial planar if G has a radial
drawing in which every two independent edges cross an even number of times; the
radial embedding has the same leveling as the radial drawing. In other words,
we establish the strong Hanani-Tutte theorem for radial planarity. This characterization
yields a very simple algorithm for radial planarity testing.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In:
Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial
planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and
Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity
II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece,
2016, vol. 9801, pp. 468–481.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity
II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801,
Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:29Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-02-23T10:05:57Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_36
ec_funded: 1
external_id:
arxiv:
- '1608.08662'
intvolume: ' 9801'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.08662
month: '12'
oa: 1
oa_version: Preprint
page: 468 - 481
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6193'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1595'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity II
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9801
year: '2016'
...
---
_id: '1165'
abstract:
- lang: eng
text: We show that c-planarity is solvable in quadratic time for flat clustered
graphs with three clusters if the combinatorial embedding of the underlying graph
is fixed. In simpler graph-theoretical terms our result can be viewed as follows.
Given a graph G with the vertex set partitioned into three parts embedded on a
2-sphere, our algorithm decides if we can augment G by adding edges without creating
an edge-crossing so that in the resulting spherical graph the vertices of each
part induce a connected sub-graph. We proceed by a reduction to the problem of
testing the existence of a perfect matching in planar bipartite graphs. We formulate
our result in a slightly more general setting of cyclic clustered graphs, i.e.,
the simple graph obtained by contracting each cluster, where we disregard loops
and multi-edges, is a cycle.
acknowledgement: "R. Fulek—The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI
would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions
that helped to improve the presentation of the result."
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer;
2016:94-106. doi:10.1007/978-3-319-50106-2_8'
apa: 'Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp.
94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens,
Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8'
chicago: Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106.
Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.
ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD:
Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp.
94–106.'
ista: 'Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing
and Network Visualization, LNCS, vol. 9801, 94–106.'
mla: Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801,
Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8.
short: R. Fulek, in:, Springer, 2016, pp. 94–106.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-09-27T12:14:48Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_8
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.01346
month: '12'
oa: 1
oa_version: Preprint
page: 94 - 106
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6192'
quality_controlled: '1'
related_material:
record:
- id: '794'
relation: later_version
status: public
scopus_import: 1
status: public
title: C-planarity of embedded cyclic c-graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '9801 '
year: '2016'
...
---
_id: '1167'
abstract:
- lang: eng
text: Evolutionary pathways describe trajectories of biological evolution in the
space of different variants of organisms (genotypes). The probability of existence
and the number of evolutionary pathways that lead from a given genotype to a better-adapted
genotype are important measures of accessibility of local fitness optima and the
reproducibility of evolution. Both quantities have been studied in simple mathematical
models where genotypes are represented as binary sequences of two types of basic
units, and the network of permitted mutations between the genotypes is a hypercube
graph. However, it is unclear how these results translate to the biologically
relevant case in which genotypes are represented by sequences of more than two
units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the
mutational graph is not the hypercube. Here we investigate accessibility of the
best-adapted genotype in the general case of K > 2 units. Using computer generated
and experimental fitness landscapes we show that accessibility of the global fitness
maximum increases with K and can be much higher than for binary sequences. The
increase in accessibility comes from the increase in the number of indirect trajectories
exploited by evolution for higher K. As one of the consequences, the fraction
of genotypes that are accessible increases by three orders of magnitude when the
number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes.
This suggests that evolution can follow many different trajectories on such landscapes
and the reconstruction of evolutionary pathways from experimental data might be
an extremely difficult task.
acknowledgement: MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107.
BW was supported by the Scottish Government/Royal Society of Edinburgh Personal
Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading
the manuscript.
article_number: e1005218
article_processing_charge: No
author:
- 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: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational
Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the
Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational
Networks.” PLoS Computational Biology. Public Library of Science, 2016.
https://doi.org/10.1371/journal.pcbi.1005218.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks,” PLoS
Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational Biology.
