---
_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: '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: '1182'
abstract:
- lang: eng
text: 'Balanced knockout tournaments are ubiquitous in sports competitions and are
also used in decisionmaking and elections. The traditional computational question,
that asks to compute a draw (optimal draw) that maximizes the winning probability
for a distinguished player, has received a lot of attention. Previous works consider
the problem where the pairwise winning probabilities are known precisely, while
we study how robust is the winning probability with respect to small errors in
the pairwise winning probabilities. First, we present several illuminating examples
to establish: (a) there exist deterministic tournaments (where the pairwise winning
probabilities are 0 or 1) where one optimal draw is much more robust than the
other; and (b) in general, there exist tournaments with slightly suboptimal draws
that are more robust than all the optimal draws. The above examples motivate the
study of the computational problem of robust draws that guarantee a specified
winning probability. Second, we present a polynomial-time algorithm for approximating
the robustness of a draw for sufficiently small errors in pairwise winning probabilities,
and obtain that the stated computational problem is NP-complete. We also show
that two natural cases of deterministic tournaments where the optimal draw could
be computed in polynomial time also admit polynomial-time algorithms to compute
robust optimal draws.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout
tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in
balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the
IJCAI: International Joint Conference on Artificial Intelligence, New York, NY,
USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust
Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced
knockout tournaments,” presented at the IJCAI: International Joint Conference
on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.'
ista: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout
tournaments. IJCAI: International Joint Conference on Artificial Intelligence
vol. 2016–January, 172–179.'
mla: Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments.
Vol. 2016–January, AAAI Press, 2016, pp. 172–79.
short: K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.
conference:
end_date: 2016-07-15
location: New York, NY, USA
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2016-07-09
date_created: 2018-12-11T11:50:35Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-02-21T10:04:26Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05090v1
month: '01'
oa: 1
oa_version: Preprint
page: 172 - 179
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: AAAI Press
publist_id: '6171'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://www.ijcai.org/proceedings/2016
scopus_import: 1
status: public
title: Robust draws in balanced knockout tournaments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-January
year: '2016'
...
---
_id: '1184'
abstract:
- lang: eng
text: Across multicellular organisms, the costs of reproduction and self-maintenance
result in a life history trade-off between fecundity and longevity. Queens of
perennial social Hymenoptera are both highly fertile and long-lived, and thus,
this fundamental trade-off is lacking. Whether social insect males similarly evade
the fecundity/longevity trade-off remains largely unstudied. Wingless males of
the ant genus Cardiocondyla stay in their natal colonies throughout their relatively
long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla
obscurior males that were allowed to mate with large numbers of female sexuals
had a shortened life span compared to males that mated at a low frequency or virgin
males. Although frequent mating negatively affects longevity, males clearly benefit
from a “live fast, die young strategy” by inseminating as many female sexuals
as possible at a cost to their own survival.
acknowledgement: 'German Science Foundation. Grant Number: SCHR 1135/2-1. We thank
M. Adam for handling part of the setups and J. Zoellner for behavioral observations.'
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology
and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474
apa: Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in
ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474
chicago: Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity
in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.
ieee: S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,”
Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906,
2016.
ista: Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males.
Ecology and Evolution. 6(24), 8903–8906.
mla: Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution,
vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.
short: S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:55Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1002/ece3.2474
file:
- access_level: open_access
checksum: 789026eb9e1be2a0da08376f29f569cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:12Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5062'
file_name: IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf
file_size: 328414
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 8903 - 8906
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6169'
pubrep_id: '736'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mating and longevity in ant males
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: '1186'
abstract:
- lang: eng
text: The human pathogen Streptococcus pneumoniae is decorated with a special class
of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine
(PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography,
NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies,
we provide structural information of choline-binding protein L (CbpL) and demonstrate
its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated
three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported
in this work for the very first time-, (ii) an unprecedented anchorage module
showing alternate disposition of canonical and non-canonical choline-binding sites
that allows vine-like binding of fully-PCho-substituted teichoic acids (with two
choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural
and infection assays indicate an important role of the whole multimodular protein
allowing both to locate CbpL at specific places on the cell wall and to interact
with host components in order to facilitate pneumococcal lung infection and transmigration
from nasopharynx to the lungs and blood. CbpL implication in both resistance against
killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein
as relevant among the pathogenic arsenal of the pneumococcus.
acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann,
for technical assistance and Lothar Petruschka for in silico analysis (all Dept.
of Genetics, University of Greifswald). We are further grateful to the staff from
SLS synchrotron beamline for help in data collection. This work was supported by
grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish
Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P
to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to
JAH and FG).
article_number: '38094'
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Malek
full_name: Saleh, Malek
last_name: Saleh
- first_name: Martín
full_name: Alcorlo, Martín
last_name: Alcorlo
- first_name: Alejandro
full_name: Gómez Mejóa, Alejandro
last_name: Gómez Mejóa
- first_name: David
full_name: Pantoja Uceda, David
last_name: Pantoja Uceda
- first_name: Miguel
full_name: Treviño, Miguel
last_name: Treviño
- first_name: Franziska
full_name: Vob, Franziska
last_name: Vob
- first_name: Mohammed
full_name: Abdullah, Mohammed
last_name: Abdullah
- first_name: Sergio
full_name: Galán Bartual, Sergio
last_name: Galán Bartual
- first_name: Jolien
full_name: Seinen, Jolien
last_name: Seinen
- first_name: Pedro
full_name: Sánchez Murcia, Pedro
last_name: Sánchez Murcia
- first_name: Federico
full_name: Gago, Federico
last_name: Gago
- first_name: Marta
full_name: Bruix, Marta
last_name: Bruix
- first_name: Sven
full_name: Hammerschmidt, Sven
last_name: Hammerschmidt
- first_name: Juan
full_name: Hermoso, Juan
last_name: Hermoso
citation:
ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and
unique teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094
apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda,
D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094
chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez
Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture
and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL
Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature
Publishing Group, 2016. https://doi.org/10.1038/srep38094.
ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.
ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D,
Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago
F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique
teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 6, 38094.
mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic
Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal
Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group,
2016, doi:10.1038/srep38094.
short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja
Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez
Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6
(2016).
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '05'
ddc:
- '576'
- '610'
department:
- _id: LeSa
doi: 10.1038/srep38094
file:
- access_level: open_access
checksum: e007d78b483bc59bf5ab98e9d42a6ec1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:18Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4804'
file_name: IST-2017-735-v1+1_srep38094.pdf
file_size: 2716045
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: '6167'
pubrep_id: '735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular architecture and unique teichoic acid recognition features of choline-binding
protein L CbpL contributing to pneumococcal pathogenesis
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: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016,
doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
intvolume: ' 2016'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_status: published
publisher: IOPscience
publist_id: '6165'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1195'
abstract:
- lang: eng
text: 'The genetic analysis of experimentally evolving populations typically relies
on short reads from pooled individuals (Pool-Seq). While this method provides
reliable allele frequency estimates, the underlying haplotype structure remains
poorly characterized. With small population sizes and adaptive variants that start
from low frequencies, the interpretation of selection signatures in most Evolve
and Resequencing studies remains challenging. To facilitate the characterization
of selection targets, we propose a new approach that reconstructs selected haplotypes
from replicated time series, using Pool-Seq data. We identify selected haplotypes
through the correlated frequencies of alleles carried by them. Computer simulations
indicate that selected haplotype-blocks of several Mb can be reconstructed with
high confidence and low error rates, even when allele frequencies change only
by 20% across three replicates. Applying this method to real data from D. melanogaster
populations adapting to a hot environment, we identify a selected haplotype-block
of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations
by experimental haplotyping, demonstrating the power and accuracy of our haplotype
reconstruction from Pool-Seq data. We propose that the combination of allele frequency
estimates with haplotype information will provide the key to understanding the
dynamics of adaptive alleles. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected
during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184.
doi:10.1093/molbev/msw210
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during
Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no.
1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2021-01-12T06:49:00Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1093/molbev/msw210
ec_funded: 1
file:
- access_level: open_access
checksum: 1e78d3aaffcb40dc8b02b7b4666019e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:35Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5223'
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creator: system
date_created: 2018-12-12T10:16:36Z
date_updated: 2020-07-14T12:44:38Z
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creator: system
date_created: 2018-12-12T10:16:37Z
date_updated: 2020-07-14T12:44:38Z
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creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5226'
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checksum: e47b2a0c32142f423b3100150c0294f8
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creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5227'
file_name: IST-2017-770-v1+5_Fig4.pdf
file_size: 50045
relation: main_file
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checksum: a5a7d6b32e7e17d35d337d7ec2a9f6c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:39Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5228'
file_name: IST-2017-770-v1+6_Fig5.pdf
file_size: 50705
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 174 - 184
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6155'
pubrep_id: '770'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2016'
...
---
_id: '1200'
acknowledgement: C.H. acknowledges generous support from the ISTFELLOW program.
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Arne
full_name: Traulsen, Arne
last_name: Traulsen
citation:
ama: 'Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations
can leverage the full potential of evolutionary modeling: Comment on “Evolutionary
game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze.
Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004'
apa: 'Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics
and agent based simulations can leverage the full potential of evolutionary modeling:
Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J.
Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004'
chicago: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.'
ieee: 'C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau
and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31,
2016.'
ista: 'Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau
and A. Hintze. Physics of Life Reviews. 19, 29–31.'
mla: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016,
pp. 29–31, doi:10.1016/j.plrev.2016.10.004.'
short: C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31.
date_created: 2018-12-11T11:50:40Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
ddc:
- '530'
department:
- _id: KrCh
doi: 10.1016/j.plrev.2016.10.004
ec_funded: 1
file:
- access_level: open_access
checksum: 95e6dc78278334b99dacbf8822509364
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4855'
file_name: IST-2017-798-v1+1_comment_adami.pdf
file_size: 171352
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 29 - 31
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6150'
pubrep_id: '798'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Only the combination of mathematics and agent based simulations can leverage
the full potential of evolutionary modeling: Comment on “Evolutionary game theory
using agent-based methods” by C. Adami, J. Schossau and A. Hintze'
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: 19
year: '2016'
...
---
_id: '1202'
acknowledgement: The authors thank Sophie A.O. Armitage and Jan N. Offenborn for helpful
comments on the figures, and two anonymous reviewers for their helpful comments.
The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2)
within the priority programme SPP 1399 “Host–Parasite Coevolution”.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Kevin
full_name: Ferro, Kevin
last_name: Ferro
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. Immune priming in arthropods: an
update focusing on the red flour beetle. Zoology . 2016;119(4):254-261.
doi:10.1016/j.zool.2016.03.006'
apa: 'Milutinovic, B., Peuß, R., Ferro, K., & Kurtz, J. (2016). Immune priming
in arthropods: an update focusing on the red flour beetle. Zoology . Elsevier.
https://doi.org/10.1016/j.zool.2016.03.006'
chicago: 'Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune
Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology
. Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006.'
ieee: 'B. Milutinovic, R. Peuß, K. Ferro, and J. Kurtz, “Immune priming in arthropods:
an update focusing on the red flour beetle,” Zoology , vol. 119, no. 4.
Elsevier, pp. 254–261, 2016.'
ista: 'Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods:
an update focusing on the red flour beetle. Zoology . 119(4), 254–261.'
mla: 'Milutinovic, Barbara, et al. “Immune Priming in Arthropods: An Update Focusing
on the Red Flour Beetle.” Zoology , vol. 119, no. 4, Elsevier, 2016, pp.
254–61, doi:10.1016/j.zool.2016.03.006.'
short: B. Milutinovic, R. Peuß, K. Ferro, J. Kurtz, Zoology 119 (2016) 254–261.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1016/j.zool.2016.03.006
file:
- access_level: open_access
checksum: 8396d5bd95f9c4295857162f902afabf
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T13:00:20Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5885'
file_name: 2016_Elsevier_Milutinovic.pdf
file_size: 1473211
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 119'
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 254 - 261
project:
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: 'Zoology '
publication_status: published
publisher: Elsevier
publist_id: '6147'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Immune priming in arthropods: an update focusing on the red flour beetle'
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: 119
year: '2016'
...
---
_id: '1203'
abstract:
- lang: eng
text: Haemophilus haemolyticus has been recently discovered to have the potential
to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae
(NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified
because none of the existing tests targeting the known phenotypes of H. haemolyticus
are able to specifically identify H. haemolyticus. Through comparative genomic
analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to
H. haemolyticus that can be used as targets for the identification of H. haemolyticus.
A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase
2 in the purine synthesis pathway) was developed and evaluated. The lower limit
of detection was 40 genomes/PCR; the sensitivity and specificity in detecting
H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination
of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets
(H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was
also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification
of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification
of H. influenzae, respectively. The dual-target testing scheme can be used for
the diagnosis and surveillance of infection and disease caused by H. haemolyticus
and NT H. influenzae.
acknowledgement: We are grateful to ABCs for providing strains and the Bacterial Meningitis
Laboratory for technical support.
author:
- first_name: Fang
full_name: Hu, Fang
last_name: Hu
- first_name: Lavanya
full_name: Rishishwar, Lavanya
last_name: Rishishwar
- first_name: Ambily
full_name: Sivadas, Ambily
last_name: Sivadas
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Jordan
full_name: King, Jordan
last_name: King
- first_name: Timothy
full_name: Murphy, Timothy
last_name: Murphy
- first_name: Janet
full_name: Gilsdorf, Janet
last_name: Gilsdorf
- first_name: Leonard
full_name: Mayer, Leonard
last_name: Mayer
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
citation:
ama: Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus
haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for
their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017.
doi:10.1128/JCM.01511-16
apa: Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., …
Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16
chicago: Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan
King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative
Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae
and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology.
American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.
ieee: F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus
and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,”
Journal of Clinical Microbiology, vol. 54, no. 12. American Society for
Microbiology, pp. 3010–3017, 2016.
ista: Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer
L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and
nontypeable Haemophilus influenzae and a new testing scheme for their discrimination.
Journal of Clinical Microbiology. 54(12), 3010–3017.
mla: Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus
and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.”
Journal of Clinical Microbiology, vol. 54, no. 12, American Society for
Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.
short: F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf,
L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:04Z
day: '01'
department:
- _id: GaTk
doi: 10.1128/JCM.01511-16
intvolume: ' 54'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/
month: '12'
oa: 1
oa_version: Submitted Version
page: 3010 - 3017
publication: Journal of Clinical Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '6146'
quality_controlled: '1'
scopus_import: 1
status: public
title: Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus
influenzae and a new testing scheme for their discrimination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2016'
...
---
_id: '1204'
abstract:
- lang: eng
text: In science, as in life, "surprises" can be adequately appreciated
only in the presence of a null model, what we expect a priori. In physics, theories
sometimes express the values of dimensionless physical constants as combinations
of mathematical constants like π or e. The inverse problem also arises, whereby
the measured value of a physical constant admits a "surprisingly" simple
approximation in terms of well-known mathematical constants. Can we estimate the
probability for this to be a mere coincidence, rather than an inkling of some
theory? We answer the question in the most naive form.
author:
- first_name: Ariel
full_name: Amir, Ariel
last_name: Amir
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Tadashi
full_name: Tokieda, Tadashi
last_name: Tokieda
citation:
ama: Amir A, Lemeshko M, Tokieda T. Surprises in numerical expressions of physical
constants. American Mathematical Monthly. 2016;123(6):609-612. doi:10.4169/amer.math.monthly.123.6.609
apa: Amir, A., Lemeshko, M., & Tokieda, T. (2016). Surprises in numerical expressions
of physical constants. American Mathematical Monthly. Mathematical Association
of America. https://doi.org/10.4169/amer.math.monthly.123.6.609
chicago: Amir, Ariel, Mikhail Lemeshko, and Tadashi Tokieda. “Surprises in Numerical
Expressions of Physical Constants.” American Mathematical Monthly. Mathematical
Association of America, 2016. https://doi.org/10.4169/amer.math.monthly.123.6.609.
ieee: A. Amir, M. Lemeshko, and T. Tokieda, “Surprises in numerical expressions
of physical constants,” American Mathematical Monthly, vol. 123, no. 6.
Mathematical Association of America, pp. 609–612, 2016.
ista: Amir A, Lemeshko M, Tokieda T. 2016. Surprises in numerical expressions of
physical constants. American Mathematical Monthly. 123(6), 609–612.
mla: Amir, Ariel, et al. “Surprises in Numerical Expressions of Physical Constants.”
American Mathematical Monthly, vol. 123, no. 6, Mathematical Association
of America, 2016, pp. 609–12, doi:10.4169/amer.math.monthly.123.6.609.
short: A. Amir, M. Lemeshko, T. Tokieda, American Mathematical Monthly 123 (2016)
609–612.
date_created: 2018-12-11T11:50:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:04Z
day: '01'
department:
- _id: MiLe
doi: 10.4169/amer.math.monthly.123.6.609
intvolume: ' 123'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.00299
month: '06'
oa: 1
oa_version: Preprint
page: 609 - 612
publication: American Mathematical Monthly
publication_status: published
publisher: Mathematical Association of America
publist_id: '6143'
quality_controlled: '1'
scopus_import: 1
status: public
title: Surprises in numerical expressions of physical constants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2016'
...
---
_id: '1206'
abstract:
- lang: eng
text: We study a polar molecule immersed in a superfluid environment, such as a
helium nanodroplet or a Bose–Einstein condensate, in the presence of a strong
electrostatic field. We show that coupling of the molecular pendular motion, induced
by the field, to the fluctuating bath leads to formation of pendulons—spherical
harmonic librators dressed by a field of many-particle excitations. We study the
behavior of the pendulon in a broad range of molecule–bath and molecule–field
interaction strengths, and reveal that its spectrum features a series of instabilities
which are absent in the field-free case of the angulon quasiparticle. Furthermore,
we show that an external field allows to fine-tune the positions of these instabilities
in the molecular rotational spectrum. This opens the door to detailed experimental
studies of redistribution of orbital angular momentum in many-particle systems.
© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Redchenko E, Lemeshko M. Libration of strongly oriented polar molecules inside
a superfluid. ChemPhysChem. 2016;17(22):3649-3654. doi:10.1002/cphc.201601042
apa: Redchenko, E., & Lemeshko, M. (2016). Libration of strongly oriented polar
molecules inside a superfluid. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201601042
chicago: Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented
Polar Molecules inside a Superfluid.” ChemPhysChem. Wiley-Blackwell, 2016.
https://doi.org/10.1002/cphc.201601042.
ieee: E. Redchenko and M. Lemeshko, “Libration of strongly oriented polar molecules
inside a superfluid,” ChemPhysChem, vol. 17, no. 22. Wiley-Blackwell, pp.
3649–3654, 2016.
ista: Redchenko E, Lemeshko M. 2016. Libration of strongly oriented polar molecules
inside a superfluid. ChemPhysChem. 17(22), 3649–3654.
mla: Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented Polar
Molecules inside a Superfluid.” ChemPhysChem, vol. 17, no. 22, Wiley-Blackwell,
2016, pp. 3649–54, doi:10.1002/cphc.201601042.
short: E. Redchenko, M. Lemeshko, ChemPhysChem 17 (2016) 3649–3654.
date_created: 2018-12-11T11:50:43Z
date_published: 2016-09-18T00:00:00Z
date_updated: 2021-01-12T06:49:05Z
day: '18'
department:
- _id: JoFi
- _id: MiLe
doi: 10.1002/cphc.201601042
ec_funded: 1
intvolume: ' 17'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08161
month: '09'
oa: 1
oa_version: Preprint
page: 3649 - 3654
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6140'
quality_controlled: '1'
scopus_import: 1
status: public
title: Libration of strongly oriented polar molecules inside a superfluid
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1209'
abstract:
- lang: eng
text: 'NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the
least characterized complex of the mitochondrial electron transport chain. Because
of the ease of sample availability, previous work has focused almost exclusively
on bovine complex I. However, only medium resolution structural analyses of this
complex have been reported. Working with other mammalian complex I homologues
is a potential approach for overcoming these limitations. Due to the inherent
difficulty of expressing large membrane protein complexes, screening of complex
I homologues is limited to large mammals reared for human consumption. The high
sequence identity among these available sources may preclude the benefits of screening.
Here, we report the characterization of complex I purified from Ovis aries (ovine)
heart mitochondria. All 44 unique subunits of the intact complex were identified
by mass spectrometry. We identified differences in the subunit composition of
subcomplexes of ovine complex I as compared with bovine, suggesting differential
stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa
subunit, which is easily lost from the bovine enzyme, remains tightly bound to
ovine complex I. Additionally, we developed a novel purification protocol for
highly active and stable mitochondrial complex I using the branched-chain detergent
lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related,
significant differences exist between the biochemical properties of complex I
prepared from ovine and bovine mitochondria and that ovine complex I represents
a suitable alternative target for further structural studies. '
acknowledgement: "J.A.S supported in part by a Medical Research D.G.Council UK Ph.D.
fellowship.\r\nThis work was supported in part by European Union's 2020 Research
and Innovation Program under Grant 701309. \r\n"
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Gianluca
full_name: Degliesposti, Gianluca
last_name: Degliesposti
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification
of ovine respiratory complex i results in a highly active and stable preparation.
Journal of Biological Chemistry. 2016;291(47):24657-24675. doi:10.1074/jbc.M116.735142
apa: Letts, J. A., Degliesposti, G., Fiedorczuk, K., Skehel, M., & Sazanov,
L. A. (2016). Purification of ovine respiratory complex i results in a highly
active and stable preparation. Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.735142
chicago: Letts, James A, Gianluca Degliesposti, Karol Fiedorczuk, Mark Skehel, and
Leonid A Sazanov. “Purification of Ovine Respiratory Complex i Results in a Highly
Active and Stable Preparation.” Journal of Biological Chemistry. American
Society for Biochemistry and Molecular Biology, 2016. https://doi.org/10.1074/jbc.M116.735142.
ieee: J. A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, and L. A. Sazanov,
“Purification of ovine respiratory complex i results in a highly active and stable
preparation,” Journal of Biological Chemistry, vol. 291, no. 47. American
Society for Biochemistry and Molecular Biology, pp. 24657–24675, 2016.
ista: Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. 2016. Purification
of ovine respiratory complex i results in a highly active and stable preparation.