12(12), e1005218.
mla: Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility
of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational
Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.
short: M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-23T14:11:22Z
day: '09'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218
file:
- access_level: open_access
checksum: 84f44ae92866c52ff1ca8a574558dca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:08Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4926'
file_name: IST-2017-740-v1+1_journal.pcbi.1005218.pdf
file_size: 3822299
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6190'
pubrep_id: '740'
quality_controlled: '1'
related_material:
record:
- id: '9866'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Beyond the hypercube evolutionary accessibility of fitness landscapes with
realistic mutational networks
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 12
year: '2016'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1177'
abstract:
- lang: eng
text: Boldyreva, Palacio and Warinschi introduced a multiple forking game as an
extension of general forking. The notion of (multiple) forking is a useful abstraction
from the actual simulation of cryptographic scheme to the adversary in a security
reduction, and is achieved through the intermediary of a so-called wrapper algorithm.
Multiple forking has turned out to be a useful tool in the security argument of
several cryptographic protocols. However, a reduction employing multiple forking
incurs a significant degradation of (Formula presented.) , where (Formula presented.)
denotes the upper bound on the underlying random oracle calls and (Formula presented.)
, the number of forkings. In this work we take a closer look at the reasons for
the degradation with a tighter security bound in mind. We nail down the exact
set of conditions for success in the multiple forking game. A careful analysis
of the cryptographic schemes and corresponding security reduction employing multiple
forking leads to the formulation of ‘dependence’ and ‘independence’ conditions
pertaining to the output of the wrapper in different rounds. Based on the (in)dependence
conditions we propose a general framework of multiple forking and a General Multiple
Forking Lemma. Leveraging (in)dependence to the full allows us to improve the
degradation factor in the multiple forking game by a factor of (Formula presented.).
By implication, the cost of a single forking involving two random oracles (augmented
forking) matches that involving a single random oracle (elementary forking). Finally,
we study the effect of these observations on the concrete security of existing
schemes employing multiple forking. We conclude that by careful design of the
protocol (and the wrapper in the security reduction) it is possible to harness
our observations to the full extent.
acknowledgement: "We are grateful to the anonymous reviewers for their insightful
comments. The\r\ndetailed reports helped us a lot to address the technical mistakes
as well as to improve the overall presentation of the paper."
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Sanjit
full_name: Chatterjee, Sanjit
last_name: Chatterjee
citation:
ama: 'Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging
(in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362.
doi:10.1007/s00453-015-9997-6'
apa: 'Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. Springer.
https://doi.org/10.1007/s00453-015-9997-6'
chicago: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer,
2016. https://doi.org/10.1007/s00453-015-9997-6.'
ieee: 'C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74,
no. 4. Springer, pp. 1321–1362, 2016.'
ista: 'Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.'
mla: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74,
no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.'
short: C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.
date_created: 2018-12-11T11:50:33Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:48:52Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00453-015-9997-6
intvolume: ' 74'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2013/651
month: '04'
oa: 1
oa_version: Submitted Version
page: 1321 - 1362
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6177'
quality_controlled: '1'
status: public
title: 'A closer look at multiple-forking: Leveraging (in)dependence for a tighter
bound'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2016'
...
---
_id: '1179'
abstract:
- lang: eng
text: "Computational notions of entropy have recently found many applications, including
leakage-resilient cryptography, deterministic encryption or memory delegation.
The two main types of results which make computational notions so useful are (1)
Chain rules, which quantify by how much the computational entropy of a variable
decreases if conditioned on some other variable (2) Transformations, which quantify
to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and
transformations typically lose a significant amount in quality of the entropy,
and are the reason why applying these results one gets rather weak quantitative
security bounds. In this paper we for the first time prove lower bounds in this
context, showing that existing results for transformations are, unfortunately,
basically optimal for non-adaptive black-box reductions (and it’s hard to imagine
how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable
X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y
with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby
distinguishing circuits of size s. A weaker notion is Metric entropy, where we
switch quantifiers, and only require that for every distinguisher of size s, such
a Y exists.\r\n\r\nWe first describe our result concerning transformations. By
definition, HILL implies Metric without any loss in quality. Metric entropy often
comes up in applications, but must be transformed to HILL for meaningful security
guarantees. The best known result states that if a variable X has k bits of Metric
entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2).
We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary.
In fact, we show the stronger result that this loss is already necessary when
transforming so called deterministic real valued Metric entropy to randomised
boolean Metric (both these variants of Metric entropy are implied by HILL without
loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has
k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length
m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We
show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still
leaves a gap of ϵ between the known bound and our lower bound."
acknowledgement: "K. Pietrzak—Supported by the European Research Council consolidator
grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland
(2015/17/N/ST6/03564)."
alternative_title:
- LNCS
author:
- 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: Skorski
full_name: Maciej, Skorski
last_name: Maciej
citation:
ama: 'Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations.
In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8'
apa: 'Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for
chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC:
Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8'
chicago: 'Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.'
ieee: 'K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules
and transformations,” presented at the TCC: Theory of Cryptography Conference,
Beijing, China, 2016, vol. 9985, pp. 183–203.'
ista: 'Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules
and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985,
183–203.'
mla: 'Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203,
doi:10.1007/978-3-662-53641-4_8.'
short: K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.
conference:
end_date: 2016-11-03
location: Beijing, China
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-10-31
date_created: 2018-12-11T11:50:34Z
date_published: 2016-10-22T00:00:00Z
date_updated: 2021-01-12T06:48:53Z
day: '22'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53641-4_8
ec_funded: 1
intvolume: ' 9985'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/159
month: '10'
oa: 1
oa_version: Preprint
page: 183 - 203
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6175'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Pseudoentropy: Lower-bounds for chain rules and transformations'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9985
year: '2016'
...
---
_id: '786'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers prefer to treat
concurrent code as if it were wait-free, guaranteeing that all operations always
make progress. Unfortunately, designing wait-free algorithms is generally a very
complex task, and the resulting algorithms are not always efficient. Although
obtaining efficient wait-free algorithms has been a long-time goal for the theory
community, most nonblocking commercial code is only lock-free. This article suggests
a simple solution to this problem.We show that for a large class of lock-free
algorithms, under scheduling conditions that approximate those found in commercial
hardware architectures, lock-free algorithms behave as if they are wait-free.
In other words, programmers can continue to design simple lock-free algorithms
instead of complex wait-free ones, and in practice, they will get wait-free progress.
Our main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes to the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1 but that in
fact a general subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes. To the best
of our knowledge, this is the first attempt to analyze progress conditions, typically
stated in relation to a worst-case adversary, in a stochastic model capturing
their expected asymptotic behavior.
acknowledgement: Part of this work was performed while the first author was a postdoctoral
associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program,
NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the
Oracle and Intel corporations. The second author was supported in part by ISF grant
1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926,
IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923,
and by equipment grants from Intel Corporation.
article_processing_charge: No
arxiv: 1
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: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 2016;63(4). doi:10.1145/2903136
apa: Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2016). Are lock free
concurrent algorithms practically wait free . Journal of the ACM. ACM.
https://doi.org/10.1145/2903136
chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free
Concurrent Algorithms Practically Wait Free .” Journal of the ACM. ACM,
2016. https://doi.org/10.1145/2903136.
ieee: D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent
algorithms practically wait free ,” Journal of the ACM, vol. 63, no. 4.
ACM, 2016.
ista: Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 63(4).
mla: Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically
Wait Free .” Journal of the ACM, vol. 63, no. 4, ACM, 2016, doi:10.1145/2903136.
short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016).
date_created: 2018-12-11T11:48:29Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-02-23T13:19:04Z
day: '01'
doi: 10.1145/2903136
extern: '1'
external_id:
arxiv:
- '1311.3200'
intvolume: ' 63'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3200
month: '09'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '6870'
quality_controlled: '1'
status: public
title: 'Are lock free concurrent algorithms practically wait free '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2016'
...
---
_id: '8020'
abstract:
- lang: eng
text: Balance of cortical excitation and inhibition (EI) is thought to be disrupted
in several neuropsychiatric conditions, yet it is not clear how it is maintained
in the healthy human brain. When EI balance is disturbed during learning and memory
in animal models, it can be restabilized via formation of inhibitory replicas
of newly formed excitatory connections. Here we assess evidence for such selective
inhibitory rebalancing in humans. Using fMRI repetition suppression we measure
newly formed cortical associations in the human brain. We show that expression
of these associations reduces over time despite persistence in behavior, consistent
with inhibitory rebalancing. To test this, we modulated excitation/inhibition
balance with transcranial direct current stimulation (tDCS). Using ultra-high-field
(7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations
to be re-expressed. This suggests that in humans associative memories are stored
in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory
connections are unmasked.
article_processing_charge: No
article_type: original
author:
- first_name: H.C.
full_name: Barron, H.C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: U.E.
full_name: Emir, U.E.
last_name: Emir
- first_name: T.R.