Journal of Biological Chemistry. 291(47), 24657–24675.
mla: Letts, James A., et al. “Purification of Ovine Respiratory Complex i Results
in a Highly Active and Stable Preparation.” Journal of Biological Chemistry,
vol. 291, no. 47, American Society for Biochemistry and Molecular Biology, 2016,
pp. 24657–75, doi:10.1074/jbc.M116.735142.
short: J.A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, L.A. Sazanov, Journal
of Biological Chemistry 291 (2016) 24657–24675.
date_created: 2018-12-11T11:50:44Z
date_published: 2016-11-18T00:00:00Z
date_updated: 2021-01-12T06:49:06Z
day: '18'
department:
- _id: LeSa
doi: 10.1074/jbc.M116.735142
ec_funded: 1
intvolume: ' 291'
issue: '47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114416/
month: '11'
oa: 1
oa_version: Submitted Version
page: 24657 - 24675
project:
- _id: 2593EBD6-B435-11E9-9278-68D0E5697425
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(FEBS)
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '6139'
quality_controlled: '1'
scopus_import: 1
status: public
title: Purification of ovine respiratory complex i results in a highly active and
stable preparation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 291
year: '2016'
...
---
_id: '1212'
abstract:
- lang: eng
text: 'Plants adjust their growth according to gravity. Gravitropism involves gravity
perception, signal transduction, and asymmetric growth response, with organ bending
as a consequence [1]. Asymmetric growth results from the asymmetric distribution
of the plant-specific signaling molecule auxin [2] that is generated by lateral
transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3
(PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal
cells, correlating with increased auxin accumulation in adjacent tissues at the
lower side of the stimulated organ, where auxin induces cell elongation and, hence,
organ bending. A curvature response allows the hypocotyl to resume straight growth
at a defined angle [6], implying that at some point auxin symmetry is restored
to prevent overbending. Here, we present initial insights into cellular and molecular
mechanisms that lead to the termination of the tropic response. We identified
an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry
of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization
events redirect auxin fluxes at different time points of the gravity response:
first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower
hypocotyl side, where auxin gradually accumulates and promotes growth, and later
PIN3 polarization to the opposite cell side, depleting this auxin maximum to end
the bending. Accordingly, genetic or pharmacological interference with the late
PIN3 polarization prevents termination of the response and leads to hypocotyl
overbending. This observation reveals a role of auxin feedback on PIN polarity
in the termination of the tropic response. © 2016 Elsevier Ltd'
acknowledgement: "We thank Dr. Jie Li (Key Laboratory of Plant Molecular Physiology,
Chinese Academy of Science, China) for the pPIN3::PIN3-GFP/DII::VENUS line and Martine
De Cock for help in preparing the manuscript. This work was supported by the European
Research Council (project ERC-2011-StG-20101109-PSDP), by the Czech Science Foundation
GAČR (GA13-40637S) to J.F., and by the Ministry of Education, Youth and Sports of
the Czech Republic under the project CEITEC 2020 (LQ1601) to H.S.R. H.R. is indebted
to the Agency for Innovation by Science and Technology (IWT) for a predoctoral fellowship.\r\n"
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Mohamad
full_name: Abbas, Mohamad
id: 47E8FC1C-F248-11E8-B48F-1D18A9856A87
last_name: Abbas
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Siyuan
full_name: Song, Siyuan
last_name: Song
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. Termination of shoot
gravitropic responses by auxin feedback on PIN3 polarity. Current Biology.
2016;26(22):3026-3032. doi:10.1016/j.cub.2016.08.067
apa: Rakusová, H., Abbas, M., Han, H., Song, S., Robert, H., & Friml, J. (2016).
Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.08.067
chicago: Rakusová, Hana, Mohamad Abbas, Huibin Han, Siyuan Song, Hélène Robert,
and Jiří Friml. “Termination of Shoot Gravitropic Responses by Auxin Feedback
on PIN3 Polarity.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2016.08.067.
ieee: H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, and J. Friml, “Termination
of shoot gravitropic responses by auxin feedback on PIN3 polarity,” Current
Biology, vol. 26, no. 22. Cell Press, pp. 3026–3032, 2016.
ista: Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. 2016. Termination of
shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology.
26(22), 3026–3032.
mla: Rakusová, Hana, et al. “Termination of Shoot Gravitropic Responses by Auxin
Feedback on PIN3 Polarity.” Current Biology, vol. 26, no. 22, Cell Press,
2016, pp. 3026–32, doi:10.1016/j.cub.2016.08.067.
short: H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology
26 (2016) 3026–3032.
date_created: 2018-12-11T11:50:44Z
date_published: 2016-11-21T00:00:00Z
date_updated: 2021-01-12T06:49:08Z
day: '21'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.cub.2016.08.067
ec_funded: 1
file:
- access_level: open_access
checksum: 79ed2498185a027cf51a8f88100379e6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:33Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4757'
file_name: IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf
file_size: 5391923
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 3026 - 3032
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '6138'
pubrep_id: '1008'
quality_controlled: '1'
scopus_import: 1
status: public
title: Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1216'
abstract:
- lang: eng
text: 'A framework fo r extracting features in 2D transient flows, based on the
acceleration field to ensure Galilean invariance is proposed in this paper. The
minima of the acceleration magnitude (a superset of acceleration zeros) are extracted
and discriminated into vortices and saddle points, based on the spectral properties
of the velocity Jacobian. The extraction of topological features is performed
with purely combinatorial algorithms from discrete computational topology. The
feature points are prioritized with persistence, as a physically meaningful importance
measure. These feature points are tracked in time with a robust algorithm for
tracking features. Thus, a space-time hierarchy of the minima is built and vortex
merging events are detected. We apply the acceleration feature extraction strategy
to three two-dimensional shear flows: (1) an incompressible periodic cylinder
wake, (2) an incompressible planar mixing layer and (3) a weakly compressible
planar jet. The vortex-like acceleration feature points are shown to be well aligned
with acceleration zeros, maxima of the vorticity magnitude, minima of the pressure
field and minima of λ2.'
acknowledgement: "The authors acknowledge funding of the German Re-\r\nsearch Foundation
\ (DFG) via the Collaborative Re-\r\nsearch Center (SFB 557) \\Control of
\ Complex Turbu-\r\nlent Shear Flows\" and the Emmy Noether Program.\r\nFurther
\ funding was provided by the Zuse Institute\r\nBerlin (ZIB), the DFG-CNRS
\ research group \\Noise\r\nGeneration in Turbulent Flows\" (2003{2010), the Chaire\r\nd'Excellence
'Closed-loop control of turbulent shear ows\r\nusing reduced-order models' (TUCOROM)
of the French\r\nAgence Nationale de la Recherche (ANR), and the Eu-\r\nropean Social
\ Fund (ESF App. No. 100098251). We\r\nthank the Ambrosys Ltd. Society
\ for Complex Sys-\r\ntems Management and the Bernd R. Noack Cybernet-\r\nics
\ Foundation for additional support. A part of this\r\nwork was performed
using HPC resources from GENCI-[CCRT/CINES/IDRIS] supported by the Grant 2011-\r\n[x2011020912"
author:
- first_name: Jens
full_name: Kasten, Jens
last_name: Kasten
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Ingrid
full_name: Hotz, Ingrid
last_name: Hotz
- first_name: Hans
full_name: Hege, Hans
last_name: Hege
- first_name: Bernd
full_name: Noack, Bernd
last_name: Noack
- first_name: Guillaume
full_name: Daviller, Guillaume
last_name: Daviller
- first_name: Marek
full_name: Morzyński, Marek
last_name: Morzyński
citation:
ama: Kasten J, Reininghaus J, Hotz I, et al. Acceleration feature points of unsteady
shear flows. Archives of Mechanics. 2016;68(1):55-80.
apa: Kasten, J., Reininghaus, J., Hotz, I., Hege, H., Noack, B., Daviller, G., &
Morzyński, M. (2016). Acceleration feature points of unsteady shear flows. Archives
of Mechanics. Polish Academy of Sciences Publishing House.
chicago: Kasten, Jens, Jan Reininghaus, Ingrid Hotz, Hans Hege, Bernd Noack, Guillaume
Daviller, and Marek Morzyński. “Acceleration Feature Points of Unsteady Shear
Flows.” Archives of Mechanics. Polish Academy of Sciences Publishing House,
2016.
ieee: J. Kasten et al., “Acceleration feature points of unsteady shear flows,”
Archives of Mechanics, vol. 68, no. 1. Polish Academy of Sciences Publishing
House, pp. 55–80, 2016.
ista: Kasten J, Reininghaus J, Hotz I, Hege H, Noack B, Daviller G, Morzyński M.
2016. Acceleration feature points of unsteady shear flows. Archives of Mechanics.
68(1), 55–80.
mla: Kasten, Jens, et al. “Acceleration Feature Points of Unsteady Shear Flows.”
Archives of Mechanics, vol. 68, no. 1, Polish Academy of Sciences Publishing
House, 2016, pp. 55–80.
short: J. Kasten, J. Reininghaus, I. Hotz, H. Hege, B. Noack, G. Daviller, M. Morzyński,
Archives of Mechanics 68 (2016) 55–80.
date_created: 2018-12-11T11:50:46Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:09Z
day: '01'
department:
- _id: HeEd
intvolume: ' 68'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://am.ippt.pan.pl/am/article/viewFile/v68p55/pdf
month: '01'
oa: 1
oa_version: Published Version
page: 55 - 80
publication: Archives of Mechanics
publication_status: published
publisher: Polish Academy of Sciences Publishing House
publist_id: '6118'
quality_controlled: '1'
scopus_import: 1
status: public
title: Acceleration feature points of unsteady shear flows
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2016'
...
---
_id: '1218'
abstract:
- lang: eng
text: Investigating the physiology of cyanobacteria cultured under a diel light
regime is relevant for a better understanding of the resulting growth characteristics
and for specific biotechnological applications that are foreseen for these photosynthetic
organisms. Here, we present the results of a multiomics study of the model cyanobacterium
Synechocystis sp. strain PCC 6803, cultured in a lab-scale photobioreactor in
physiological conditions relevant for large-scale culturing. The culture was sparged
withN2 andCO2, leading to an anoxic environment during the dark period. Growth
followed the availability of light. Metabolite analysis performed with 1Hnuclear
magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur
assimilation showed elevated levels in the light. Most protein levels, analyzed
through mass spectrometry, remained rather stable. However, several high-light-response
proteins and stress-response proteins showed distinct changes at the onset of
the light period. Microarray-based transcript analysis found common patterns of~56%
of the transcriptome following the diel regime. These oscillating transcripts
could be grouped coarsely into genes that were upregulated and downregulated in
the dark period. The accumulated glycogen was degraded in the anaerobic environment
in the dark. A small part was degraded gradually, reflecting basic maintenance
requirements of the cells in darkness. Surprisingly, the largest part was degraded
rapidly in a short time span at the end of the dark period. This degradation could
allow rapid formation of metabolic intermediates at the end of the dark period,
preparing the cells for the resumption of growth at the start of the light period.
acknowledgement: "Dutch Ministry of Economic Affairs, Agriculture, and Innovation
through the program BioSolar CellsS. Andreas Angermayr,Pascal van Alphen, Klaas
J. Hellingwerf\r\nWe thank Naira Quintana (presently at Rousselot, Belgium) for
the ini-\r\ntiative at the 10th Cyanobacterial Molecular Biology Workshop\r\n(CMBW),
June 2010, Lake Arrowhead, Los Angeles, CA, USA, to start the\r\ncollaborative endeavor
reported here. We thank Timo Maarleveld from\r\nCWI/VU (Amsterdam) for a custom-made
Python script handling the output from the NMR analysis and for evaluating and visualizing
the\r\nseparate metabolites for their evaluation. We thank Rob Verpoorte from\r\nLeiden
University (metabolome analysis) and Hans Aerts from the AMC\r\n(proteome analysis)
for lab space and equipment. We thank Robert Leh-\r\nmann (Humboldt University Berlin)
and Ilka Axmann (University of\r\nDüsseldorf) for sharing the R-code for the LOS
transformation of the\r\ntranscript data. We thank Hans C. P. Matthijs from IBED
for inspiring\r\ndialogues and insightful thoughts on continuous culturing of cyanobac-\r\nteria.
We thank Sandra Waaijenborg for performing the transcript nor-\r\nmalization and
Johan Westerhuis from BDA, Jeroen van der Steen and\r\nFilipe Branco dos Santos
from MMP, and Lucas Stal from IBED/NIOZ for\r\nhelpful discussions. We thank Milou
Schuurmans from MMP for help\r\nwith sampling and glycogen determination. We thank
the members of the\r\nRNA Biology & Applied Bioinformatics group at SILS, in particular
Selina\r\nvan Leeuwen, Elisa Hoekstra, and Martijs Jonker, for the microarray anal-\r\nysis.
We thank the reviewers of this work for their insightful comments\r\nwhich improved
the quality of the manuscript. This work, including the efforts of S. Andreas Angermayr,
Pascal van\r\nAlphen, and Klaas J. Hellingwerf, was funded by Dutch Ministry of
Eco-\r\nnomic Affairs, Agriculture, and Innovation through the program BioSolar\r\nCells."
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Pascal
full_name: Van Alphen, Pascal
last_name: Van Alphen
- first_name: Dicle
full_name: Hasdemir, Dicle
last_name: Hasdemir
- first_name: Gertjan
full_name: Kramer, Gertjan
last_name: Kramer
- first_name: Muzamal
full_name: Iqbal, Muzamal
last_name: Iqbal
- first_name: Wilmar
full_name: Van Grondelle, Wilmar
last_name: Van Grondelle
- first_name: Huub
full_name: Hoefsloot, Huub
last_name: Hoefsloot
- first_name: Younghae
full_name: Choi, Younghae
last_name: Choi
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
citation:
ama: Angermayr A, Van Alphen P, Hasdemir D, et al. Culturing synechocystis sp. Strain
pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics
with low maintenance costs. Applied and Environmental Microbiology. 2016;82(14):4180-4189.
doi:10.1128/AEM.00256-16
apa: Angermayr, A., Van Alphen, P., Hasdemir, D., Kramer, G., Iqbal, M., Van Grondelle,
W., … Hellingwerf, K. (2016). Culturing synechocystis sp. Strain pcc 6803 with
N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance
costs. Applied and Environmental Microbiology. American Society for Microbiology.
https://doi.org/10.1128/AEM.00256-16
chicago: Angermayr, Andreas, Pascal Van Alphen, Dicle Hasdemir, Gertjan Kramer,
Muzamal Iqbal, Wilmar Van Grondelle, Huub Hoefsloot, Younghae Choi, and Klaas
Hellingwerf. “Culturing Synechocystis Sp. Strain Pcc 6803 with N2 and CO2 in a
Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs.”
Applied and Environmental Microbiology. American Society for Microbiology,
2016. https://doi.org/10.1128/AEM.00256-16.
ieee: A. Angermayr et al., “Culturing synechocystis sp. Strain pcc 6803 with
N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance
costs,” Applied and Environmental Microbiology, vol. 82, no. 14. American
Society for Microbiology, pp. 4180–4189, 2016.
ista: Angermayr A, Van Alphen P, Hasdemir D, Kramer G, Iqbal M, Van Grondelle W,
Hoefsloot H, Choi Y, Hellingwerf K. 2016. Culturing synechocystis sp. Strain pcc
6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with
low maintenance costs. Applied and Environmental Microbiology. 82(14), 4180–4189.
mla: Angermayr, Andreas, et al. “Culturing Synechocystis Sp. Strain Pcc 6803 with
N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance
Costs.” Applied and Environmental Microbiology, vol. 82, no. 14, American
Society for Microbiology, 2016, pp. 4180–89, doi:10.1128/AEM.00256-16.
short: A. Angermayr, P. Van Alphen, D. Hasdemir, G. Kramer, M. Iqbal, W. Van Grondelle,
H. Hoefsloot, Y. Choi, K. Hellingwerf, Applied and Environmental Microbiology
82 (2016) 4180–4189.
date_created: 2018-12-11T11:50:46Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:10Z
day: '01'
department:
- _id: ToBo
doi: 10.1128/AEM.00256-16
intvolume: ' 82'
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959195/
month: '07'
oa: 1
oa_version: Submitted Version
page: 4180 - 4189
publication: Applied and Environmental Microbiology
publication_status: published
publisher: American Society for Microbiology
publist_id: '6117'
quality_controlled: '1'
scopus_import: 1
status: public
title: Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime
reveals multiphase glycogen dynamics with low maintenance costs
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2016'
...
---
_id: '1219'
abstract:
- lang: eng
text: We consider N×N random matrices of the form H = W + V where W is a real symmetric
or complex Hermitian Wigner matrix and V is a random or deterministic, real, diagonal
matrix whose entries are independent of W. We assume subexponential decay for
the matrix entries of W, and we choose V so that the eigenvalues ofW and V are
typically of the same order. For a large class of diagonal matrices V , we show
that the local statistics in the bulk of the spectrum are universal in the limit
of large N.
acknowledgement: "J.C. was supported in part by National Research Foundation of Korea
Grant 2011-0013474 and TJ Park Junior Faculty Fellowship.\r\nK.S. was supported
by ERC Advanced Grant RANMAT, No. 338804, and the \"Fund for Math.\"\r\nB.S. was
supported by NSF GRFP Fellowship DGE-1144152.\r\nH.Y. was supported in part by NSF
Grant DMS-13-07444 and Simons investigator fellowship. We thank Paul Bourgade, László
Erd ̋os and Antti Knowles for helpful comments. We are grateful to the Taida Institute
for Mathematical\r\nSciences and National Taiwan Universality for their hospitality
during part of this\r\nresearch. We thank Thomas Spencer and the Institute for Advanced
Study for their\r\nhospitality during the academic year 2013–2014. "
author:
- first_name: Jioon
full_name: Lee, Jioon
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
- first_name: Ben
full_name: Stetler, Ben
last_name: Stetler
- first_name: Horngtzer
full_name: Yau, Horngtzer
last_name: Yau
citation:
ama: Lee J, Schnelli K, Stetler B, Yau H. Bulk universality for deformed wigner
matrices. Annals of Probability. 2016;44(3):2349-2425. doi:10.1214/15-AOP1023
apa: Lee, J., Schnelli, K., Stetler, B., & Yau, H. (2016). Bulk universality
for deformed wigner matrices. Annals of Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/15-AOP1023
chicago: Lee, Jioon, Kevin Schnelli, Ben Stetler, and Horngtzer Yau. “Bulk Universality
for Deformed Wigner Matrices.” Annals of Probability. Institute of Mathematical
Statistics, 2016. https://doi.org/10.1214/15-AOP1023.
ieee: J. Lee, K. Schnelli, B. Stetler, and H. Yau, “Bulk universality for deformed
wigner matrices,” Annals of Probability, vol. 44, no. 3. Institute of Mathematical
Statistics, pp. 2349–2425, 2016.
ista: Lee J, Schnelli K, Stetler B, Yau H. 2016. Bulk universality for deformed
wigner matrices. Annals of Probability. 44(3), 2349–2425.
mla: Lee, Jioon, et al. “Bulk Universality for Deformed Wigner Matrices.” Annals
of Probability, vol. 44, no. 3, Institute of Mathematical Statistics, 2016,
pp. 2349–425, doi:10.1214/15-AOP1023.
short: J. Lee, K. Schnelli, B. Stetler, H. Yau, Annals of Probability 44 (2016)
2349–2425.
date_created: 2018-12-11T11:50:47Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:10Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/15-AOP1023
ec_funded: 1
intvolume: ' 44'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.6634
month: '01'
oa: 1
oa_version: Preprint
page: 2349 - 2425
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6115'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bulk universality for deformed wigner matrices
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2016'
...
---
_id: '1220'
abstract:
- lang: eng
text: Theoretical and numerical aspects of aerodynamic efficiency of propulsion
systems coupled to the boundary layer of a fuselage are studied. We discuss the
effects of local flow fields, which are affected both by conservative flow acceleration
as well as total pressure losses, on the efficiency of boundary layer immersed
propulsion devices. We introduce the concept of a boundary layer retardation turbine
that helps reduce skin friction over the fuselage. We numerically investigate
efficiency gains offered by boundary layer and wake interacting devices. We discuss
the results in terms of a total energy consumption framework and show that efficiency
gains of any device depend on all the other elements of the propulsion system.
author:
- first_name: Gregor
full_name: Mikić, Gregor
last_name: Mikić
- first_name: Alex
full_name: Stoll, Alex
last_name: Stoll
- first_name: Joe
full_name: Bevirt, Joe
last_name: Bevirt
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Mark
full_name: Moore, Mark
last_name: Moore
citation:
ama: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion
propulsion applied to a thin haul commuter aircraft for optimal efficiency. In:
AIAA; 2016:1-19. doi:10.2514/6.2016-3764'
apa: 'Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage
boundary layer ingestion propulsion applied to a thin haul commuter aircraft for
optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration,
and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764'
chicago: Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage
Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for
Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764.
ieee: 'G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary
layer ingestion propulsion applied to a thin haul commuter aircraft for optimal
efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations
Conference, Washington, D.C., USA, 2016, pp. 1–19.'
ista: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer
ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency.
AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.'
mla: Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied
to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19,
doi:10.2514/6.2016-3764.
short: G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.
conference:
end_date: 2016-06-17
location: Washington, D.C., USA
name: 'AIAA: Aviation Technology, Integration, and Operations Conference'
start_date: 2016-06-13
date_created: 2018-12-11T11:50:47Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-21T10:17:50Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.2514/6.2016-3764
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ntrs.nasa.gov/search.jsp?R=20160010167&hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA
month: '06'
oa: 1
oa_version: Preprint
page: 1 - 19
publication_status: published
publisher: AIAA
publist_id: '6114'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fuselage boundary layer ingestion propulsion applied to a thin haul commuter
aircraft for optimal efficiency
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1221'
abstract:
- lang: eng
text: The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in
plants. Since decades ago, it has been the prime receptor candidate for the plant
hormone auxin with a plethora of described functions in auxin signaling and development.
The developmental importance of ABP1 has recently been questioned by identification
of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes
under normal growth conditions. In this study, we examined the contradiction between
the normal growth and development of the abp1 knock-outs and the strong morphological
defects observed in three different ethanol-inducible abp1 knock-down mutants
( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out
vs. abp1 knock-down crosses we show that the strong morphological defects that
were believed to be the result of conditional down-regulation of ABP1 can be reproduced
also in the absence of the functional ABP1 protein. This data suggests that the
phenotypes in abp1 knock-down lines are due to the off-target effects and asks
for further reflections on the biological function of ABP1 or alternative explanations
for the missing phenotypic defects in the abp1 loss-of-function alleles.
acknowledgement: "This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP
to JF). JM internship was supported by the grant “Action Austria – Slovakia”. MG
was supported by the scholarship \"Stipendien der Stipendienstiftung der Republik
Österreich\". Work by EH and CPR were supported by ANR blanc ANR-14-CE11-0018. We
would like to thank Mark Estelle and Yunde Zhao for provid\r\n-\r\ning \r\nabp1-c1\r\n,
\r\nabp1-TD1 \r\nand \r\nabp1-WTc1 \r\nseeds. We thank Emeline \r\nHuault for technical
assistance."
article_number: '86'
article_processing_charge: No
article_type: original
author:
- first_name: Jaroslav
full_name: Michalko, Jaroslav
id: 483727CA-F248-11E8-B48F-1D18A9856A87
last_name: Michalko
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Catherine
full_name: Perrot Rechenmann, Catherine
last_name: Perrot Rechenmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Michalko J, Glanc M, Perrot Rechenmann C, Friml J. Strong morphological defects
in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional
ABP1 protein. F1000 Research . 2016;5. doi:10.12688/f1000research.7654.1
apa: Michalko, J., Glanc, M., Perrot Rechenmann, C., & Friml, J. (2016). Strong
morphological defects in conditional Arabidopsis abp1 knock-down mutants generated
in absence of functional ABP1 protein. F1000 Research . F1000 Research.
https://doi.org/10.12688/f1000research.7654.1
chicago: Michalko, Jaroslav, Matous Glanc, Catherine Perrot Rechenmann, and Jiří
Friml. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down
Mutants Generated in Absence of Functional ABP1 Protein.” F1000 Research .
F1000 Research, 2016. https://doi.org/10.12688/f1000research.7654.1.
ieee: J. Michalko, M. Glanc, C. Perrot Rechenmann, and J. Friml, “Strong morphological
defects in conditional Arabidopsis abp1 knock-down mutants generated in absence
of functional ABP1 protein,” F1000 Research , vol. 5. F1000 Research, 2016.
ista: Michalko J, Glanc M, Perrot Rechenmann C, Friml J. 2016. Strong morphological
defects in conditional Arabidopsis abp1 knock-down mutants generated in absence
of functional ABP1 protein. F1000 Research . 5, 86.
mla: Michalko, Jaroslav, et al. “Strong Morphological Defects in Conditional Arabidopsis
Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” F1000
Research , vol. 5, 86, F1000 Research, 2016, doi:10.12688/f1000research.7654.1.
short: J. Michalko, M. Glanc, C. Perrot Rechenmann, J. Friml, F1000 Research 5
(2016).
date_created: 2018-12-11T11:50:47Z
date_published: 2016-01-20T00:00:00Z
date_updated: 2022-03-24T09:12:49Z
day: '20'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.12688/f1000research.7654.1
ec_funded: 1
file:
- access_level: open_access
checksum: c9e50bb6096a7ba4a832969935820f19
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:33Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5154'
file_name: IST-2016-711-v1+1_770cf1e0-612f-4e85-a500-54b6349fbbab_7654_-_jaroslav_michalko.pdf
file_size: 2990459
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: 'F1000 Research '
publication_status: published
publisher: F1000 Research
publist_id: '6113'
pubrep_id: '711'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants
generated in absence of functional ABP1 protein
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: 5
year: '2016'
...
---
_id: '1222'
abstract:
- lang: eng
text: We consider packings of congruent circles on a square flat torus, i.e., periodic
(w.r.t. a square lattice) planar circle packings, with the maximal circle radius.
This problem is interesting due to a practical reason—the problem of “super resolution
of images.” We have found optimal arrangements for N=6, 7 and 8 circles. Surprisingly,
for the case N=7 there are three different optimal arrangements. Our proof is
based on a computer enumeration of toroidal irreducible contact graphs.
acknowledgement: We wish to thank Alexey Tarasov, Vladislav Volkov and Brittany Fasy
for some useful comments and remarks, and especially Thom Sulanke for modifying
surftri to suit our purposes. Oleg R. Musin was partially supported by the NSF Grant
DMS-1400876 and by the RFBR Grant 15-01-99563. Anton V. Nikitenko was supported
by the Chebyshev Laboratory (Department of Mathematics and Mechanics, St. Petersburg
State University) under RF Government Grant 11.G34.31.0026.
author:
- first_name: Oleg
full_name: Musin, Oleg
last_name: Musin
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
citation:
ama: Musin O, Nikitenko A. Optimal packings of congruent circles on a square flat
torus. Discrete & Computational Geometry. 2016;55(1):1-20. doi:10.1007/s00454-015-9742-6
apa: Musin, O., & Nikitenko, A. (2016). Optimal packings of congruent circles
on a square flat torus. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-015-9742-6
chicago: Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles
on a Square Flat Torus.” Discrete & Computational Geometry. Springer,
2016. https://doi.org/10.1007/s00454-015-9742-6.
ieee: O. Musin and A. Nikitenko, “Optimal packings of congruent circles on a square
flat torus,” Discrete & Computational Geometry, vol. 55, no. 1. Springer,
pp. 1–20, 2016.
ista: Musin O, Nikitenko A. 2016. Optimal packings of congruent circles on a square
flat torus. Discrete & Computational Geometry. 55(1), 1–20.
mla: Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles on
a Square Flat Torus.” Discrete & Computational Geometry, vol. 55, no.
1, Springer, 2016, pp. 1–20, doi:10.1007/s00454-015-9742-6.
short: O. Musin, A. Nikitenko, Discrete & Computational Geometry 55 (2016) 1–20.
date_created: 2018-12-11T11:50:48Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:11Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-015-9742-6
intvolume: ' 55'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.0649
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 20
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '6111'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal packings of congruent circles on a square flat torus
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1223'
abstract:
- lang: eng
text: We consider a random Schrödinger operator on the binary tree with a random
potential which is the sum of a random radially symmetric potential, Qr, and a
random transversally periodic potential, κQt, with coupling constant κ. Using
a new one-dimensional dynamical systems approach combined with Jensen's inequality
in hyperbolic space (our key estimate) we obtain a fractional moment estimate
proving localization for small and large κ. Together with a previous result we
therefore obtain a model with two Anderson transitions, from localization to delocalization
and back to localization, when increasing κ. As a by-product we also have a partially
new proof of one-dimensional Anderson localization at any disorder.
author:
- first_name: Richard
full_name: Froese, Richard
last_name: Froese
- first_name: Darrick
full_name: Lee, Darrick
last_name: Lee
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
- first_name: Wolfgang
full_name: Spitzer, Wolfgang
last_name: Spitzer
- first_name: Günter
full_name: Stolz, Günter
last_name: Stolz
citation:
ama: Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally
periodic random potentials on binary trees. Journal of Spectral Theory.
2016;6(3):557-600. doi:10.4171/JST/132
apa: Froese, R., Lee, D., Sadel, C., Spitzer, W., & Stolz, G. (2016). Localization
for transversally periodic random potentials on binary trees. Journal of Spectral
Theory. European Mathematical Society. https://doi.org/10.4171/JST/132
chicago: Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter
Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.”
Journal of Spectral Theory. European Mathematical Society, 2016. https://doi.org/10.4171/JST/132.
ieee: R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally
periodic random potentials on binary trees,” Journal of Spectral Theory,
vol. 6, no. 3. European Mathematical Society, pp. 557–600, 2016.
ista: Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally
periodic random potentials on binary trees. Journal of Spectral Theory. 6(3),
557–600.
mla: Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials
on Binary Trees.” Journal of Spectral Theory, vol. 6, no. 3, European Mathematical
Society, 2016, pp. 557–600, doi:10.4171/JST/132.
short: R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory
6 (2016) 557–600.
date_created: 2018-12-11T11:50:48Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:12Z
day: '01'
department:
- _id: LaEr
doi: 10.4171/JST/132
intvolume: ' 6'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.3961
month: '01'
oa: 1
oa_version: Preprint
page: 557 - 600
publication: Journal of Spectral Theory
publication_status: published
publisher: European Mathematical Society
publist_id: '6112'
quality_controlled: '1'
scopus_import: 1
status: public
title: Localization for transversally periodic random potentials on binary trees
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1226'
abstract:
- lang: eng
text: Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes
to cellular energy production by transferring electrons from NADH to ubiquinone
coupled to proton translocation across the membrane. It is the largest protein
assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we
present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial
complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking
and mass-spectrometry mapping experiments. All 14 conserved core subunits and
31 mitochondria-specific supernumerary subunits are resolved within the L-shaped
molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur
clusters involved in electron transfer, and the membrane arm contains 78 transmembrane
helices, mostly contributed by antiporter-like subunits involved in proton translocation.
Supernumerary subunits form an interlinked, stabilizing shell around the conserved
core. Tightly bound lipids (including cardiolipins) further stabilize interactions
between the hydrophobic subunits. Subunits with possible regulatory roles contain
additional cofactors, NADPH and two phosphopantetheine molecules, which are shown
to be involved in inter-subunit interactions. We observe two different conformations
of the complex, which may be related to the conformationally driven coupling mechanism
and to the active-deactive transition of the enzyme. Our structure provides insight
into the mechanism, assembly, maturation and dysfunction of mitochondrial complex
I, and allows detailed molecular analysis of disease-causing mutations.
article_processing_charge: No
article_type: original
author:
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Gianluca
full_name: Degliesposti, Gianluca
last_name: Degliesposti
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. Atomic
structure of the entire mammalian mitochondrial complex i. Nature. 2016;538(7625):406-410.
doi:10.1038/nature19794
apa: Fiedorczuk, K., Letts, J. A., Degliesposti, G., Kaszuba, K., Skehel, M., &
Sazanov, L. A. (2016). Atomic structure of the entire mammalian mitochondrial
complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19794
chicago: Fiedorczuk, Karol, James A Letts, Gianluca Degliesposti, Karol Kaszuba,
Mark Skehel, and Leonid A Sazanov. “Atomic Structure of the Entire Mammalian Mitochondrial
Complex I.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature19794.
ieee: K. Fiedorczuk, J. A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, and L.
A. Sazanov, “Atomic structure of the entire mammalian mitochondrial complex i,”
Nature, vol. 538, no. 7625. Nature Publishing Group, pp. 406–410, 2016.
ista: Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. 2016.
Atomic structure of the entire mammalian mitochondrial complex i. Nature. 538(7625),
406–410.
mla: Fiedorczuk, Karol, et al. “Atomic Structure of the Entire Mammalian Mitochondrial
Complex I.” Nature, vol. 538, no. 7625, Nature Publishing Group, 2016,
pp. 406–10, doi:10.1038/nature19794.
short: K. Fiedorczuk, J.A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, L.A. Sazanov,
Nature 538 (2016) 406–410.
date_created: 2018-12-11T11:50:49Z
date_published: 2016-10-20T00:00:00Z
date_updated: 2021-01-12T06:49:13Z
day: '20'
department:
- _id: LeSa
doi: 10.1038/nature19794
ec_funded: 1
external_id:
pmid:
- '27595392'
intvolume: ' 538'
issue: '7625'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164932/
month: '10'
oa: 1
oa_version: Submitted Version
page: 406 - 410
pmid: 1
project:
- _id: 2593EBD6-B435-11E9-9278-68D0E5697425
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(FEBS)
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6108'
quality_controlled: '1'
scopus_import: 1
status: public
title: Atomic structure of the entire mammalian mitochondrial complex i
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 538
year: '2016'
...
---
_id: '1227'
abstract:
- lang: eng
text: Many biological systems can be modeled as multiaffine hybrid systems. Due
to the nonlinearity of multiaffine systems, it is difficult to verify their properties
of interest directly. A common strategy to tackle this problem is to construct
and analyze a discrete overapproximation of the original system. However, the
conservativeness of a discrete abstraction significantly determines the level
of confidence we can have in the properties of the original system. In this paper,
in order to reduce the conservativeness of a discrete abstraction, we propose
a new method based on a sufficient and necessary decision condition for computing
discrete transitions between states in the abstract system. We assume the state
space partition of a multiaffine system to be based on a set of multivariate polynomials.
Hence, a rectangular partition defined in terms of polynomials of the form (xi
− c) is just a simple case of multivariate polynomial partition, and the new decision
condition applies naturally. We analyze and demonstrate the improvement of our
method over the existing methods using some examples.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23
(Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Kong H, Bartocci E, Bogomolov S, et al. Discrete abstraction of multiaffine
systems. In: Vol 9957. Springer; 2016:128-144. doi:10.1007/978-3-319-47151-8_9'
apa: 'Kong, H., Bartocci, E., Bogomolov, S., Grosu, R., Henzinger, T. A., Jiang,
Y., & Schilling, C. (2016). Discrete abstraction of multiaffine systems (Vol.
9957, pp. 128–144). Presented at the HSB: Hybrid Systems Biology, Grenoble, France:
Springer. https://doi.org/10.1007/978-3-319-47151-8_9'
chicago: Kong, Hui, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, Thomas A Henzinger,
Yu Jiang, and Christian Schilling. “Discrete Abstraction of Multiaffine Systems,”
9957:128–44. Springer, 2016. https://doi.org/10.1007/978-3-319-47151-8_9.
ieee: 'H. Kong et al., “Discrete abstraction of multiaffine systems,” presented
at the HSB: Hybrid Systems Biology, Grenoble, France, 2016, vol. 9957, pp. 128–144.'
ista: 'Kong H, Bartocci E, Bogomolov S, Grosu R, Henzinger TA, Jiang Y, Schilling
C. 2016. Discrete abstraction of multiaffine systems. HSB: Hybrid Systems Biology,
LNCS, vol. 9957, 128–144.'
mla: Kong, Hui, et al. Discrete Abstraction of Multiaffine Systems. Vol.
9957, Springer, 2016, pp. 128–44, doi:10.1007/978-3-319-47151-8_9.
short: H. Kong, E. Bartocci, S. Bogomolov, R. Grosu, T.A. Henzinger, Y. Jiang, C.
Schilling, in:, Springer, 2016, pp. 128–144.
conference:
end_date: 2016-10-21
location: Grenoble, France
name: 'HSB: Hybrid Systems Biology'
start_date: 2016-10-20
date_created: 2018-12-11T11:50:49Z
date_published: 2016-09-25T00:00:00Z
date_updated: 2021-01-12T06:49:13Z
day: '25'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-47151-8_9
file:
- access_level: open_access
checksum: 994e164b558c47bacf8dc066dd27c8fc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:49Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4840'
file_name: IST-2017-781-v1+1_main.pdf
file_size: 683955
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 9957'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 128 - 144
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '6107'
pubrep_id: '781'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discrete abstraction of multiaffine systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9957
year: '2016'
...
---
_id: '1231'
abstract:
- lang: eng
text: 'We study the time-and memory-complexities of the problem of computing labels
of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The
w-bit label of a node is the hash of the labels of its parents, and the hash function
is modeled as a random oracle. Specific instances of this problem underlie both
proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard
functions like scrypt. As our main tool, we introduce the new notion of a probabilistic
parallel entangled pebbling game, a new type of combinatorial pebbling game on
a graph, which is closely related to the labeling game on the same graph. As a
first application of our framework, we prove that for scrypt, when the underlying
hash function is invoked n times, the cumulative memory complexity (CMC) (a notion
recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness
for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for
adversaries that can store many natural functions of the labels (e.g., linear
combinations), but still not arbitrary functions thereof. We then introduce and
study a combinatorial quantity, and show how a sufficiently small upper bound
on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary
adversaries. We also show that such an upper bound solves the main open problem
for proofs-of-space protocols: namely, establishing that the time complexity of
computing the label of a random node in a graph on n nodes (given an initial kw-bit
state) reduces tightly to the time complexity for black pebbling on the same graph
(given an initial k-node pebbling).'
acknowledgement: "Joël Alwen, Chethan Kamath, and Krzysztof Pietrzak’s research is
partially supported by an ERC starting grant (259668-PSPC). Vladimir Kolmogorov
is partially supported by an ERC consolidator grant (616160-DOICV). Binyi Chen was
partially supported by NSF grants CNS-1423566 and CNS-1514526, and a gift from the
Gareatis Foundation. Stefano Tessaro was partially supported by NSF grants CNS-1423566,
CNS-1528178, a Hellman Fellowship, and the Glen and Susanne Culler Chair.\r\n\r\nThis
work was done in part while the authors were visiting the Simons Institute for the
Theory of Computing, supported by the Simons Foundation and by the DIMACS/Simons
Collaboration in Cryptography through NSF grant CNS-1523467."
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Binyi
full_name: Chen, Binyi
last_name: Chen
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- 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: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S.
On the complexity of scrypt and proofs of space in the parallel random oracle
model. In: Vol 9666. Springer; 2016:358-387. doi:10.1007/978-3-662-49896-5_13'
apa: 'Alwen, J. F., Chen, B., Kamath Hosdurg, C., Kolmogorov, V., Pietrzak, K. Z.,
& Tessaro, S. (2016). On the complexity of scrypt and proofs of space in the
parallel random oracle model (Vol. 9666, pp. 358–387). Presented at the EUROCRYPT:
Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer.
https://doi.org/10.1007/978-3-662-49896-5_13'
chicago: Alwen, Joel F, Binyi Chen, Chethan Kamath Hosdurg, Vladimir Kolmogorov,
Krzysztof Z Pietrzak, and Stefano Tessaro. “On the Complexity of Scrypt and Proofs
of Space in the Parallel Random Oracle Model,” 9666:358–87. Springer, 2016. https://doi.org/10.1007/978-3-662-49896-5_13.
ieee: 'J. F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K. Z. Pietrzak, and
S. Tessaro, “On the complexity of scrypt and proofs of space in the parallel random
oracle model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, Vienna, Austria, 2016, vol. 9666, pp. 358–387.'
ista: 'Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S.
2016. On the complexity of scrypt and proofs of space in the parallel random oracle
model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol.
9666, 358–387.'
mla: Alwen, Joel F., et al. On the Complexity of Scrypt and Proofs of Space in
the Parallel Random Oracle Model. Vol. 9666, Springer, 2016, pp. 358–87, doi:10.1007/978-3-662-49896-5_13.
short: J.F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K.Z. Pietrzak, S.
Tessaro, in:, Springer, 2016, pp. 358–387.
conference:
end_date: 2016-05-12
location: Vienna, Austria
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2016-05-08
date_created: 2018-12-11T11:50:51Z
date_published: 2016-04-28T00:00:00Z
date_updated: 2021-01-12T06:49:15Z
day: '28'
department:
- _id: KrPi
- _id: VlKo
doi: 10.1007/978-3-662-49896-5_13
ec_funded: 1
intvolume: ' 9666'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/100
month: '04'
oa: 1
oa_version: Submitted Version
page: 358 - 387
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_status: published
publisher: Springer
publist_id: '6103'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the complexity of scrypt and proofs of space in the parallel random oracle
model
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9666
year: '2016'
...
---
_id: '1233'
abstract:
- lang: eng
text: About three decades ago it was realized that implementing private channels
between parties which can be adaptively corrupted requires an encryption scheme
that is secure against selective opening attacks. Whether standard (IND-CPA) security
implies security against selective opening attacks has been a major open question
since. The only known reduction from selective opening to IND-CPA security loses
an exponential factor. A polynomial reduction is only known for the very special
case where the distribution considered in the selective opening security experiment
is a product distribution, i.e., the messages are sampled independently from each
other. In this paper we give a reduction whose loss is quantified via the dependence
graph (where message dependencies correspond to edges) of the underlying message
distribution. In particular, for some concrete distributions including Markov
distributions, our reduction is polynomial.
acknowledgement: G. Fuchsbauer and K. Pietrzak are supported by the European Research
Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja
Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for
BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von
Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074).
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Felix
full_name: Heuer, Felix
last_name: Heuer
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply
security against selective opening for markov distributions. In: Vol 9562. Springer;
2016:282-305. doi:10.1007/978-3-662-49096-9_12'
apa: 'Fuchsbauer, G., Heuer, F., Kiltz, E., & Pietrzak, K. Z. (2016). Standard
security does imply security against selective opening for markov distributions
(Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-662-49096-9_12'
chicago: Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard
Security Does Imply Security against Selective Opening for Markov Distributions,”
9562:282–305. Springer, 2016. https://doi.org/10.1007/978-3-662-49096-9_12.
ieee: 'G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security
does imply security against selective opening for markov distributions,” presented
at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562,
pp. 282–305.'
ista: 'Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does
imply security against selective opening for markov distributions. TCC: Theory
of Cryptography Conference, LNCS, vol. 9562, 282–305.'
mla: Fuchsbauer, Georg, et al. Standard Security Does Imply Security against
Selective Opening for Markov Distributions. Vol. 9562, Springer, 2016, pp.
282–305, doi:10.1007/978-3-662-49096-9_12.
short: G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp.
282–305.
conference:
end_date: 2016-01-13
location: Tel Aviv, Israel
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-01-10
date_created: 2018-12-11T11:50:51Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:16Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-49096-9_12
ec_funded: 1
intvolume: ' 9562'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/853
month: '01'
oa: 1
oa_version: Submitted Version
page: 282 - 305
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '6100'
quality_controlled: '1'
scopus_import: 1
status: public
title: Standard security does imply security against selective opening for markov
distributions
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9562
year: '2016'
...