full_name: Makin, T.R.
last_name: Makin
- first_name: J.
full_name: O’Shea, J.
last_name: O’Shea
- first_name: S.
full_name: Clare, S.
last_name: Clare
- first_name: S.
full_name: Jbabdi, S.
last_name: Jbabdi
- first_name: R.J.
full_name: Dolan, R.J.
last_name: Dolan
- first_name: T.E.J.
full_name: Behrens, T.E.J.
last_name: Behrens
citation:
ama: Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections
in human cortex to reveal dormant cortical memories. Neuron. 2016;90(1):191-203.
doi:10.1016/j.neuron.2016.02.031
apa: Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare,
S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.02.031
chicago: Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare,
S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections
in Human Cortex to Reveal Dormant Cortical Memories.” Neuron. Elsevier,
2016. https://doi.org/10.1016/j.neuron.2016.02.031.
ieee: H. C. Barron et al., “Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories,” Neuron, vol. 90, no. 1. Elsevier,
pp. 191–203, 2016.
ista: Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan
RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex
to reveal dormant cortical memories. Neuron. 90(1), 191–203.
mla: Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex
to Reveal Dormant Cortical Memories.” Neuron, vol. 90, no. 1, Elsevier,
2016, pp. 191–203, doi:10.1016/j.neuron.2016.02.031.
short: H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S.
Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.
date_created: 2020-06-25T13:05:33Z
date_published: 2016-04-06T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '06'
ddc:
- '570'
doi: 10.1016/j.neuron.2016.02.031
extern: '1'
external_id:
pmid:
- '26996082'
file:
- access_level: open_access
checksum: 9ce7a1c64986dce0435c070285a7ef9b
content_type: application/pdf
creator: cziletti
date_created: 2020-07-09T09:57:04Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8104'
file_name: 2016_Neuron_Barron.pdf
file_size: 5334136
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 90'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 191-203
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Unmasking latent inhibitory connections in human cortex to reveal dormant cortical
memories
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 90
year: '2016'
...
---
_id: '8094'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. The idea is that the controller controls the world---the body plus
its environment---as reliably as possible. This paper focuses on new lines of
self-organization for developmental robotics. We apply the recently developed
differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder
system from the Myorobotics toolkit. In the experiments, we observe a vast variety
of self-organized behavior patterns: when left alone, the arm realizes pseudo-random
sequences of different poses. By applying physical forces, the system can be entrained
into definite motion patterns like wiping a table. Most interestingly, after attaching
an object, the controller gets in a functional resonance with the object''s internal
dynamics, starting to shake spontaneously bottles half-filled with water or sensitively
driving an attached pendulum into a circular mode. When attached to the crank
of a wheel the neural system independently discovers how to rotate it. In this
way, the robot discovers affordances of objects its body is interacting with.'
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Rafael
full_name: Hostettler, Rafael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon
driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial
Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized
control of an tendon driven arm by differential extrinsic plasticity. In Proceedings
of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico:
MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029'
chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized
Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings
of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control
of an tendon driven arm by differential extrinsic plasticity,” in Proceedings
of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp.
142–143.
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of
an tendon driven arm by differential extrinsic plasticity. Proceedings of the
Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on
the Synthesis and Simulation of Living Systems vol. 28, 142–143.'
mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by
Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference
2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial
Life Conference 2016, MIT Press, 2016, pp. 142–143.
conference:
end_date: 2016-07-08
location: Cancun, Mexico
name: 'ALIFE 2016: 15th International Conference on the Synthesis and Simulation
of Living Systems'
start_date: 2016-07-04
date_created: 2020-07-05T22:00:47Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:16:53Z
day: '01'
ddc:
- '610'
department:
- _id: ChLa
- _id: GaTk
doi: 10.7551/978-0-262-33936-0-ch029
ec_funded: 1
file:
- access_level: open_access
checksum: cff63e7a4b8ac466ba51a9c84153a940
content_type: application/pdf
creator: cziletti
date_created: 2020-07-06T12:59:09Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8096'
file_name: 2016_ProcALIFE_Martius.pdf
file_size: 678670
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 28'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 142-143
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the Artificial Life Conference 2016
publication_identifier:
isbn:
- '9780262339360'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Self-organized control of an tendon driven arm by differential extrinsic plasticity
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2016'
...