---
_id: '1238'
abstract:
- lang: eng
text: The dynamic localization of endosomal compartments labeled with targeted fluorescent
protein tags is routinely followed by time lapse fluorescence microscopy approaches
and single particle tracking algorithms. In this way trajectories of individual
endosomes can be mapped and linked to physiological processes as cell growth.
However, other aspects of dynamic behavior including endosomal interactions are
difficult to follow in this manner. Therefore, we characterized the localization
and dynamic properties of early and late endosomes throughout the entire course
of root hair formation by means of spinning disc time lapse imaging and post-acquisition
automated multitracking and quantitative analysis. Our results show differential
motile behavior of early and late endosomes and interactions of late endosomes
that may be specified to particular root hair domains. Detailed data analysis
revealed a particular transient interaction between late endosomes—termed herein
as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially
located in the root hair tip interacted as dancing-endosomes and traveled short
distances during this interaction. Finally, sizes of early and late endosomes
were addressed by means of super-resolution structured illumination microscopy
(SIM) to corroborate measurements on the spinning disc. This is a first study
providing quantitative microscopic data on dynamic spatio-temporal interactions
of endosomes during root hair tip growth.
acknowledgement: "This work was supported by National Program for Sustainability I
(grant no. LO1204) provided by the Czech Ministry of Education and by Institutional
Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help
with the statistics."
article_number: '1262'
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Amparo
full_name: Rosero, Amparo
last_name: Rosero
- first_name: George
full_name: Komis, George
last_name: Komis
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Miroslav
full_name: Ovečka, Miroslav
last_name: Ovečka
- first_name: Boris
full_name: Voigt, Boris
last_name: Voigt
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
citation:
ama: von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root
hair growth. Frontiers in Plant Science. 2016;6(JAN2016). doi:10.3389/fpls.2015.01262
apa: von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt,
B., & Šamaj, J. (2016). Endosomal interactions during root hair growth. Frontiers
in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.01262
chicago: Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav
Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair
Growth.” Frontiers in Plant Science. Frontiers Research Foundation, 2016.
https://doi.org/10.3389/fpls.2015.01262.
ieee: D. von Wangenheim et al., “Endosomal interactions during root hair
growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research
Foundation, 2016.
ista: von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj
J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science.
6(JAN2016), 1262.
mla: von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.”
Frontiers in Plant Science, vol. 6, no. JAN2016, 1262, Frontiers Research
Foundation, 2016, doi:10.3389/fpls.2015.01262.
short: D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt,
J. Šamaj, Frontiers in Plant Science 6 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T06:49:18Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.3389/fpls.2015.01262
file:
- access_level: open_access
checksum: 3127eab844d53564bf47e2b6b42f1ca0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:36Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4760'
file_name: IST-2016-710-v1+1_fpls-06-01262.pdf
file_size: 1640550
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 6'
issue: JAN2016
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6094'
pubrep_id: '710'
quality_controlled: '1'
scopus_import: 1
status: public
title: Endosomal interactions during root hair growth
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: '1240'
abstract:
- lang: eng
text: 'Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as
gene regulators and may ultimately be more numerous than protein-coding genes
in the human genome. Despite large numbers of reported lncRNAs, reference annotations
are likely incomplete due to their lower and tighter tissue-specific expression
compared to mRNAs. An unexplored factor potentially confounding lncRNA identification
is inter-individual expression variability. Here, we characterize lncRNA natural
expression variability in human primary granulocytes. Results: We annotate granulocyte
lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple
lncRNAs absent from reference annotations, and use this to investigate three known
features (higher tissue-specificity, lower expression, and reduced splicing efficiency)
of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals
sampled three times at 1- or more than 1-month intervals. We show that lncRNAs
display significantly more inter-individual expression variability compared to
mRNAs. We confirm this finding in two independent human datasets by analyzing
multiple tissues from the GTEx project and lymphoblastoid cell lines from the
GEUVADIS project. Using the latter dataset we also show that including more human
donors into the transcriptome annotation pipeline allows identification of an
increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions:
A comprehensive annotation of lncRNAs is known to require an approach that is
sensitive to low and tight tissue-specific expression. Here we show that increased
inter-individual expression variability is an additional general lncRNA feature
to consider when creating a comprehensive annotation of human lncRNAs or proposing
their use as prognostic or disease markers.'
acknowledgement: "This study was partly funded by the Austrian Science Fund (FWF F43-B09,
FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of
Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth
Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the
CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe
Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing
and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions,
Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript."
article_number: '14'
author:
- first_name: Aleksandra
full_name: Kornienko, Aleksandra
last_name: Kornienko
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
- first_name: Philipp
full_name: Guenzl, Philipp
last_name: Guenzl
- first_name: Heinz
full_name: Gisslinger, Heinz
last_name: Gisslinger
- first_name: Bettina
full_name: Gisslinger, Bettina
last_name: Gisslinger
- first_name: Ciara
full_name: Cleary, Ciara
last_name: Cleary
- first_name: Robert
full_name: Kralovics, Robert
last_name: Kralovics
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
citation:
ama: Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher
natural expression variation than protein-coding genes in healthy humans. Genome
Biology. 2016;17(1). doi:10.1186/s13059-016-0873-8
apa: Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary,
C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans. Genome Biology.
BioMed Central. https://doi.org/10.1186/s13059-016-0873-8
chicago: Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger,
Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise
Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than
Protein-Coding Genes in Healthy Humans.” Genome Biology. BioMed Central,
2016. https://doi.org/10.1186/s13059-016-0873-8.
ieee: A. Kornienko et al., “Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans,” Genome Biology,
vol. 17, no. 1. BioMed Central, 2016.
ista: Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics
R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression
variation than protein-coding genes in healthy humans. Genome Biology. 17(1),
14.
mla: Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural
Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology,
vol. 17, no. 1, 14, BioMed Central, 2016, doi:10.1186/s13059-016-0873-8.
short: A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary,
R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '29'
ddc:
- '576'
department:
- _id: GaNo
doi: 10.1186/s13059-016-0873-8
file:
- access_level: open_access
checksum: a268beee1a690801c83ec6729f9ebc5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4789'
file_name: IST-2016-709-v1+1_s13059-016-0873-8.pdf
file_size: 2914601
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '6093'
pubrep_id: '709'
quality_controlled: '1'
scopus_import: 1
status: public
title: Long non-coding RNAs display higher natural expression variation than protein-coding
genes in healthy humans
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: 17
year: '2016'
...
---
_id: '1242'
abstract:
- lang: eng
text: A crucial step in the regulation of gene expression is binding of transcription
factor (TF) proteins to regulatory sites along the DNA. But transcription factors
act at nanomolar concentrations, and noise due to random arrival of these molecules
at their binding sites can severely limit the precision of regulation. Recent
work on the optimization of information flow through regulatory networks indicates
that the lower end of the dynamic range of concentrations is simply inaccessible,
overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain
proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest
a scheme in which transcription factors also act as indirect translational regulators,
binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule
acts as an independent sensor of the input concentration, and averaging over these
multiple sensors reduces the noise. We analyze information flow through this scheme
and identify conditions under which it outperforms direct transcriptional regulation.
Our results suggest that the dual role of homeodomain proteins is not just a historical
accident, but a solution to a crucial physics problem in the regulation of gene
expression.
acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions.
This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370
from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W.
acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561.
G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S."
article_number: '022404'
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aleksandra
full_name: Walczak, Aleksandra
last_name: Walczak
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of
transcription factor action by translational regulation. Physical Review E
Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404
apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending
the dynamic range of transcription factor action by translational regulation.
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404
chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik.
“Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”
Physical Review E Statistical Nonlinear and Soft Matter Physics. American
Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.
ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic
range of transcription factor action by translational regulation,” Physical
Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American
Institute of Physics, 2016.
ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic
range of transcription factor action by translational regulation. Physical Review
E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.
mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription
Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022404.
short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical
Nonlinear and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-04T00:00:00Z
date_updated: 2021-01-12T06:49:20Z
day: '04'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.93.022404
intvolume: ' 93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.02562
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6088'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extending the dynamic range of transcription factor action by translational
regulation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1241'
abstract:
- lang: eng
text: 'How likely is it that a population escapes extinction through adaptive evolution?
The answer to this question is of great relevance in conservation biology, where
we aim at species’ rescue and the maintenance of biodiversity, and in agriculture
and medicine, where we seek to hamper the emergence of pesticide or drug resistance.
By reshuffling the genome, recombination has two antagonistic effects on the probability
of evolutionary rescue: It generates and it breaks up favorable gene combinations.
Which of the two effects prevails depends on the fitness effects of mutations
and on the impact of stochasticity on the allele frequencies. In this article,
we analyze a mathematical model for rescue after a sudden environmental change
when adaptation is contingent on mutations at two loci. The analysis reveals a
complex nonlinear dependence of population survival on recombination. We moreover
find that, counterintuitively, a fast eradication of the wild type can promote
rescue in the presence of recombination. The model also shows that two-step rescue
is not unlikely to happen and can even be more likely than single-step rescue
(where adaptation relies on a single mutation), depending on the circumstances.'
acknowledgement: This work was made possible by a “For Women in Science” fellowship
(L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations
Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences
with financial support from the Federal Ministry for Science and Research Austria)
and European Research Council grant 250152 (to Nick Barton).
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics.
2016;202(2):721-732. doi:10.1534/genetics.115.180299
apa: Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary
rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299
chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in
Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.
ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,”
Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.
ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue.
Genetics. 202(2), 721–732.
mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary
Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016,
pp. 721–32, doi:10.1534/genetics.115.180299.
short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2023-02-21T10:24:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.115.180299
ec_funded: 1
intvolume: ' 202'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2015/07/06/022020.abstract
month: '02'
oa: 1
oa_version: Preprint
page: 721 - 732
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: L'OREAL Fellowship
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6091'
quality_controlled: '1'
scopus_import: 1
status: public
title: The role of recombination in evolutionary rescue
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1247'
abstract:
- lang: eng
text: The shaping of organs in plants depends on the intercellular flow of the phytohormone
auxin, of which the directional signaling is determined by the polar subcellular
localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics
of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID
kinase, which act antagonistically to mediate their apical-basal polar delivery.
Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase
activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting
from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding
for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant
phenotypes [i.e., reduced apical dominance, primary root length, lateral root
emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia;
decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems;
hypergravitropic root growth and response; increased IAA levels in shoot apices;
and reduced auxin accumulation in root meristems] support a role for RON3 in auxin
biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3
might act in PIN transporter trafficking. Indeed, pharmacological interference
with vesicle trafficking processes revealed that single ron3-2 and double ron3-2
rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our
data indicate that RON3 contributes to auxin-mediated development by playing a
role in PIN recycling and polarity establishment through regulation of the PP2A
complex activity.
acknowledgement: "This work was supported by the Ghent University Special Research
Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP)
(to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted
to the Agency for Science and Technology for\r\na predoctoral fellowship."
author:
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Pia
full_name: Neyt, Pia
last_name: Neyt
- first_name: Steven
full_name: De Groeve, Steven
last_name: De Groeve
- first_name: Stijn
full_name: Aesaert, Stijn
last_name: Aesaert
- first_name: Griet
full_name: Coussens, Griet
last_name: Coussens
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Leonardo
full_name: Bruno, Leonardo
last_name: Bruno
- first_name: Nancy
full_name: De Winne, Nancy
last_name: De Winne
- first_name: Annemie
full_name: Van Minnebruggen, Annemie
last_name: Van Minnebruggen
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Maria
full_name: Ponce, Maria
last_name: Ponce
- first_name: José
full_name: Micol, José
last_name: Micol
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Mieke
full_name: Van Lijsebettens, Mieke
last_name: Van Lijsebettens
citation:
ama: Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development
by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS.
2016;113(10):2768-2773. doi:10.1073/pnas.1501343112
apa: Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík,
J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1501343112
chicago: Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet
Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development
by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.
ieee: M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase
2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113,
no. 10. National Academy of Sciences, pp. 2768–2773, 2016.
ista: Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno
L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De
Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by
phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10),
2768–2773.
mla: Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase
2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113,
no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112.
short: M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík,
L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol,
J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-08T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '08'
department:
- _id: JiFr
doi: 10.1073/pnas.1501343112
ec_funded: 1
intvolume: ' 113'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/
month: '03'
oa: 1
oa_version: Submitted Version
page: 2768 - 2773
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6081'
quality_controlled: '1'
scopus_import: 1
status: public
title: ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation
of auxin transporter recycling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1246'
abstract:
- lang: eng
text: Near-field imaging is a powerful tool to investigate the complex structure
of light at the nanoscale. Recent advances in near-field imaging have indicated
the possibility for the complete reconstruction of both electric and magnetic
components of the evanescent field. Here we study the electro-magnetic field structure
of surface plasmon polariton waves propagating along subwavelength gold nanowires
by performing phase- and polarization-resolved near-field microscopy in collection
mode. By applying the optical reciprocity theorem, we describe the signal collected
by the probe as an overlap integral of the nanowire's evanescent field and the
probe's response function. As a result, we find that the probe's sensitivity to
the magnetic field is approximately equal to its sensitivity to the electric field.
Through rigorous modeling of the nanowire mode as well as the aperture probe response
function, we obtain a good agreement between experimentally measured signals and
a numerical model. Our findings provide a better understanding of aperture-based
near-field imaging of the nanoscopic plasmonic and photonic structures and are
helpful for the interpretation of future near-field experiments.
acknowledgement: 'This work is supported part of the research program of the Netherlands
Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization
for Scientific Research (NWO), and part of this work has been funded by the project
‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging
Technologies (FET) program within the Seventh Framework Programme for Research of
the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges
funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).'
article_number: '22665'
author:
- first_name: Irina
full_name: Kabakova, Irina
last_name: Kabakova
- first_name: Anouk
full_name: De Hoogh, Anouk
last_name: De Hoogh
- first_name: Ruben
full_name: Van Der Wel, Ruben
last_name: Van Der Wel
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Boris
full_name: Le Feber, Boris
last_name: Le Feber
- first_name: Laurens
full_name: Kuipers, Laurens
last_name: Kuipers
citation:
ama: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging
of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
2016;6. doi:10.1038/srep22665
apa: Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., &
Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665
chicago: Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris
Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665.
ieee: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers,
“Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific
Reports, vol. 6. Nature Publishing Group, 2016.
ista: Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016.
Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports.
6, 22665.
mla: Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic
Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group,
2016, doi:10.1038/srep22665.
short: I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers,
Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:55Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '07'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/srep22665
file:
- access_level: open_access
checksum: ca76236cb1aae22cb90c65313e2c5e98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5061'
file_name: IST-2016-707-v1+1_srep22665.pdf
file_size: 1425165
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6082'
pubrep_id: '707'
quality_controlled: '1'
scopus_import: 1
status: public
title: Imaging of electric and magnetic fields near plasmonic nanowires
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: '1244'
abstract:
- lang: eng
text: Cell polarity refers to a functional spatial organization of proteins that
is crucial for the control of essential cellular processes such as growth and
division. To establish polarity, cells rely on elaborate regulation networks that
control the distribution of proteins at the cell membrane. In fission yeast cells,
a microtubule-dependent network has been identified that polarizes the distribution
of signaling proteins that restricts growth to cell ends and targets the cytokinetic
machinery to the middle of the cell. Although many molecular components have been
shown to play a role in this network, it remains unknown which molecular functionalities
are minimally required to establish a polarized protein distribution in this system.
Here we show that a membrane-binding protein fragment, which distributes homogeneously
in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching
it to a cytoplasmic microtubule end-binding protein. This concentration results
in a polarized pattern of chimera proteins with a spatial extension that is very
reminiscent of natural polarity patterns in fission yeast. However, chimera levels
fluctuate in response to microtubule dynamics, and disruption of microtubules
leads to disappearance of the pattern. Numerical simulations confirm that the
combined functionality of membrane anchoring and microtubule tip affinity is in
principle sufficient to create polarized patterns. Our chimera protein may thus
represent a simple molecular functionality that is able to polarize the membrane,
onto which additional layers of molecular complexity may be built to provide the
temporal robustness that is typical of natural polarity patterns.
acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian
Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong
Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions;
and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the
manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor
Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse
organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”"
author:
- first_name: Pierre
full_name: Recouvreux, Pierre
last_name: Recouvreux
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Aristea
full_name: Grammoustianou, Aristea
last_name: Grammoustianou
- first_name: Pieter
full_name: Tenwolde, Pieter
last_name: Tenwolde
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
citation:
ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera
proteins with affinity for membranes and microtubule tips polarize in the membrane
of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113
apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &
Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule
tips polarize in the membrane of fission yeast cells. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1419248113
chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter
Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes
and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS.
National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113.
ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom,
“Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy
of Sciences, pp. 1811–1816, 2016.
ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016.
Chimera proteins with affinity for membranes and microtubule tips polarize in
the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.
mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and
Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS,
vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.
short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom,
PNAS 113 (2016) 1811–1816.
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-16T00:00:00Z
date_updated: 2021-01-12T06:49:21Z
day: '16'
department:
- _id: GaTk
doi: 10.1073/pnas.1419248113
intvolume: ' 113'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/
month: '02'
oa: 1
oa_version: Submitted Version
page: 1811 - 1816
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6085'
quality_controlled: '1'
scopus_import: 1
status: public
title: Chimera proteins with affinity for membranes and microtubule tips polarize
in the membrane of fission yeast cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1248'
abstract:
- lang: eng
text: Life depends as much on the flow of information as on the flow of energy.
Here we review the many efforts to make this intuition precise. Starting with
the building blocks of information theory, we explore examples where it has been
possible to measure, directly, the flow of information in biological networks,
or more generally where information-theoretic ideas have been used to guide the
analysis of experiments. Systems of interest range from single molecules (the
sequence diversity in families of proteins) to groups of organisms (the distribution
of velocities in flocks of birds), and all scales in between. Many of these analyses
are motivated by the idea that biological systems may have evolved to optimize
the gathering and representation of information, and we review the experimental
evidence for this optimization, again across a wide range of scales.
acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation
(PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651),
by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations."
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review
of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803
apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems.
Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803
chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803.
ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual
Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.
ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual
Review of Condensed Matter Physics. 7, 89–117.
mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.”
Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016,
pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.
short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016)
89–117.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '10'
department:
- _id: GaTk
doi: 10.1146/annurev-conmatphys-031214-014803
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.8752
month: '03'
oa: 1
oa_version: Preprint
page: 89 - 117
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Annual Review of Condensed Matter Physics
publication_status: published
publisher: Annual Reviews
publist_id: '6080'
quality_controlled: '1'
scopus_import: 1
status: public
title: Information processing in living systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1249'
abstract:
- lang: eng
text: 'Actin and myosin assemble into a thin layer of a highly dynamic network underneath
the membrane of eukaryotic cells. This network generates the forces that drive
cell- and tissue-scale morphogenetic processes. The effective material properties
of this active network determine large-scale deformations and other morphogenetic
events. For example, the characteristic time of stress relaxation (the Maxwell
time τM) in the actomyosin sets the timescale of large-scale deformation of the
cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic
length λ) sets the length scale of slow deformations, and a large hydrodynamic
length is a prerequisite for long-ranged cortical flows. Here we introduce a method
to determine physical parameters of the actomyosin cortical layer in vivo directly
from laser ablation experiments. For this we investigate the cortical response
to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the
gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained
physical description of the cortex in terms of a two-dimensional thin film of
an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic
length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated
the response to laser ablation in two different ways: by quantifying flow and
density fields as a function of space and time, and by determining the time evolution
of the shape of the ablated region. Importantly, both methods provide best-fit
physical parameters that are in close agreement with each other and that are similar
to previous estimates in the two systems. Our method provides an accurate and
robust means for measuring physical parameters of the actomyosin cortical layer.
It can be useful for investigations of actomyosin mechanics at the cellular-scale,
but also for providing insights into the active mechanics processes that govern
tissue-scale morphogenesis.'
acknowledgement: S.W.G. acknowledges support by grant no. 281903 from the European
Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft.
S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung
der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20).
We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We
thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.
author:
- first_name: Arnab
full_name: Saha, Arnab
last_name: Saha
- first_name: Masatoshi
full_name: Nishikawa, Masatoshi
last_name: Nishikawa
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Stephan
full_name: Grill, Stephan
last_name: Grill
citation:
ama: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining
physical properties of the cell cortex. Biophysical Journal. 2016;110(6):1421-1429.
doi:10.1016/j.bpj.2016.02.013
apa: Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., &
Grill, S. (2016). Determining physical properties of the cell cortex. Biophysical
Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2016.02.013
chicago: Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg,
Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell
Cortex.” Biophysical Journal. Biophysical Society, 2016. https://doi.org/10.1016/j.bpj.2016.02.013.
ieee: A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S.
Grill, “Determining physical properties of the cell cortex,” Biophysical Journal,
vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.
ista: Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016.
Determining physical properties of the cell cortex. Biophysical Journal. 110(6),
1421–1429.
mla: Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” Biophysical
Journal, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:10.1016/j.bpj.2016.02.013.
short: A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill,
Biophysical Journal 110 (2016) 1421–1429.
date_created: 2018-12-11T11:50:56Z
date_published: 2016-03-29T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '29'
ddc:
- '572'
- '576'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2016.02.013
file:
- access_level: open_access
checksum: c408cf2e25a25c8d711cffea524bda55
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:54Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4845'
file_name: IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf
file_size: 1965645
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 110'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1421 - 1429
project:
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '6079'
pubrep_id: '706'
quality_controlled: '1'
scopus_import: 1
status: public
title: Determining physical properties of the cell cortex
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: 110
year: '2016'
...
---
_id: '1251'
abstract:
- lang: eng
text: Plant growth and architecture is regulated by the polar distribution of the
hormone auxin. Polarity and flexibility of this process is provided by constant
cycling of auxin transporter vesicles along actin filaments, coordinated by a
positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling
are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic
acid (NPA), counteracting the effect of auxin; however, underlying targets and
mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis
thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant,
although likely indirect, TWD1 interactor, and show TWD1-dependent regulation
of actin filament organization and dynamics and that TWD1 is required for NPA-mediated
actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence
of efflux transporters, and as a consequence act7 and twd1 share developmental
and physiological phenotypes indicative of defects in auxin transport. These can
be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide
evidence that TWD1 determines downstreamlocations of auxin efflux transporters
by adjusting actin filament debundling and dynamizing processes and mediating
NPA action on the latter. This function appears to be evolutionary conserved since
TWD1 expression in budding yeast alters actin polarization and cell polarity and
provides NPA sensitivity.
acknowledgement: ' This work was supported by grants from the European Social Fund
(CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F.
and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under
the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and
Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program
for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the
Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all
to M.G.). '
author:
- first_name: Jinsheng
full_name: Zhu, Jinsheng
last_name: Zhu
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Valpuri
full_name: Sovero, Valpuri
last_name: Sovero
- first_name: Martin
full_name: Di Donato, Martin
last_name: Di Donato
- first_name: Pei
full_name: Ge, Pei
last_name: Ge
- first_name: Jacqueline
full_name: Oehri, Jacqueline
last_name: Oehri
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Pengchao
full_name: Hao, Pengchao
last_name: Hao
- first_name: Miriam
full_name: Linnert, Miriam
last_name: Linnert
- first_name: Noelia
full_name: Burgardt, Noelia
last_name: Burgardt
- first_name: Christian
full_name: Lücke, Christian
last_name: Lücke
- first_name: Matthias
full_name: Weiwad, Matthias
last_name: Weiwad
- first_name: Max
full_name: Michel, Max
last_name: Michel
- first_name: Oliver
full_name: Weiergräber, Oliver
last_name: Weiergräber
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Noel
full_name: Ferro, Noel
last_name: Ferro
- first_name: Yoichiro
full_name: Fukao, Yoichiro
last_name: Fukao
- first_name: Céline
full_name: Hoffmann, Céline
last_name: Hoffmann
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Clément
full_name: Thomas, Clément
last_name: Thomas
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin
transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948.
doi:10.1105/tpc.15.00726
apa: Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler,
M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on
actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.15.00726
chicago: Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di
Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of
Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell.
American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726.
ieee: J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport
inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4.
American Society of Plant Biologists, pp. 930–948, 2016.
ista: Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B,
Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann
S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml
J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport
inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.
mla: Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport
Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4,
American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726.
short: J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri,
B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O.
Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann,
R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:24Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.15.00726
intvolume: ' 28'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/
month: '04'
oa: 1
oa_version: Submitted Version
page: 930 - 948
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6078'
quality_controlled: '1'
scopus_import: 1
status: public
title: TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton
dynamics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '1252'
abstract:
- lang: eng
text: We study the homomorphism induced in homology by a closed correspondence between
topological spaces, using projections from the graph of the correspondence to
its domain and codomain. We provide assumptions under which the homomorphism induced
by an outer approximation of a continuous map coincides with the homomorphism
induced in homology by the map. In contrast to more classical results we do not
require that the projection to the domain have acyclic preimages. Moreover, we
show that it is possible to retrieve correct homological information from a correspondence
even if some data is missing or perturbed. Finally, we describe an application
to combinatorial maps that are either outer approximations of continuous maps
or reconstructions of such maps from a finite set of data points.
acknowledgement: "The authors gratefully acknowledge the support of the Lorenz Center
which\r\nprovided an opportunity for us to discuss in depth the work of this paper.
Research leading to these results has received funding from Fundo Europeu de Desenvolvimento
Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
(POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia
e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie
Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 622033 (supporting PP). The work of the first and
third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019,
1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second
author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029),
Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan."
article_processing_charge: No
article_type: original
author:
- first_name: Shaun
full_name: Harker, Shaun
last_name: Harker
- first_name: Hiroshi
full_name: Kokubu, Hiroshi
last_name: Kokubu
- first_name: Konstantin
full_name: Mischaikow, Konstantin
last_name: Mischaikow
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from
a correspondence. Proceedings of the American Mathematical Society. 2016;144(4):1787-1801.
doi:10.1090/proc/12812
apa: Harker, S., Kokubu, H., Mischaikow, K., & Pilarczyk, P. (2016). Inducing
a map on homology from a correspondence. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12812
chicago: Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk.
“Inducing a Map on Homology from a Correspondence.” Proceedings of the American
Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12812.
ieee: S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on
homology from a correspondence,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.
ista: Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology
from a correspondence. Proceedings of the American Mathematical Society. 144(4),
1787–1801.
mla: Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” Proceedings
of the American Mathematical Society, vol. 144, no. 4, American Mathematical
Society, 2016, pp. 1787–801, doi:10.1090/proc/12812.
short: S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American
Mathematical Society 144 (2016) 1787–1801.
date_created: 2018-12-11T11:50:57Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2022-05-24T09:35:58Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/12812
ec_funded: 1
external_id:
arxiv:
- '1411.7563'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.7563
month: '04'
oa: 1
oa_version: Preprint
page: 1787 - 1801
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 1088-6826
publication_status: published
publisher: American Mathematical Society
publist_id: '6075'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inducing a map on homology from a correspondence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1254'
abstract:
- lang: eng
text: We use rigorous numerical techniques to compute a lower bound for the exponent
of expansivity outside a neighborhood of the critical point for thousands of intervals
of parameter values in the quadratic family. We first compute a radius of the
critical neighborhood outside which the map is uniformly expanding. This radius
is taken as small as possible, yet large enough for our numerical procedure to
succeed in proving that the expansivity exponent outside this neighborhood is
positive. Then, for each of the intervals, we compute a lower bound for this expansivity
exponent, valid for all the parameters in that interval. We illustrate and study
the distribution of the radii and the expansivity exponents. The results of our
computations are mathematically rigorous. The source code of the software and
the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.
acknowledgement: "AG and PP were partially supported by Abdus Salam International
Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS,
and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento
Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade
(POFC) and from the Portuguese national funds through Fundação para a Ciência e
a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645
(ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics
\ of Kyoto University for providing access\r\nto their server for conducting
\ computations for this\r\nproject."
author:
- first_name: Ali
full_name: Golmakani, Ali
last_name: Golmakani
- first_name: Stefano
full_name: Luzzatto, Stefano
last_name: Luzzatto
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical
neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124.
doi:10.1080/10586458.2015.1048011
apa: Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity
outside a critical neighborhood in the quadratic family. Experimental Mathematics.
Taylor and Francis. https://doi.org/10.1080/10586458.2015.1048011
chicago: Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity
Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics.
Taylor and Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011.
ieee: A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside
a critical neighborhood in the quadratic family,” Experimental Mathematics,
vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.
ista: Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a
critical neighborhood in the quadratic family. Experimental Mathematics. 25(2),
116–124.
mla: Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood
in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor
and Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.
short: A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016)
116–124.
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-02T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '02'
department:
- _id: HeEd
doi: 10.1080/10586458.2015.1048011
ec_funded: 1
intvolume: ' 25'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.00116
month: '04'
oa: 1
oa_version: Preprint
page: 116 - 124
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Experimental Mathematics
publication_status: published
publisher: Taylor and Francis
publist_id: '6071'
quality_controlled: '1'
scopus_import: 1
status: public
title: Uniform expansivity outside a critical neighborhood in the quadratic family
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '1255'
abstract:
- lang: eng
text: Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital
neuronal functions although the role it plays in insect and crustacean immunity
is less well understood. In this study, we combine different approaches to understand
the roles that Dscam1 plays in fitness-related contexts in two model insect species.
Contrary to our expectations, we found no short-term modulation of Dscam1 gene
expression after haemocoelic or oral bacterial exposure in Tribolium castaneum,
or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore,
RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce
T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion
defects, as well as dramatically reduced fecundity in males and females. We suggest
that Dscam1 does not always play a straightforward role in immunity, but strongly
influences behaviour and fecundity. This study takes a step towards understanding
more about the role of this intriguing gene from different phenotypic perspectives.
acknowledgement: "We thank Dietmar Schmucker for reading a draft of this manuscript
and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert,
Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions.
We also thank two anonymous reviewers for their comments. This study was supported
by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.)
and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2
to R.P. and J.K.)."
article_number: '160138'
author:
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Kristina
full_name: Wensing, Kristina
last_name: Wensing
- first_name: Luisa
full_name: Woestmann, Luisa
last_name: Woestmann
- first_name: Hendrik
full_name: Eggert, Hendrik
last_name: Eggert
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Marlene
full_name: Sroka, Marlene
last_name: Sroka
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: 'Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule
1: Testing for a role in insect immunity, behaviour and reproduction. Royal
Society Open Science. 2016;3(4). doi:10.1098/rsos.160138'
apa: 'Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka,
M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for
a role in insect immunity, behaviour and reproduction. Royal Society Open Science.
Royal Society, The. https://doi.org/10.1098/rsos.160138'
chicago: 'Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara
Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage.
“Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity,
Behaviour and Reproduction.” Royal Society Open Science. Royal Society,
The, 2016. https://doi.org/10.1098/rsos.160138.'
ieee: 'R. Peuß et al., “Down syndrome cell adhesion molecule 1: Testing for
a role in insect immunity, behaviour and reproduction,” Royal Society Open
Science, vol. 3, no. 4. Royal Society, The, 2016.'
ista: 'Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack
J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing
for a role in insect immunity, behaviour and reproduction. Royal Society Open
Science. 3(4), 160138.'
mla: 'Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for
a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open
Science, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:10.1098/rsos.160138.'
short: R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J.
Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:49:25Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rsos.160138
file:
- access_level: open_access
checksum: c3cd84666c8dc0ce6a784f1c82c1cf68
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:01Z
date_updated: 2020-07-14T12:44:41Z
file_id: '5049'
file_name: IST-2016-704-v1+1_160138.full.pdf
file_size: 627377
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_status: published
publisher: Royal Society, The
publist_id: '6070'
pubrep_id: '704'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity,
behaviour and reproduction'
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: 3
year: '2016'
...
---
_id: '1256'
abstract:
- lang: eng
text: Simulink is widely used for model driven development (MDD) of industrial software
systems. Typically, the Simulink based development is initiated from Stateflow
modeling, followed by simulation, validation and code generation mapped to physical
execution platforms. However, recent industrial trends have raised the demands
of rigorous verification on safety-critical applications, which is unfortunately
challenging for Simulink. In this paper, we present an approach to bridge the
Stateflow based model driven development and a well- defined rigorous verification.
First, we develop a self- contained toolkit to translate Stateflow model into
timed automata, where major advanced modeling features in Stateflow are supported.
Taking advantage of the strong verification capability of Uppaal, we can not only
find bugs in Stateflow models which are missed by Simulink Design Verifier, but
also check more important temporal properties. Next, we customize a runtime verifier
for the generated nonintrusive VHDL and C code of Stateflow model for monitoring.
The major strength of the customization is the flexibility to collect and analyze
runtime properties with a pure software monitor, which opens more opportunities
for engineers to achieve high reliability of the target system compared with the
traditional act that only relies on Simulink Polyspace. We incorporate these two
parts into original Stateflow based MDD seamlessly. In this way, safety-critical
properties are both verified at the model level, and at the consistent system
implementation level with physical execution environment in consideration. We
apply our approach on a train controller design, and the verified implementation
is tested and deployed on a real hardware platform.
acknowledgement: This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886,
NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.
article_number: '7461337'
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Yixiao
full_name: Yang, Yixiao
last_name: Yang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ming
full_name: Gu, Ming
last_name: Gu
- first_name: Jiaguang
full_name: Sun, Jiaguang
last_name: Sun
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: 'Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation:
A verification approach and a real-time train controller design. In: IEEE; 2016.
doi:10.1109/RTAS.2016.7461337'
apa: 'Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016).
From stateflow simulation to verified implementation: A verification approach
and a real-time train controller design. Presented at the RTAS: Real-time and
Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. https://doi.org/10.1109/RTAS.2016.7461337'
chicago: 'Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and
Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification
Approach and a Real-Time Train Controller Design.” IEEE, 2016. https://doi.org/10.1109/RTAS.2016.7461337.'
ieee: 'Y. Jiang et al., “From stateflow simulation to verified implementation:
A verification approach and a real-time train controller design,” presented at
the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna,
Austria, 2016.'
ista: 'Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow
simulation to verified implementation: A verification approach and a real-time
train controller design. RTAS: Real-time and Embedded Technology and Applications
Symposium, 7461337.'
mla: 'Jiang, Yu, et al. From Stateflow Simulation to Verified Implementation:
A Verification Approach and a Real-Time Train Controller Design. 7461337,
IEEE, 2016, doi:10.1109/RTAS.2016.7461337.'
short: Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016.
conference:
end_date: 2016-04-14
location: Vienna, Austria
name: 'RTAS: Real-time and Embedded Technology and Applications Symposium'
start_date: 2016-04-11
date_created: 2018-12-11T11:50:58Z
date_published: 2016-04-27T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '27'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1109/RTAS.2016.7461337
file:
- access_level: open_access
checksum: 42f0462911cc9957f2356b12fb33b4b6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:31Z
date_updated: 2020-07-14T12:44:41Z
file_id: '4949'
file_name: IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf
file_size: 1293599
relation: main_file
file_date_updated: 2020-07-14T12:44:41Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '6069'
pubrep_id: '780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'From stateflow simulation to verified implementation: A verification approach
and a real-time train controller design'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1257'
abstract:
- lang: eng
text: We consider products of random matrices that are small, independent identically
distributed perturbations of a fixed matrix (Formula presented.). Focusing on
the eigenvalues of (Formula presented.) of a particular size we obtain a limit
to a SDE in a critical scaling. Previous results required (Formula presented.)
to be a (conjugated) unitary matrix so it could not have eigenvalues of different
modulus. From the result we can also obtain a limit SDE for the Markov process
given by the action of the random products on the flag manifold. Applying the
result to random Schrödinger operators we can improve some results by Valko and
Virag showing GOE statistics for the rescaled eigenvalue process of a sequence
of Anderson models on long boxes. In particular, we solve a problem posed in their
work.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010
RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework
Programme FP7/2007-2013, REA Grant 291734.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
- first_name: Bálint
full_name: Virág, Bálint
last_name: Virág
citation:
ama: Sadel C, Virág B. A central limit theorem for products of random matrices and
GOE statistics for the Anderson model on long boxes. Communications in Mathematical
Physics. 2016;343(3):881-919. doi:10.1007/s00220-016-2600-4
apa: Sadel, C., & Virág, B. (2016). A central limit theorem for products of
random matrices and GOE statistics for the Anderson model on long boxes. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2600-4
chicago: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products
of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications
in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2600-4.
ieee: C. Sadel and B. Virág, “A central limit theorem for products of random matrices
and GOE statistics for the Anderson model on long boxes,” Communications in
Mathematical Physics, vol. 343, no. 3. Springer, pp. 881–919, 2016.
ista: Sadel C, Virág B. 2016. A central limit theorem for products of random matrices
and GOE statistics for the Anderson model on long boxes. Communications in Mathematical
Physics. 343(3), 881–919.
mla: Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of
Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications
in Mathematical Physics, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:10.1007/s00220-016-2600-4.
short: C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.
date_created: 2018-12-11T11:50:59Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:49:26Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2600-4
ec_funded: 1
file:
- access_level: open_access
checksum: 4fb2411d9c2f56676123165aad46c828
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:02Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5119'
file_name: IST-2016-703-v1+1_s00220-016-2600-4.pdf
file_size: 800792
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 343'
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 881 - 919
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6067'
pubrep_id: '703'
quality_controlled: '1'
scopus_import: 1
status: public
title: A central limit theorem for products of random matrices and GOE statistics
for the Anderson model on long boxes
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: 343
year: '2016'
...
---
_id: '1259'
abstract:
- lang: eng
text: We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body
system with two-body interactions. For suitable interaction potentials that have
a strong enough attractive tail in order to allow for two-body bound states, but
are otherwise sufficiently repulsive to guarantee stability of the system, we
show that in the low-density limit the ground state of this model consists of
a Bose–Einstein condensate of fermion pairs. The latter can be described by means
of the Gross–Pitaevskii energy functional.
acknowledgement: Partial financial support from the DFG grant GRK 1838, as well as
the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged.
article_number: '13'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Gerhard
full_name: Bräunlich, Gerhard
last_name: Bräunlich
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly
interacting fermions in the low density limit. Mathematical Physics, Analysis
and Geometry. 2016;19(2). doi:10.1007/s11040-016-9209-x
apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2016). Bogolubov–Hartree–Fock
theory for strongly interacting fermions in the low density limit. Mathematical
Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9209-x
chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock
Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical
Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9209-x.
ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory
for strongly interacting fermions in the low density limit,” Mathematical Physics,
Analysis and Geometry, vol. 19, no. 2. Springer, 2016.
ista: Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for
strongly interacting fermions in the low density limit. Mathematical Physics,
Analysis and Geometry. 19(2), 13.
mla: Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting
Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry,
vol. 19, no. 2, 13, Springer, 2016, doi:10.1007/s11040-016-9209-x.
short: G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and
Geometry 19 (2016).
date_created: 2018-12-11T11:50:59Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:27Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11040-016-9209-x
file:
- access_level: open_access
checksum: 9954f685cc25c58d7f1712c67b47ad8d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:13Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4736'
file_name: IST-2016-702-v1+1_s11040-016-9209-x.pdf
file_size: 506242
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '6066'
pubrep_id: '702'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low
density limit
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: 19
year: '2016'
...
---
_id: '1260'
abstract:
- lang: eng
text: In this work, the Gardner problem of inferring interactions and fields for
an Ising neural network from given patterns under a local stability hypothesis
is addressed under a dual perspective. By means of duality arguments, an integer
linear system is defined whose solution space is the dual of the Gardner space
and whose solutions represent mutually unstable patterns. We propose and discuss
Monte Carlo methods in order to find and remove unstable patterns and uniformly
sample the space of interactions thereafter. We illustrate the problem on a set
of real data and perform ensemble calculation that shows how the emergence of
phase dominated by unstable patterns can be triggered in a nonlinear discontinuous
way.
article_number: '1650067'
article_processing_charge: No
article_type: original
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. The dual of the space of interactions in neural network models.
International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674
apa: De Martino, D. (2016). The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. World Scientific Publishing.
https://doi.org/10.1142/S0129183116500674
chicago: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C. World Scientific Publishing,
2016. https://doi.org/10.1142/S0129183116500674.
ieee: D. De Martino, “The dual of the space of interactions in neural network models,”
International Journal of Modern Physics C, vol. 27, no. 6. World Scientific
Publishing, 2016.
ista: De Martino D. 2016. The dual of the space of interactions in neural network
models. International Journal of Modern Physics C. 27(6), 1650067.
mla: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network
Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067,
World Scientific Publishing, 2016, doi:10.1142/S0129183116500674.
short: D. De Martino, International Journal of Modern Physics C 27 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:28Z
day: '01'
department:
- _id: GaTk
doi: 10.1142/S0129183116500674
external_id:
arxiv:
- '1505.02963'
intvolume: ' 27'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.02963
month: '06'
oa: 1
oa_version: Preprint
publication: International Journal of Modern Physics C
publication_status: published
publisher: World Scientific Publishing
publist_id: '6065'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dual of the space of interactions in neural network models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2016'
...
---
_id: '1261'
abstract:
- lang: eng
text: 'We consider a non-standard finite-volume discretization of a strongly non-linear
fourth order diffusion equation on the d-dimensional cube, for arbitrary . The
scheme preserves two important structural properties of the equation: the first
is the interpretation as a gradient flow in a mass transportation metric, and
the second is an intimate relation to a linear Fokker-Planck equation. Thanks
to these structural properties, the scheme possesses two discrete Lyapunov functionals.
These functionals approximate the entropy and the Fisher information, respectively,
and their dissipation rates converge to the optimal ones in the discrete-to-continuous
limit. Using the dissipation, we derive estimates on the long-time asymptotics
of the discrete solutions. Finally, we present results from numerical experiments
which indicate that our discretization is able to capture significant features
of the complex original dynamics, even with a rather coarse spatial resolution.'
acknowledgement: This research was supported by the DFG Collaborative Research Centers TRR 109, ‘
Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent
Effects ’ .
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Daniel
full_name: Matthes, Daniel
last_name: Matthes
citation:
ama: Maas J, Matthes D. Long-time behavior of a finite volume discretization for
a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023.
doi:10.1088/0951-7715/29/7/1992
apa: Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization
for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd.
https://doi.org/10.1088/0951-7715/29/7/1992
chicago: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization
for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd.,
2016. https://doi.org/10.1088/0951-7715/29/7/1992.
ieee: J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization
for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP
Publishing Ltd., pp. 1992–2023, 2016.
ista: Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization
for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.
mla: Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization
for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP
Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992.
short: J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-01-12T06:49:28Z
day: '10'
department:
- _id: JaMa
doi: 10.1088/0951-7715/29/7/1992
intvolume: ' 29'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1505.03178
month: '06'
oa: 1
oa_version: Preprint
page: 1992 - 2023
publication: Nonlinearity
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6062'
quality_controlled: '1'
scopus_import: 1
status: public
title: Long-time behavior of a finite volume discretization for a fourth order diffusion
equation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1264'
abstract:
- lang: eng
text: n contrast with the wealth of recent reports about the function of μ-adaptins
and clathrin adaptor protein (AP) complexes, there is very little information
about the motifs that determine the sorting of membrane proteins within clathrin-coated
vesicles in plants. Here, we investigated putative sorting signals in the large
cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin
transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking
and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are
involved in the binding of different μ-adaptins in vitro. However, only Phe-165,
which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking
and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis
but also localized to intracellular structures containing several layers of membranes
and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER
or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin
mutant, it accumulated in big intracellular structures containing LysoTracker
in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants
of other subunits of the AP-3 complex. Our data suggest that Phe-165, through
the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis
and for PIN1 trafficking along the secretory pathway, respectively.
acknowledgement: "We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL
construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing
the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive
GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis;
Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the
Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed
Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy
section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance."
author:
- first_name: Gloria
full_name: Sancho Andrés, Gloria
last_name: Sancho Andrés
- first_name: Esther
full_name: Soriano Ortega, Esther
last_name: Soriano Ortega
- first_name: Caiji
full_name: Gao, Caiji
last_name: Gao
- first_name: Joan
full_name: Bernabé Orts, Joan
last_name: Bernabé Orts
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Anna
full_name: Müller, Anna
id: 420AB15A-F248-11E8-B48F-1D18A9856A87
last_name: Müller
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Liwen
full_name: Jiang, Liwen
last_name: Jiang
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Fernando
full_name: Aniento, Fernando
last_name: Aniento
- first_name: Maria
full_name: Marcote, Maria
last_name: Marcote
citation:
ama: Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in
the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology.
2016;171(3):1965-1982. doi:10.1104/pp.16.00373
apa: Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan,
M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking
and localization of the PIN1 auxin efflux carrier. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373
chicago: Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts,
Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved
in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant
Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373.
ieee: G. Sancho Andrés et al., “Sorting motifs involved in the trafficking
and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol.
171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.
ista: Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller
A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved
in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology.
171(3), 1965–1982.
mla: Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and
Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol.
171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.
short: G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan,
A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology
171 (2016) 1965–1982.
date_created: 2018-12-11T11:51:01Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:29Z
day: '01'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1104/pp.16.00373
ec_funded: 1
intvolume: ' 171'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/
month: '07'
oa: 1
oa_version: Submitted Version
page: 1965 - 1982
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6059'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sorting motifs involved in the trafficking and localization of the PIN1 auxin
efflux carrier
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2016'
...
---
_id: '1266'
abstract:
- lang: eng
text: 'Cortical networks exhibit ‘global oscillations’, in which neural spike times
are entrained to an underlying oscillatory rhythm, but where individual neurons
fire irregularly, on only a fraction of cycles. While the network dynamics underlying
global oscillations have been well characterised, their function is debated. Here,
we show that such global oscillations are a direct consequence of optimal efficient
coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary
spikes, neurons need to share information about the network state. Ideally, membrane
potentials should be strongly correlated and reflect a ‘prediction error’ while
the spikes themselves are uncorrelated and occur rarely. We show that the most
efficient representation is when: (i) spike times are entrained to a global Gamma
rhythm (implying a consistent representation of the error); but (ii) few neurons
fire on each cycle (implying high efficiency), while (iii) excitation and inhibition
are tightly balanced. This suggests that cortical networks exhibiting such dynamics
are tuned to achieve a maximally efficient population code.'
acknowledgement: Boris Gutkin acknowledges funding by the Russian Academic Excellence
Project '5-100’.
article_number: e13824
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient
coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824
apa: Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a
signature of efficient coding in the presence of synaptic delays. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.13824
chicago: Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations
as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife.
eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.
ieee: M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature
of efficient coding in the presence of synaptic delays,” eLife, vol. 5,
no. 2016JULY. eLife Sciences Publications, 2016.
ista: Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of
efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.
mla: Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient
Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY,
e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.
short: M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).
date_created: 2018-12-11T11:51:02Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.7554/eLife.13824
file:
- access_level: open_access
checksum: dc52d967dc76174477bb258d84be2899
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4874'
file_name: IST-2016-700-v1+1_e13824-download.pdf
file_size: 2819055
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 5'
issue: 2016JULY
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6056'
pubrep_id: '700'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neural oscillations as a signature of efficient coding in the presence of synaptic
delays
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: 5
year: '2016'
...
---
_id: '1269'
abstract:
- lang: eng
text: Plants are continuously exposed to a myriad of external signals such as fluctuating
nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks
that can severely affect their development, growth, and fertility. As sessile
organisms, plants must therefore be able to sense and rapidly react to these external
inputs, activate efficient responses, and adjust development to changing conditions.
In recent years, significant progress has been made towards understanding the
molecular mechanisms underlying the intricate and complex communication between
plants and the environment. It is now becoming increasingly evident that hormones
have an important regulatory role in plant adaptation and defense mechanisms.
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Benková E. Plant hormones in interactions with the environment. Plant Molecular
Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8
apa: Benková, E. (2016). Plant hormones in interactions with the environment. Plant
Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8
chicago: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant
Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8.
ieee: E. Benková, “Plant hormones in interactions with the environment,” Plant
Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.
ista: Benková E. 2016. Plant hormones in interactions with the environment. Plant
Molecular Biology. 91(6), 597.
mla: Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant
Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.
short: E. Benková, Plant Molecular Biology 91 (2016) 597.
date_created: 2018-12-11T11:51:03Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:31Z
day: '01'
ddc:
- '581'
department:
- _id: EvBe
doi: 10.1007/s11103-016-0501-8
file:
- access_level: open_access
checksum: 0ffb7a15c5336b3a55248cc67021a825
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:28Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5349'
file_name: IST-2016-697-v1+1_s11103-016-0501-8.pdf
file_size: 297282
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 91'
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '597'
publication: Plant Molecular Biology
publication_status: published
publisher: Springer
publist_id: '6052'
pubrep_id: '697'
quality_controlled: '1'
scopus_import: 1
status: public
title: Plant hormones in interactions with the environment
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: 91
year: '2016'
...
---
_id: '1267'
abstract:
- lang: eng
text: We give a simplified proof of the nonexistence of large nuclei in the liquid
drop model and provide an explicit bound. Our bound is within a factor of 2.3
of the conjectured value and seems to be the first quantitative result.
acknowledgement: "Open access funding provided by Institute of Science and Technology
Austria.\r\n"
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Rowan
full_name: Killip, Rowan
last_name: Killip
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
citation:
ama: Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model.
Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8
apa: Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in
the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8
chicago: Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei
in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016.
https://doi.org/10.1007/s11005-016-0860-8.
ieee: R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid
drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer,
pp. 1033–1036, 2016.
ista: Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid
drop model. Letters in Mathematical Physics. 106(8), 1033–1036.
mla: Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.”
Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36,
doi:10.1007/s11005-016-0860-8.
short: R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.
date_created: 2018-12-11T11:51:02Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0860-8
file:
- access_level: open_access
checksum: d740a6a226e0f5f864f40e3e269d3cc0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:09Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4863'
file_name: IST-2016-698-v1+1_s11005-016-0860-8.pdf
file_size: 349464
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 106'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1033 - 1036
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6054'
pubrep_id: '698'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonexistence of large nuclei in the liquid drop model
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: 106
year: '2016'
...
---
_id: '1271'
abstract:
- lang: eng
text: 'Background: High directional persistence is often assumed to enhance the
efficiency of chemotactic migration. Yet, cells in vivo usually display meandering
trajectories with relatively low directional persistence, and the control and
function of directional persistence during cell migration in three-dimensional
environments are poorly understood. Results: Here, we use mesendoderm progenitors
migrating during zebrafish gastrulation as a model system to investigate the control
of directional persistence during migration in vivo. We show that progenitor cells
alternate persistent run phases with tumble phases that result in cell reorientation.
Runs are characterized by the formation of directed actin-rich protrusions and
tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions
or blebs leads to longer or shorter run phases, respectively. Importantly, both
reducing and increasing run phases result in larger spatial dispersion of the
cells, indicative of reduced migration precision. A physical model quantitatively
recapitulating the migratory behavior of mesendoderm progenitors indicates that
the ratio of tumbling to run times, and thus the specific degree of directional
persistence of migration, are critical for optimizing migration precision. Conclusions:
Together, our experiments and model provide mechanistic insight into the control
of migration directionality for cells moving in three-dimensional environments
that combine different protrusion types, whereby the proportion of blebs to actin-rich
protrusions determines the directional persistence and precision of movement by
regulating the ratio of tumbling to run times.'
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch
lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor
discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM.
Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand
imaging facilities for help and advice at various stages of this project. This work
was supported by the Max Planck Society, the Medical Research Council UK (core funding
to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education
(454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and
PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010)
to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also
supported by the Francis Crick Institute which receives its core funding from Cancer
Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome
Trust (FC001317) to GS."
article_number: '74'
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Pawel
full_name: Romanczuk, Pawel
last_name: Romanczuk
- first_name: Weimiao
full_name: Yu, Weimiao
last_name: Yu
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Kenzo
full_name: Ivanovitch, Kenzo
last_name: Ivanovitch
- first_name: Guillame
full_name: Salbreux, Guillame
last_name: Salbreux
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
citation:
ama: Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating
blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x
apa: Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux,
G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich
protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x
chicago: Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch,
Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration
by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central,
2016. https://doi.org/10.1186/s12915-016-0294-x.
ieee: A. Diz Muñoz et al., “Steering cell migration by alternating blebs
and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central,
2016.
ista: Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg
C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich
protrusions. BMC Biology. 14(1), 74.
mla: Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich
Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x.
short: A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux,
C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-02T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '02'
ddc:
- '572'
- '576'
department:
- _id: CaHe
doi: 10.1186/s12915-016-0294-x
file:
- access_level: open_access
checksum: 0bfa484ac69a0a560fb9a4589aeda7f6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5002'
file_name: IST-2016-695-v1+1_s12915-016-0294-x.pdf
file_size: 1875695
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 252064B8-B435-11E9-9278-68D0E5697425
grant_number: HE_3231/6-1
name: Analysis of the Formation and Function of Different Cell Protusion Types During
Cell Migration in Vivo
publication: BMC Biology
publication_status: published
publisher: BioMed Central
publist_id: '6049'
pubrep_id: '695'
quality_controlled: '1'
scopus_import: 1
status: public
title: Steering cell migration by alternating blebs and actin-rich protrusions
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: '1273'
abstract:
- lang: eng
text: Lateral root primordia (LRP) originate from pericycle stem cells located deep
within parental root tissues. LRP emerge through overlying root tissues by inducing
auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible
auxin influx carrier LAX3 plays a key role concentrating this signal in cells
overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying
new LRP is crucial to ensure that auxin-regulated cell separation occurs solely
along their shared walls. Multiscale modeling has predicted that this highly focused
pattern of expression requires auxin to sequentially induce auxin efflux and influx
carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report
that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE
FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound
by the transcription factor LBD29, which is a direct target for regulation by
ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX
transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral
root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin
is required to coordinate cell separation and organ emergence.
acknowledgement: "We acknowledge the support of glasshouse technicians at the University
of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock
Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported
by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and
M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and
FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship
awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS)
Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development
under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a
European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and
a European Reintegration Grant under the 7th framework of the European Commission
[ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated
by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.);
The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan:
Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and
a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research
performed by S.M.B. and A.G. were provided by University of California, Davis startup
funds."
author:
- first_name: Silvana
full_name: Porco, Silvana
last_name: Porco
- first_name: Antoine
full_name: Larrieu, Antoine
last_name: Larrieu
- first_name: Yujuan
full_name: Du, Yujuan
last_name: Du
- first_name: Allison
full_name: Gaudinier, Allison
last_name: Gaudinier
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Kamal
full_name: Swarup, Kamal
last_name: Swarup
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Britta
full_name: Kuempers, Britta
last_name: Kuempers
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Julien
full_name: Lavenus, Julien
last_name: Lavenus
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Kristine
full_name: Hill, Kristine
last_name: Hill
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Hidehiro
full_name: Fukaki, Hidehiro
last_name: Fukaki
- first_name: Siobhan
full_name: Brady, Siobhan
last_name: Brady
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Benjamin
full_name: Peéet, Benjamin
last_name: Peéet
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
citation:
ama: Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development.
2016;143(18):3340-3349. doi:10.1242/dev.136283
apa: Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett,
M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription
factor LBD29 regulation of auxin influx carrier LAX3. Development. Company
of Biologists. https://doi.org/10.1242/dev.136283
chicago: Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki
Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis
Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier
LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.
ieee: S. Porco et al., “Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development,
vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016.
ista: Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers
B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres
B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent
on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development.
143(18), 3340–3349.
mla: Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent
on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development,
vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.
short: S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup,
B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki,
S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '13'
department:
- _id: EvBe
doi: 10.1242/dev.136283
intvolume: ' 143'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01595056/
month: '09'
oa: 1
oa_version: Preprint
page: 3340 - 3349
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6044'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lateral root emergence in Arabidopsis is dependent on transcription factor
LBD29 regulation of auxin influx carrier LAX3
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1272'
abstract:
- lang: eng
text: We study different means to extend offsetting based on skeletal structures
beyond the well-known constant-radius and mitered offsets supported by Voronoi
diagrams and straight skeletons, for which the orthogonal distance of offset elements
to their respective input elements is constant and uniform over all input elements.
Our main contribution is a new geometric structure, called variable-radius Voronoi
diagram, which supports the computation of variable-radius offsets, i.e., offsets
whose distance to the input is allowed to vary along the input. We discuss properties
of this structure and sketch a prototype implementation that supports the computation
of variable-radius offsets based on this new variant of Voronoi diagrams.
acknowledgement: 'This work was supported by Austrian Science Fund (FWF): P25816-N15.'
author:
- first_name: Martin
full_name: Held, Martin
last_name: Held
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using
skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721.
doi:10.1080/16864360.2016.1150718
apa: Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of
planar structures using skeletons. Computer-Aided Design and Applications.
Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718
chicago: Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting
of Planar Structures Using Skeletons.” Computer-Aided Design and Applications.
Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718.
ieee: M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures
using skeletons,” Computer-Aided Design and Applications, vol. 13, no.
5. Taylor and Francis, pp. 712–721, 2016.
ista: Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures
using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.
mla: Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.”
Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis,
2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.
short: M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13
(2016) 712–721.
date_created: 2018-12-11T11:51:04Z
date_published: 2016-09-02T00:00:00Z
date_updated: 2021-01-12T06:49:32Z
day: '02'
ddc:
- '004'
- '516'
department:
- _id: HeEd
doi: 10.1080/16864360.2016.1150718
file:
- access_level: open_access
checksum: c746f3a48edb62b588d92ea5d0fd2c0e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:20Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5206'
file_name: IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf
file_size: 1678369
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 712 - 721
publication: Computer-Aided Design and Applications
publication_status: published
publisher: Taylor and Francis
publist_id: '6048'
pubrep_id: '694'
quality_controlled: '1'
scopus_import: 1
status: public
title: Generalized offsetting of planar structures using skeletons
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: 13
year: '2016'
...
---
_id: '1279'
abstract:
- lang: eng
text: During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory
inputdriven neuronal firing patterns are replayed. Such replay is thought to be
important for plasticity- related processes and consolidation of memory traces.
It has previously been shown that the electrical stimulation-induced disruption
of SWR events interferes with learning in rodents in different experimental paradigms.
On the other hand, the cognitive map theory posits that the plastic changes of
the firing of hippocampal place cells constitute the electrophysiological counterpart
of the spatial learning, observable at the behavioral level. Therefore, we tested
whether intact SWR events occurring during the sleep/rest session after the first
exploration of a novel environment are needed for the stabilization of the CA1
code, which process requires plasticity. We found that the newly-formed representation
in the CA1 has the same level of stability with optogenetic SWR blockade as with
a control manipulation that delivered the same amount of light into the brain.
Therefore our results suggest that at least in the case of passive exploratory
behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles.
acknowledgement: '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 n° [291734] via the IST FELLOWSHIP
awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant
(acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We
thank Lauri Viljanto for technical help in building the ripple detector.'
article_number: e0164675
author:
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Markku
full_name: Penttonen, Markku
last_name: Penttonen
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari
JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere
with the formation of stable spatial representation in the CA1 area of the hippocampus.
PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675
apa: Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero,
D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple
events in sleep does not interfere with the formation of stable spatial representation
in the CA1 area of the hippocampus. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0164675
chicago: Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen,
Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp
Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial
Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pone.0164675.
ieee: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero,
and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep
does not interfere with the formation of stable spatial representation in the
CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library
of Science, 2016.
ista: Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari
JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not
interfere with the formation of stable spatial representation in the CA1 area
of the hippocampus. PLoS One. 11(10), e0164675.
mla: Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events
in Sleep Does Not Interfere with the Formation of Stable Spatial Representation
in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675,
Public Library of Science, 2016, doi:10.1371/journal.pone.0164675.
short: K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero,
J.L. Csicsvari, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:06Z
date_published: 2016-10-19T00:00:00Z
date_updated: 2021-01-12T06:49:35Z
day: '19'
ddc:
- '570'
- '571'
department:
- _id: JoCs
doi: 10.1371/journal.pone.0164675
ec_funded: 1
file:
- access_level: open_access
checksum: 395895ecb2216e9c39135abaa56b28b3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:26Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5009'
file_name: IST-2016-690-v1+1_journal.pone.0164675.PDF
file_size: 4353592
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6037'
pubrep_id: '690'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optogenetically blocking sharp wave ripple events in sleep does not interfere
with the formation of stable spatial representation in the CA1 area of the hippocampus
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: 11
year: '2016'
...
---
_id: '1278'
abstract:
- lang: eng
text: Adaptations of vestibulo-ocular and optokinetic response eye movements have
been studied as an experimental model of cerebellum-dependent motor learning.
Several previous physiological and pharmacological studies have consistently suggested
that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular
nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively
maintain the memory traces of short- and long-term adaptation. To study the basic
structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy
(EM), we injected green florescence protein (GFP)-expressing lentivirus into FL
to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal
boutons were distributed in the magnocellular MVN and in the border region of
parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the
FL-P cell axons mainly terminated on somata and proximal dendrites. On the other
hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly
terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN
neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH
neurons were determined to be glutamatergic by immunocytochemistry and in-situ
hybridization of GFP expressing transgenic mice. To further examine the spatial
relationship between the synapses of FL P-cells and those of vestibular nerve
on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated
dextran amine into the semicircular canal and anterogradely labeled vestibular
nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic
boutons often closely apposed vestibular nerve synaptic boutons in both LM and
EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with
those of vestibular nerve axons in the distal dendrites of MVN neurons suggests
that inhibitory synapses of FL P-cells may influence the function of neighboring
excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.
acknowledgement: This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan
Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112
to SN].
article_number: e0164037
article_processing_charge: No
article_type: original
author:
- first_name: Hitomi
full_name: Matsuno, Hitomi
last_name: Matsuno
- first_name: Moeko
full_name: Kudoh, Moeko
last_name: Kudoh
- first_name: Akiya
full_name: Watakabe, Akiya
last_name: Watakabe
- first_name: Tetsuo
full_name: Yamamori, Tetsuo
last_name: Yamamori
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Soichi
full_name: Nagao, Soichi
last_name: Nagao
citation:
ama: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution
and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar
flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy
studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037'
apa: 'Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao,
S. (2016). Distribution and structure of synapses on medial vestibular nuclear
neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in
mice: Light and electron microscopy studies. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0164037'
chicago: 'Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi
Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial
Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and
Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One.
Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037.'
ieee: 'H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao,
“Distribution and structure of synapses on medial vestibular nuclear neurons targeted
by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and
electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library
of Science, 2016.'
ista: 'Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution
and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar
flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy
studies. PLoS One. 11(10), e0164037.'
mla: 'Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial
Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and
Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One,
vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.'
short: H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS
One 11 (2016).
date_created: 2018-12-11T11:51:06Z
date_published: 2016-10-06T00:00:00Z
date_updated: 2021-01-12T06:49:34Z
day: '06'
ddc:
- '570'
- '571'
department:
- _id: RySh
doi: 10.1371/journal.pone.0164037
file:
- access_level: open_access
checksum: 7c0ba0ca6d79844059158059d2a38d25
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:16Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5269'
file_name: IST-2016-689-v1+1_journal.pone.0164037.PDF
file_size: 3657084
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6038'
pubrep_id: '689'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Distribution and structure of synapses on medial vestibular nuclear neurons
targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light
and electron microscopy studies'
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: 11
year: '2016'
...
---
_id: '1276'
abstract:
- lang: eng
text: The cytochrome (cyt) bc 1 complex is an integral component of the respiratory
electron transfer chain sustaining the energy needs of organisms ranging from
humans to bacteria. Due to its ubiquitous role in the energy metabolism, both
the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied
vigorously. Here, this vast amount of data is reassessed after probing the substrate
reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus
using atomistic molecular dynamics simulations. The simulations suggest that the
Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated
semiquinone-a reaction intermediate that is potentially formed during substrate
reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252,
thus making direct proton transfer possible. In the neutral state, the lysine
side chain stays close to the conserved binding location of cardiolipin (CL).
This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions
as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching,
which represents a refinement to the previously described CL/K pathway, fine-tunes
the proton transfer process. Lastly, the simulation data was used to formulate
a mechanism for reducing the substrate at the Q i-site.
acknowledgement: We wish to thank CSC – IT Centre for Science (Espoo, Finland) for
computational resources. For financial support, we wish to thank the Academy of
Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)),
the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius
Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV,
TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust
International Senior Research Fellowship.
article_number: '33607'
author:
- first_name: Pekka
full_name: Postila, Pekka
last_name: Postila
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Patryk
full_name: Kuleta, Patryk
last_name: Kuleta
- first_name: Ilpo
full_name: Vattulainen, Ilpo
last_name: Vattulainen
- first_name: Marcin
full_name: Sarewicz, Marcin
last_name: Sarewicz
- first_name: Artur
full_name: Osyczka, Artur
last_name: Osyczka
- first_name: Tomasz
full_name: Róg, Tomasz
last_name: Róg
citation:
ama: Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme
Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports.
2016;6. doi:10.1038/srep33607
apa: Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka,
A., & Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the
Qi-site of the cytochrome bc1 complex. Scientific Reports. Nature Publishing
Group. https://doi.org/10.1038/srep33607
chicago: Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin
Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme
Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports.
Nature Publishing Group, 2016. https://doi.org/10.1038/srep33607.
ieee: P. Postila et al., “Atomistic determinants of co-enzyme Q reduction
at the Qi-site of the cytochrome bc1 complex,” Scientific Reports, vol.
6. Nature Publishing Group, 2016.
ista: Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg
T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the
cytochrome bc1 complex. Scientific Reports. 6, 33607.
mla: Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at
the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports, vol. 6,
33607, Nature Publishing Group, 2016, doi:10.1038/srep33607.
short: P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka,
T. Róg, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:51:05Z
date_published: 2016-09-26T00:00:00Z
date_updated: 2021-01-12T06:49:34Z
day: '26'
ddc:
- '576'
department:
- _id: LeSa
doi: 10.1038/srep33607
file:
- access_level: open_access
checksum: 07c591c1250ebef266333cbc3228b4dd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:09Z
date_updated: 2020-07-14T12:44:42Z
file_id: '5261'
file_name: IST-2016-691-v1+1_srep33607.pdf
file_size: 1960563
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6040'
pubrep_id: '691'
quality_controlled: '1'
scopus_import: 1
status: public
title: Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome
bc1 complex
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: '1277'
abstract:
- lang: eng
text: "The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released
into the apoplast after cellular damage caused by pathogens or wounding to induce
innate immunity by direct binding to the membrane-localized leucine-rich repeat
receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated
signaling components and responses have been studied extensively, the contributions
of the subcellular localization and dynamics of the active PEPRs remain largely
unknown. We used live-cell imaging of the fluorescently labeled and bioactive
pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root
meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent
manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes
to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized
vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation
factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different
TGN/EE markers colocalized only rarely, implying that the intracellular route
of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression
of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits
clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization
and compromised AtPep1-mediated responses. Our results show that clathrin function
at the PM is required to induce plant defense responses, likely through CME of
cell surface-located signaling components.\r\n"
acknowledgement: "F.A.O.-M. was supported by special\r\nresearch funding from the
Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and
funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the
Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for
a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted
to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor
predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships
from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders
Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation
and the National Council\r\nfor Scientific and Technological Development (CNPq)
(D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme,
E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice
and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson,
and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych
for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line."
author:
- first_name: Fausto
full_name: Ortiz Morea, Fausto
last_name: Ortiz Morea
- first_name: Daniel
full_name: Savatin, Daniel
last_name: Savatin
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Rahul
full_name: Kumar, Rahul
last_name: Kumar
- first_name: Yu
full_name: Luo, Yu
last_name: Luo
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Jos
full_name: Van Begin, Jos
last_name: Van Begin
- first_name: Keini
full_name: Dressano, Keini
last_name: Dressano
- first_name: Guilherme
full_name: De Oliveira, Guilherme
last_name: De Oliveira
- first_name: Xiuyang
full_name: Zhao, Xiuyang
last_name: Zhao
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniel
full_name: De Moura, Daniel
last_name: De Moura
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling
in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113
apa: Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski,
M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis
requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113
chicago: Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo,
Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in
Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016.
https://doi.org/10.1073/pnas.1605588113.
ieee: F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis
requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences,
pp. 11028–11033, 2016.
ista: Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin
J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova
E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin.
PNAS. 113(39), 11028–11033.
mla: Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis
Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences,
2016, pp. 11028–33, doi:10.1073/pnas.1605588113.
short: F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski,
J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml,
D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.
date_created: 2018-12-11T11:51:06Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2021-01-12T06:49:34Z
day: '27'
department:
- _id: JiFr
doi: 10.1073/pnas.1605588113
intvolume: ' 113'
issue: '39'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/
month: '09'
oa: 1
oa_version: Preprint
page: 11028 - 11033
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6039'
quality_controlled: '1'
scopus_import: 1
status: public
title: Danger-associated peptide signaling in Arabidopsis requires clathrin
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1281'
abstract:
- lang: eng
text: Plants are able to modulate root growth and development to optimize their
nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response
to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses
emergence of lateral root primordia (LRPs) at low concentration or absence of
NO3 - through its auxin transport activity that lowers auxin accumulation in LR.
However, these functional data strongly contrast with the known transcriptional
regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3
-. To explain this discrepancy, we investigated in detail the spatiotemporal expression
pattern of the NRT1.1 protein during LRP development and combined local transcript
analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our
results show that although NO3 - stimulates NRT1.1 transcription and probably
mRNA stability both in primary root tissues and in LRPs, it acts differentially
on protein accumulation, depending on the tissues considered with stimulation
in cortex and epidermis of the primary root and a strong repression in LRPs and
to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly
regulated at the posttranscriptional level by tissue-specific mechanisms. These
mechanisms are crucial for controlling the large palette of adaptive responses
to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the
proper tissue under the specific conditions where it plays a signaling role in
this particular tissue.
acknowledgement: "This work was supported by the Agropolis Foundation (RHIZOPOLIS
project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge
Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement
to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G.,
and P.N.). We thank Carine Alcon for the help with analysis of confocal images,
Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members
of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance
with biological\r\nmaterial culture, and students and trainees for assistance with
laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging
facility."
author:
- first_name: Eléonore
full_name: Bouguyon, Eléonore
last_name: Bouguyon
- first_name: Francine
full_name: Perrine Walker, Francine
last_name: Perrine Walker
- first_name: Marjorie
full_name: Pervent, Marjorie
last_name: Pervent
- first_name: Juliette
full_name: Rochette, Juliette
last_name: Rochette
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Lien
full_name: Bach, Lien
last_name: Bach
- first_name: Gabriel
full_name: Krouk, Gabriel
last_name: Krouk
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Philippe
full_name: Nacry, Philippe
last_name: Nacry
citation:
ama: Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development
through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor.
Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047
apa: Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková,
E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional
regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American
Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047
chicago: Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette
Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls
Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter
Sensor.” Plant Physiology. American Society of Plant Biologists, 2016.
https://doi.org/10.1104/pp.16.01047.
ieee: E. Bouguyon et al., “Nitrate controls root development through posttranscriptional
regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology,
vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.
ista: Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E,
Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development
through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor.
Plant Physiology. 172(2), 1237–1248.
mla: Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional
Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology,
vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047.
short: E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková,
A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016)
1237–1248.
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:36Z
day: '01'
department:
- _id: EvBe
doi: 10.1104/pp.16.01047
intvolume: ' 172'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/
month: '10'
oa: 1
oa_version: Preprint
page: 1237 - 1248
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6035'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nitrate controls root development through posttranscriptional regulation of
the NRT1.1/NPF6.3 transporter sensor
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 172
year: '2016'
...
---
_id: '1282'
abstract:
- lang: eng
text: 'We consider higher-dimensional generalizations of the normalized Laplacian
and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam
model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We
show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s.
concentrated around two values. The main tool, which goes back to the work of
Garland, are arguments that relate the eigenvalues of these matrices to those
of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns
the Laplacian; we develop an analogous result for the adjacency matrix. The same
arguments apply to other models of random complexes which allow for dependencies
between the choices of k-dimensional simplices. In the second part of the paper,
we apply this to the question of possible higher-dimensional analogues of the
discrete Cheeger inequality, which in the classical case of graphs relates the
eigenvalues of a graph and its edge expansion. It is very natural to ask whether
this generalizes to higher dimensions and, in particular, whether the eigenvalues
of the higher-dimensional Laplacian capture the notion of coboundary expansion—a
higher-dimensional generalization of edge expansion that arose in recent work
of Linial and Meshulam and of Gromov; this question was raised, for instance,
by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional
discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and
n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral
expansion properties (all nontrivial eigenvalues of the normalised k-dimensional
Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion
is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn
k can be taken to have vanishing integer homology in dimension less than k.'
author:
- first_name: Anna
full_name: Gundert, Anna
last_name: Gundert
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal
of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1
apa: Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel
Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1
chicago: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel
Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1.
ieee: A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel
Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016.
ista: Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal
of Mathematics. 216(2), 545–582.
mla: Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel
Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1.
short: A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:36Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-016-1419-1
intvolume: ' 216'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.4906
month: '10'
oa: 1
oa_version: Preprint
page: 545 - 582
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '6034'
quality_controlled: '1'
scopus_import: 1
status: public
title: On eigenvalues of random complexes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 216
year: '2016'
...
---
_id: '1280'
abstract:
- lang: eng
text: We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of
the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous
results concerning the universality of random matrices either require an averaging
in the energy parameter or they hold only for Hermitian matrices if the energy
parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion
and show that microscopic universality follows from mesoscopic statistics.
acknowledgement: "The work of P.B. was partially supported by National Sci-\r\nence
Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC
Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by
National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award.
\ The work of J.Y. was partially supported by National Science\r\nFoundation Grant
DMS-1207961. The major part of this research was conducted\r\nwhen all authors
were visiting IAS and were also supported by National Science\r\nFoundation Grant
DMS-1128255."
author:
- first_name: Paul
full_name: Bourgade, Paul
last_name: Bourgade
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horngtzer
full_name: Yau, Horngtzer
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized
wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881.
doi:10.1002/cpa.21624
apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality
for generalized wigner matrices. Communications on Pure and Applied Mathematics.
Wiley-Blackwell. https://doi.org/10.1002/cpa.21624
chicago: Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy
Universality for Generalized Wigner Matrices.” Communications on Pure and Applied
Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624.
ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for
generalized wigner matrices,” Communications on Pure and Applied Mathematics,
vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.
ista: Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized
wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.
mla: Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.”
Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell,
2016, pp. 1815–81, doi:10.1002/cpa.21624.
short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied
Mathematics 69 (2016) 1815–1881.
date_created: 2018-12-11T11:51:07Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:35Z
day: '01'
department:
- _id: LaEr
doi: 10.1002/cpa.21624
ec_funded: 1
intvolume: ' 69'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1407.5606
month: '10'
oa: 1
oa_version: Preprint
page: 1815 - 1881
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6036'
scopus_import: 1
status: public
title: Fixed energy universality for generalized wigner matrices
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 69
year: '2016'
...
---
_id: '1286'
abstract:
- lang: eng
text: We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys.
Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to
study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein
condensates of rubidium and strontium. Based on ab initio potential energy surfaces,
we provide a detailed study of the rotational Lamb shift and many-body-induced
fine structure which arise due to dressing of molecular rotation by a field of
phonon excitations. We demonstrate that the magnitude of these effects is large
enough in order to be observed in modern experiments on cold molecular ions. Furthermore,
we introduce a novel method to construct pseudopotentials starting from the ab
initio potential energy surfaces, which provides a means to obtain effective coupling
constants for low-energy polaron models.
acknowledgement: The work was supported by the NSF through a grant for the Institute
for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and
the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges
support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG
OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P)
and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex,
the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.
article_number: '041601'
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Michał
full_name: Tomza, Michał
last_name: Tomza
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside
a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical
Physics. 2016;94(4). doi:10.1103/PhysRevA.94.041601
apa: Midya, B., Tomza, M., Schmidt, R., & Lemeshko, M. (2016). Rotation of cold
molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.94.041601
chicago: Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko.
“Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical
Review A - Atomic, Molecular, and Optical Physics. American Physical Society,
2016. https://doi.org/10.1103/PhysRevA.94.041601.
ieee: B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular
ions inside a Bose-Einstein condensate,” Physical Review A - Atomic, Molecular,
and Optical Physics, vol. 94, no. 4. American Physical Society, 2016.
ista: Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular
ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular,
and Optical Physics. 94(4), 041601.
mla: Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein
Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 94, no. 4, 041601, American Physical Society, 2016, doi:10.1103/PhysRevA.94.041601.
short: B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic,
Molecular, and Optical Physics 94 (2016).
date_created: 2018-12-11T11:51:09Z
date_published: 2016-10-13T00:00:00Z
date_updated: 2021-01-12T06:49:37Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.94.041601
ec_funded: 1
intvolume: ' 94'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.06092
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '6030'
quality_controlled: '1'
scopus_import: 1
status: public
title: Rotation of cold molecular ions inside a Bose-Einstein condensate
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2016'
...
---
_id: '1291'
abstract:
- lang: eng
text: We consider Ising models in two and three dimensions, with short range ferromagnetic
and long range, power-law decaying, antiferromagnetic interactions. We let J be
the ratio between the strength of the ferromagnetic to antiferromagnetic interactions.
The competition between these two kinds of interactions induces the system to
form domains of minus spins in a background of plus spins, or vice versa. If the
decay exponent p of the long range interaction is larger than d + 1, with d
the space dimension, this happens for all values of J smaller than a critical
value Jc(p), beyond which the ground state is homogeneous. In this paper, we give
a characterization of the infinite volume ground states of the system, for pÂ
>Â 2d and J in a left neighborhood of Jc(p). In particular, we prove that the
quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs
(d = 3), all of the same optimal width and orientation, and alternating magnetization,
are infinite volume ground states. Our proof is based on localization bounds combined
with reflection positivity.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria). The\r\nresearch leading to these results has received funding from
the European Research Council under the European\r\nUnion’s Seventh Framework Programme
ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN
National Grant Geometric and analytic theory of Hamiltonian systems in finite and
infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27.
Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute
for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems,
random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully
acknowledged."
author:
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Giuliani A, Seiringer R. Periodic striped ground states in Ising models with
competing interactions. Communications in Mathematical Physics. 2016;347(3):983-1007.
doi:10.1007/s00220-016-2665-0
apa: Giuliani, A., & Seiringer, R. (2016). Periodic striped ground states in
Ising models with competing interactions. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-016-2665-0
chicago: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States
in Ising Models with Competing Interactions.” Communications in Mathematical
Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2665-0.
ieee: A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models
with competing interactions,” Communications in Mathematical Physics, vol.
347, no. 3. Springer, pp. 983–1007, 2016.
ista: Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models
with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007.
mla: Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States
in Ising Models with Competing Interactions.” Communications in Mathematical
Physics, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:10.1007/s00220-016-2665-0.
short: A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016)
983–1007.
date_created: 2018-12-11T11:51:11Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:49:40Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1007/s00220-016-2665-0
file:
- access_level: open_access
checksum: 3c6e08c048fc462e312788be72874bb1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:02Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4725'
file_name: IST-2016-688-v1+1_s00220-016-2665-0.pdf
file_size: 794983
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 347'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 983 - 1007
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '6025'
pubrep_id: '688'
quality_controlled: '1'
scopus_import: 1
status: public
title: Periodic striped ground states in Ising models with competing interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 347
year: '2016'
...
---
_id: '1293'
abstract:
- lang: eng
text: For a graph G with p vertices the closed convex cone S⪰0(G) consists of all
real positive semidefinite p×p matrices whose sparsity pattern is given by G,
that is, those matrices with zeros in the off-diagonal entries corresponding to
nonedges of G. The extremal rays of this cone and their associated ranks have
applications to matrix completion problems, maximum likelihood estimation in Gaussian
graphical models in statistics, and Gauss elimination for sparse matrices. While
the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of
G, has been characterized for different classes of graphs, we here study all possible
extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope
of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G).
For a graph G without K5 minors, we show that appropriately chosen normal vectors
to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of
extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars
the constant term of the linear equation of each facet-supporting hyperplane is
the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show
that if G is series-parallel then this gives a complete characterization of all
possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for
series-parallel graphs can be solved in terms of polyhedral geometry.
acknowledgement: We wish to thank Alexander Engström and Bernd Sturmfels for various
valuable discussions and insights. We also thank the two anonymous referees for
their thoughtful feedback on the paper. CU was partially supported by the Austrian
Science Fund (FWF) Y 903-N35.
author:
- first_name: Liam T
full_name: Solus, Liam T
id: 2AADA620-F248-11E8-B48F-1D18A9856A87
last_name: Solus
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Ruriko
full_name: Yoshida, Ruriko
last_name: Yoshida
citation:
ama: Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose
sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its
Applications. 2016;509:247-275. doi:10.1016/j.laa.2016.07.026
apa: Solus, L. T., Uhler, C., & Yoshida, R. (2016). Extremal positive semidefinite
matrices whose sparsity pattern is given by graphs without K5 minors. Linear
Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2016.07.026
chicago: Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite
Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear
Algebra and Its Applications. Elsevier, 2016. https://doi.org/10.1016/j.laa.2016.07.026.
ieee: L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices
whose sparsity pattern is given by graphs without K5 minors,” Linear Algebra
and Its Applications, vol. 509. Elsevier, pp. 247–275, 2016.
ista: Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices
whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and
Its Applications. 509, 247–275.
mla: Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity
Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications,
vol. 509, Elsevier, 2016, pp. 247–75, doi:10.1016/j.laa.2016.07.026.
short: L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509
(2016) 247–275.
date_created: 2018-12-11T11:51:11Z
date_published: 2016-11-15T00:00:00Z
date_updated: 2021-01-12T06:49:40Z
day: '15'
department:
- _id: CaUh
doi: 10.1016/j.laa.2016.07.026
intvolume: ' 509'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1506.06702.pdf
month: '11'
oa: 1
oa_version: Preprint
page: 247 - 275
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Linear Algebra and Its Applications
publication_status: published
publisher: Elsevier
publist_id: '6024'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extremal positive semidefinite matrices whose sparsity pattern is given by
graphs without K5 minors
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 509
year: '2016'
...
---
_id: '1290'
abstract:
- lang: eng
text: We developed a competition-based screening strategy to identify compounds
that invert the selective advantage of antibiotic resistance. Using our assay,
we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance
efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram.
Treating a tetracycline-resistant population with β-thujaplicin selects for loss
of the resistance gene, enabling an effective second-phase treatment with doxycycline.
acknowledgement: "This work was supported in part by National Institute of Allergy
and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants
R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC
grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to
L.K.S.).\r\n"
author:
- first_name: Laura
full_name: Stone, Laura
last_name: Stone
- first_name: Michael
full_name: Baym, Michael
last_name: Baym
- first_name: Tami
full_name: Lieberman, Tami
last_name: Lieberman
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Jon
full_name: Clardy, Jon
last_name: Clardy
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that
select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
2016;12(11):902-904. doi:10.1038/nchembio.2176
apa: Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony,
R. (2016). Compounds that select against the tetracycline-resistance efflux pump.
Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176
chicago: Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and
Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux
Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.
ieee: L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds
that select against the tetracycline-resistance efflux pump,” Nature Chemical
Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.
ista: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds
that select against the tetracycline-resistance efflux pump. Nature Chemical Biology.
12(11), 902–904.
mla: Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance
Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing
Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.
short: L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature
Chemical Biology 12 (2016) 902–904.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:49:39Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/nchembio.2176
intvolume: ' 12'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/
month: '11'
oa: 1
oa_version: Preprint
page: 902 - 904
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6026'
quality_controlled: '1'
scopus_import: 1
status: public
title: Compounds that select against the tetracycline-resistance efflux pump
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '1292'
abstract:
- lang: eng
text: We give explicit formulas and algorithms for the computation of the Thurston–Bennequin
invariant of a nullhomologous Legendrian knot on a page of a contact open book
and on Heegaard surfaces in convex position. Furthermore, we extend the results
to rationally nullhomologous knots in arbitrary 3-manifolds.
acknowledgement: "The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful
discussions and advice and Christian Evers for helpful remarks on a draft version."
author:
- first_name: Sebastian
full_name: Durst, Sebastian
last_name: Durst
- first_name: Marc
full_name: Kegel, Marc
last_name: Kegel
- first_name: Mirko D
full_name: Klukas, Mirko D
id: 34927512-F248-11E8-B48F-1D18A9856A87
last_name: Klukas
citation:
ama: Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in
open books. Acta Mathematica Hungarica. 2016;150(2):441-455. doi:10.1007/s10474-016-0648-4
apa: Durst, S., Kegel, M., & Klukas, M. D. (2016). Computing the Thurston–Bennequin
invariant in open books. Acta Mathematica Hungarica. Springer. https://doi.org/10.1007/s10474-016-0648-4
chicago: Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin
Invariant in Open Books.” Acta Mathematica Hungarica. Springer, 2016. https://doi.org/10.1007/s10474-016-0648-4.
ieee: S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant
in open books,” Acta Mathematica Hungarica, vol. 150, no. 2. Springer,
pp. 441–455, 2016.
ista: Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant
in open books. Acta Mathematica Hungarica. 150(2), 441–455.
mla: Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open
Books.” Acta Mathematica Hungarica, vol. 150, no. 2, Springer, 2016, pp.
441–55, doi:10.1007/s10474-016-0648-4.
short: S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.
date_created: 2018-12-11T11:51:11Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:40Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10474-016-0648-4
intvolume: ' 150'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.00794
month: '12'
oa: 1
oa_version: Preprint
page: 441 - 455
publication: Acta Mathematica Hungarica
publication_status: published
publisher: Springer
publist_id: '6023'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing the Thurston–Bennequin invariant in open books
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2016'
...
---
_id: '1323'
abstract:
- lang: eng
text: Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that
reliably discharge postsynaptic targets. The 'conditional' nature implies that
burst activity in dentate gyrus granule cells is required for detonation. Whether
single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3
neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term
facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether
PTP could convert mossy fiber synapses from subdetonator into detonator mode,
using a recently developed method to selectively and noninvasively stimulate individual
presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a
spike in CA3 neurons under control conditions, but reliably discharged them after
induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy
fiber synapses into full detonators for tens of seconds. Plasticity-dependent
detonation may be critical for efficient coding, storage, and recall of information
in the granule cell–CA3 cell network.
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
article_number: e17977
author:
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vyleta N, Borges Merjane C, Jonas PM. Plasticity-dependent, full detonation
at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 2016;5.
doi:10.7554/eLife.17977
apa: Vyleta, N., Borges Merjane, C., & Jonas, P. M. (2016). Plasticity-dependent,
full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.17977
chicago: Vyleta, Nicholas, Carolina Borges Merjane, and Peter M Jonas. “Plasticity-Dependent,
Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife.
eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.17977.
ieee: N. Vyleta, C. Borges Merjane, and P. M. Jonas, “Plasticity-dependent, full
detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses,” eLife,
vol. 5. eLife Sciences Publications, 2016.
ista: Vyleta N, Borges Merjane C, Jonas PM. 2016. Plasticity-dependent, full detonation
at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 5, e17977.
mla: Vyleta, Nicholas, et al. “Plasticity-Dependent, Full Detonation at Hippocampal
Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife, vol. 5, e17977, eLife
Sciences Publications, 2016, doi:10.7554/eLife.17977.
short: N. Vyleta, C. Borges Merjane, P.M. Jonas, ELife 5 (2016).
date_created: 2018-12-11T11:51:22Z
date_published: 2016-10-25T00:00:00Z
date_updated: 2023-02-21T10:34:24Z
day: '25'
ddc:
- '571'
- '572'
department:
- _id: PeJo
doi: 10.7554/eLife.17977
ec_funded: 1
file:
- access_level: open_access
checksum: a7201280c571bed88ebd459ce5ce6a47
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:05Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5257'
file_name: IST-2016-715-v1+1_e17977-download.pdf
file_size: 1477891
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5947'
pubrep_id: '715'
quality_controlled: '1'
scopus_import: 1
status: public
title: Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal
neuron synapses
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: 5
year: '2016'
...
---
_id: '1325'
abstract:
- lang: eng
text: We study graphs and two-player games in which rewards are assigned to states,
and the goal of the players is to satisfy or dissatisfy certain property of the
generated outcome, given as a mean payoff property. Since the notion of mean-payoff
does not reflect possible fluctuations from the mean-payoff along a run, we propose
definitions and algorithms for capturing the stability of the system, and give
algorithms for deciding if a given mean payoff and stability objective can be
ensured in the system.
acknowledgement: "The work has been supported by the Czech Science Foundation, grant
No. 15-17564S, by EPSRC grant\r\nEP/M023656/1, and by the People Programme (Marie
Curie Actions) of the European Union’s Seventh\r\nFramework Programme (FP7/2007-2013)
under REA grant agreement no [291734]"
alternative_title:
- LIPIcs
article_number: '10'
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Brázdil T, Forejt V, Kučera A, Novotný P. Stability in graphs and games. In:
Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.10'
apa: 'Brázdil, T., Forejt, V., Kučera, A., & Novotný, P. (2016). Stability in
graphs and games (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec
City, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10'
chicago: Brázdil, Tomáš, Vojtěch Forejt, Antonín Kučera, and Petr Novotný. “Stability
in Graphs and Games,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10.
ieee: 'T. Brázdil, V. Forejt, A. Kučera, and P. Novotný, “Stability in graphs and
games,” presented at the CONCUR: Concurrency Theory, Quebec City, Canada, 2016,
vol. 59.'
ista: 'Brázdil T, Forejt V, Kučera A, Novotný P. 2016. Stability in graphs and games.
CONCUR: Concurrency Theory, LIPIcs, vol. 59, 10.'
mla: Brázdil, Tomáš, et al. Stability in Graphs and Games. Vol. 59, 10, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.10.
short: T. Brázdil, V. Forejt, A. Kučera, P. Novotný, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City, Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:51:23Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:53Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2016.10
ec_funded: 1
file:
- access_level: open_access
checksum: 3c2dc6ab0358f8aa8f7aa7d6c1293159
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:40Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5229'
file_name: IST-2016-665-v1+1_Forejt_et_al__Stability_in_graphs_and_games.pdf
file_size: 553648
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5944'
pubrep_id: '665'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stability in graphs and games
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1329'
abstract:
- lang: eng
text: Daphnia species have become models for ecological genomics and exhibit interesting
features, such as high phenotypic plasticity and a densely packed genome with
many lineage-specific genes. They are also cyclic parthenogenetic, with alternating
asexual and sexual cycles and environmental sex determination. Here, we present
a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to
investigate gene expression in females and spontaneously produced males of two
clonal lines derived from lakes in Germany and the Czech Republic. We find that
only a low percentage (18%) of genes shows sex-biased expression and that there
are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore,
FBGs tend to be more conserved between species than MBGs in both sequence and
expression. These patterns may be a consequence of cyclic parthenogenesis leading
to a relaxation of purifying selection on MBGs. The two clonal lines show considerable
differences in both number and identity of sex-biased genes, suggesting that they
may have reproductive strategies differing in their investment in sexual reproduction.
Orthologs of key genes in the sex determination and juvenile hormone pathways,
which are thought to be important for the transition from asexual to sexual reproduction,
are present in D. galeata and highly conserved among Daphnia species.
acknowledgement: This study was financially supported by individual grants from the
Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6
to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L.
Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and
K. Otte for providing the necessary resources and help for maintaining Daphnia cultures
in the laboratory. H. Lainer supported us for the molecular laboratory work. D.
Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and
L. Hardulak did the orthology mapping including more insect species. This study
was financially supported by individual grants from the Volkswagen Stiftung (to
M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD
(to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Alberto
full_name: López Ezquerra, Alberto
last_name: López Ezquerra
- first_name: John
full_name: Parsch, John
last_name: Parsch
- first_name: Mathilde
full_name: Cordellier, Mathilde
last_name: Cordellier
citation:
ama: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome
assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia
galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221
apa: Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016).
De novo transcriptome assembly and sex-biased gene expression in the cyclical
parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evw221
chicago: Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier.
“De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical
Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford
University Press, 2016. https://doi.org/10.1093/gbe/evw221.
ieee: A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo
transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic
Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford
University Press, pp. 3120–3139, 2016.
ista: Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome
assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia
galeata. Genome Biology and Evolution. 8(10), 3120–3139.
mla: Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene
Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology
and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39,
doi:10.1093/gbe/evw221.
short: A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology
and Evolution 8 (2016) 3120–3139.
date_created: 2018-12-11T11:51:24Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:55Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1093/gbe/evw221
file:
- access_level: open_access
checksum: 25c7adcb452d39d3b6343ff4b57a652d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:06Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4924'
file_name: IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf
file_size: 1406265
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3120 - 3139
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5940'
pubrep_id: '663'
quality_controlled: '1'
scopus_import: 1
status: public
title: De novo transcriptome assembly and sex-biased gene expression in the cyclical
parthenogenetic Daphnia galeata
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2016'
...
---
_id: '1327'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and positive integer costs associated with every transition.
The traditional optimization objective (stochastic shortest path) asks to minimize
the expected total cost until the target set is reached. We extend the traditional
framework of POMDPs to model energy consumption, which represents a hard constraint.
The energy levels may increase and decrease with transitions, and the hard constraint
requires that the energy level must remain positive in all steps till the target
is reached. First, we present a novel algorithm for solving POMDPs with energy
levels, developing on existing POMDP solvers and using RTDP as its main method.
Our second contribution is related to policy representation. For larger POMDP
instances the policies computed by existing solvers are too large to be understandable.
We present an automated procedure based on machine learning techniques that automatically
extracts important decisions of the policy allowing us to compute succinct human
readable policies. Finally, we show experimentally that our algorithm performs
well and computes succinct policies on a number of POMDP instances from the literature
that were naturally enhanced with energy levels. '
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Anchit
full_name: Gupta, Anchit
last_name: Gupta
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest
path with energy constraints in POMDPs. In: Proceedings of the 15th International
Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.'
apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016).
Stochastic shortest path with energy constraints in POMDPs. In Proceedings
of the 15th International Conference on Autonomous Agents and Multiagent Systems
(pp. 1465–1466). Singapore: ACM.'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and
Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In
Proceedings of the 15th International Conference on Autonomous Agents and Multiagent
Systems, 1465–66. ACM, 2016.
ieee: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic
shortest path with energy constraints in POMDPs,” in Proceedings of the 15th
International Conference on Autonomous Agents and Multiagent Systems, Singapore,
2016, pp. 1465–1466.
ista: 'Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic
shortest path with energy constraints in POMDPs. Proceedings of the 15th International
Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents
& Multiagent Systems, 1465–1466.'
mla: Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in
POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents
and Multiagent Systems, ACM, 2016, pp. 1465–66.
short: T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings
of the 15th International Conference on Autonomous Agents and Multiagent Systems,
ACM, 2016, pp. 1465–1466.
conference:
end_date: 2016-05-13
location: Singapore
name: 'AAMAS: Autonomous Agents & Multiagent Systems'
start_date: 2016-05-09
date_created: 2018-12-11T11:51:23Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:54Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.07565
month: '01'
oa: 1
oa_version: Preprint
page: 1465 - 1466
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the 15th International Conference on Autonomous Agents
and Multiagent Systems
publication_status: published
publisher: ACM
publist_id: '5942'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stochastic shortest path with energy constraints in POMDPs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1326'
abstract:
- lang: eng
text: 'Energy Markov Decision Processes (EMDPs) are finite-state Markov decision
processes where each transition is assigned an integer counter update and a rational
payoff. An EMDP configuration is a pair s(n), where s is a control state and n
is the current counter value. The configurations are changed by performing transitions
in the standard way. We consider the problem of computing a safe strategy (i.e.,
a strategy that keeps the counter non-negative) which maximizes the expected mean
payoff. '
acknowledgement: The research was funded by the Czech Science Foundation Grant No.
P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s
Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy
Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:10.1007/978-3-319-46520-3_3'
apa: 'Brázdil, T., Kučera, A., & Novotný, P. (2016). Optimizing the expected
mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented
at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan:
Springer. https://doi.org/10.1007/978-3-319-46520-3_3'
chicago: Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected
Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016.
https://doi.org/10.1007/978-3-319-46520-3_3.
ieee: 'T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff
in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology
for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49.'
ista: 'Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff
in Energy Markov Decision Processes. ATVA: Automated Technology for Verification
and Analysis, LNCS, vol. 9938, 32–49.'
mla: Brázdil, Tomáš, et al. Optimizing the Expected Mean Payoff in Energy Markov
Decision Processes. Vol. 9938, Springer, 2016, pp. 32–49, doi:10.1007/978-3-319-46520-3_3.
short: T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.
conference:
end_date: 2016-10-20
location: Chiba, Japan
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2016-10-17
date_created: 2018-12-11T11:51:23Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2021-01-12T06:49:53Z
day: '22'
department:
- _id: KrCh
doi: 10.1007/978-3-319-46520-3_3
ec_funded: 1
intvolume: ' 9938'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00678
month: '09'
oa: 1
oa_version: Preprint
page: 32 - 49
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: '5943'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimizing the expected mean payoff in Energy Markov Decision Processes
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9938
year: '2016'
...
---
_id: '1330'
abstract:
- lang: eng
text: In this paper we investigate the existence of closed billiard trajectories
in not necessarily smooth convex bodies. In particular, we show that if a body
K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K
is acute (in a certain sense), then there is a closed billiard trajectory in K.
acknowledgement: Supported by People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734].
Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a
ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part
by the Moebius Contest Foundation for Young Scientists, and in part by the Simons
Foundation.
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
citation:
ama: Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel
Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z
apa: Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute
angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z
chicago: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with
Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z.
ieee: A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,”
Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845,
2016.
ista: Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles.
Israel Journal of Mathematics. 216(2), 833–845.
mla: Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute
Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016,
pp. 833–45, doi:10.1007/s11856-016-1429-z.
short: A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845.
date_created: 2018-12-11T11:51:24Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2021-01-12T06:49:56Z
day: '15'
department:
- _id: HeEd
doi: 10.1007/s11856-016-1429-z
ec_funded: 1
intvolume: ' 216'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.06014
month: '10'
oa: 1
oa_version: Preprint
page: 833 - 845
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '5938'
quality_controlled: '1'
scopus_import: 1
status: public
title: Billiards in convex bodies with acute angles
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 216
year: '2016'
...
---
_id: '1334'
abstract:
- lang: eng
text: Hippocampal neurons encode a cognitive map of space. These maps are thought
to be updated during learning and in response to changes in the environment through
activity-dependent synaptic plasticity. Here we examine how changes in activity
influence spatial coding in rats using halorhodopsin-mediated, spatially selective
optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression
in many place cells and interneurons; some place cells increase their firing through
disinhibition, whereas some show no effect. We find that place fields of the unaffected
subpopulation remain stable. On the other hand, place fields of suppressed place
cells were unstable, showing remapping across sessions before and after optogenetic
inhibition. Disinhibited place cells had stable maps but sustained an elevated
firing rate. These findings suggest that place representation in the hippocampus
is constantly governed by activity-dependent processes, and that disinhibition
may provide a mechanism for rate remapping.
article_number: '11824'
author:
- first_name: Philipp
full_name: Schönenberger, Philipp
id: 3B9D816C-F248-11E8-B48F-1D18A9856A87
last_name: Schönenberger
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of
hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824
apa: Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent
plasticity of hippocampal place maps. Nature Communications. Nature Publishing
Group. https://doi.org/10.1038/ncomms11824
chicago: Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity
Dependent Plasticity of Hippocampal Place Maps.” Nature Communications.
Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824.
ieee: P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity
of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing
Group, 2016.
ista: Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity
of hippocampal place maps. Nature Communications. 7, 11824.
mla: Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal
Place Maps.” Nature Communications, vol. 7, 11824, Nature Publishing Group,
2016, doi:10.1038/ncomms11824.
short: P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:26Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-01-12T06:49:57Z
day: '10'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1038/ncomms11824
ec_funded: 1
file:
- access_level: open_access
checksum: e43307754abe65b840a21939fe163618
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:10Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5196'
file_name: IST-2016-660-v1+1_ncomms11824.pdf
file_size: 1793846
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 257D4372-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2072-B27
name: Interneuron plasticity during spatial learning
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5934'
pubrep_id: '660'
quality_controlled: '1'
scopus_import: 1
status: public
title: Activity dependent plasticity of hippocampal place maps
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: 7
year: '2016'
...
---
_id: '1331'
abstract:
- lang: eng
text: 'Cytokinin is a phytohormone that is well known for its roles in numerous
plant growth and developmental processes, yet it has also been linked to abiotic
stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin
Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription
factor that, through the cytokinin signaling pathway, plays a key role in the
inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative
stress, and here we show a novel function for CRF6 in relation to oxidative stress
and identify downstream transcriptional targets of CRF6 that are repressed in
response to oxidative stress. Analysis of transcriptomic changes in wild-type
and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially
expressed transcripts, many of which were repressed rather than induced. Moreover,
many repressed genes also show decreased expression in 35S:CRF6 overexpressing
plants. Together, these findings suggest that CRF6 functions largely as a transcriptional
repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts
was a set of five genes associated with cytokinin processes: (signaling) ARR6,
ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants
of these cytokinin-associated target genes to reveal novel connections to oxidative
stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate
its targets both directly and indirectly. Together, this shows that CRF6 functions
during oxidative stress as a negative regulator to control this cytokinin-associated
module of CRF6- dependent genes and establishes a novel connection between cytokinin
and oxidative stress response.'
acknowledgement: "This work was financially supported by the following: The Alabama
Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055
for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported
by an Auburn University Cellular and Molecular Biosciences Research Fellowship.
I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043)
and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants
from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated
by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research
Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W)."
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Zwack, Paul
last_name: Zwack
- first_name: Inge
full_name: De Clercq, Inge
last_name: De Clercq
- first_name: Timothy
full_name: Howton, Timothy
last_name: Howton
- first_name: H Tucker
full_name: Hallmark, H Tucker
last_name: Hallmark
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
- first_name: Erika
full_name: Keshishian, Erika
last_name: Keshishian
- first_name: Alyssa
full_name: Parish, Alyssa
last_name: Parish
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: M Shahid
full_name: Mukhtar, M Shahid
last_name: Mukhtar
- first_name: Frank
full_name: Van Breusegem, Frank
last_name: Van Breusegem
- first_name: Aaron
full_name: Rashotte, Aaron
last_name: Rashotte
citation:
ama: Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses
cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258.
doi:10.1104/pp.16.00415
apa: Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian,
E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated
genes during oxidative stress. Plant Physiology. American Society of Plant
Biologists. https://doi.org/10.1104/pp.16.00415
chicago: Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej
Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses
Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology.
American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415.
ieee: P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated
genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American
Society of Plant Biologists, pp. 1249–1258, 2016.
ista: Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish
A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response
factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology.
172(2), 1249–1258.
mla: Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated
Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American
Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415.
short: P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian,
A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology
172 (2016) 1249–1258.
date_created: 2018-12-11T11:51:25Z
date_published: 2016-10-02T00:00:00Z
date_updated: 2022-05-24T09:26:03Z
day: '02'
department:
- _id: EvBe
doi: 10.1104/pp.16.00415
intvolume: ' 172'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.16.00415
month: '10'
oa: 1
oa_version: Published Version
page: 1249 - 1258
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5937'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin response factor 6 represses cytokinin-associated genes during oxidative
stress
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 172
year: '2016'
...
---
_id: '1333'
abstract:
- lang: eng
text: Social dilemmas force players to balance between personal and collective gain.
In many dilemmas, such as elected governments negotiating climate-change mitigation
measures, the decisions are made not by individual players but by their representatives.
However, the behaviour of representatives in social dilemmas has not been investigated
experimentally. Here inspired by the negotiations for greenhouse-gas emissions
reductions, we experimentally study a collective-risk social dilemma that involves
representatives deciding on behalf of their fellow group members. Representatives
can be re-elected or voted out after each consecutive collective-risk game. Selfish
players are preferentially elected and are hence found most frequently in the
"representatives" treatment. Across all treatments, we identify the
selfish players as extortioners. As predicted by our mathematical model, their
steadfast strategies enforce cooperation from fair players who finally compensate
almost completely the deficit caused by the extortionate co-players. Everybody
gains, but the extortionate representatives and their groups gain the most.
acknowledgement: We thank the students for participation; H.-J. Krambeck for writing
the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler
and T. Reusch for support; and the Max Planck Society for the Advancement of Science
for funding.
article_number: '10915'
author:
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Dirk
full_name: Semmann, Dirk
last_name: Semmann
- first_name: Ralf
full_name: Sommerfeld, Ralf
last_name: Sommerfeld
- first_name: Jochem
full_name: Marotzke, Jochem
last_name: Marotzke
citation:
ama: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives
who enforce cooperation in social dilemmas through extortion. Nature Communications.
2016;7. doi:10.1038/ncomms10915
apa: Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016).
Humans choose representatives who enforce cooperation in social dilemmas through
extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915
chicago: Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and
Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social
Dilemmas through Extortion.” Nature Communications. Nature Publishing Group,
2016. https://doi.org/10.1038/ncomms10915.
ieee: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans
choose representatives who enforce cooperation in social dilemmas through extortion,”
Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose
representatives who enforce cooperation in social dilemmas through extortion.
Nature Communications. 7, 10915.
mla: Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation
in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915,
Nature Publishing Group, 2016, doi:10.1038/ncomms10915.
short: M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:25Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:49:57Z
day: '07'
ddc:
- '519'
- '530'
- '599'
department:
- _id: KrCh
doi: 10.1038/ncomms10915
file:
- access_level: open_access
checksum: 9ea0d7ce59a555a1cb8353d5559407cb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:44Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4834'
file_name: IST-2016-661-v1+1_ncomms10915.pdf
file_size: 1432577
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5935'
pubrep_id: '661'
quality_controlled: '1'
scopus_import: 1
status: public
title: Humans choose representatives who enforce cooperation in social dilemmas through
extortion
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: 7
year: '2016'
...
---
_id: '1332'
abstract:
- lang: eng
text: Antibiotic-sensitive and -resistant bacteria coexist in natural environments
with low, if detectable, antibiotic concentrations. Except possibly around localized
antibiotic sources, where resistance can provide a strong advantage, bacterial
fitness is dominated by stresses unaffected by resistance to the antibiotic. How
do such mixed and heterogeneous conditions influence the selective advantage or
disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels
of tetracyclines potentiate selection for or against tetracycline resistance around
localized sources of almost any toxin or stress. Furthermore, certain stresses
generate alternating rings of selection for and against resistance around a localized
source of the antibiotic. In these conditions, localized antibiotic sources, even
at high strengths, can actually produce a net selection against resistance to
the antibiotic. Our results show that interactions between the effects of an antibiotic
and other stresses in inhomogeneous environments can generate pervasive, complex
patterns of selection both for and against antibiotic resistance.
acknowledgement: This work was partially supported by US National Institutes of Health
grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant
No. 152/11, and the European Research Council FP7 ERC Grant 281891.
article_number: '10333'
author:
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Adam
full_name: Palmer, Adam
last_name: Palmer
- first_name: Idan
full_name: Yelin, Idan
last_name: Yelin
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against
antibiotic resistance in inhomogeneous multistress environments. Nature Communications.
2016;7. doi:10.1038/ncomms10333
apa: Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection
for and against antibiotic resistance in inhomogeneous multistress environments.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333
chicago: Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection
for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.”
Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.
ieee: R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for
and against antibiotic resistance in inhomogeneous multistress environments,”
Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and
against antibiotic resistance in inhomogeneous multistress environments. Nature
Communications. 7, 10333.
mla: Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance
in Inhomogeneous Multistress Environments.” Nature Communications, vol.
7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333.
short: R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:25Z
date_published: 2016-01-20T00:00:00Z
date_updated: 2021-01-12T06:49:57Z
day: '20'
ddc:
- '570'
- '579'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/ncomms10333
file:
- access_level: open_access
checksum: ef147bcbb8bd37e9079cf3ce06f5815d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:52Z
date_updated: 2020-07-14T12:44:44Z
file_id: '5039'
file_name: IST-2016-662-v1+1_ncomms10333.pdf
file_size: 1844107
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5936'
pubrep_id: '662'
quality_controlled: '1'
scopus_import: 1
status: public
title: Pervasive selection for and against antibiotic resistance in inhomogeneous
multistress environments
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: 7
year: '2016'
...
---
_id: '1335'
abstract:
- lang: eng
text: In this paper we review various automata-theoretic formalisms for expressing
quantitative properties. We start with finite-state Boolean automata that express
the traditional regular properties. We then consider weighted ω-automata that
can measure the average density of events, which finite-state Boolean automata
cannot. However, even weighted ω-automata cannot express basic performance properties
like average response time. We finally consider two formalisms of weighted ω-automata
with monitors, where the monitors are either (a) counters or (b) weighted automata
themselves. We present a translation result to establish that these two formalisms
are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata,
and can express average response time property. They present a natural, robust,
and expressive framework for quantitative specifications, with important decidable
properties.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol
9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor
automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium,
Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative
Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2.
ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,”
presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016,
vol. 9837, pp. 23–38.'
ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata.
SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.'
mla: Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837,
Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38.
conference:
end_date: 2016-09-10
location: Edinburgh, United Kingdom
name: 'SAS: Static Analysis Symposium'
start_date: 2016-09-08
date_created: 2018-12-11T11:51:26Z
date_published: 2016-08-31T00:00:00Z
date_updated: 2021-01-12T06:49:58Z
day: '31'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-53413-7_2
ec_funded: 1
intvolume: ' 9837'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06764
month: '08'
oa: 1
oa_version: Preprint
page: 23 - 38
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Springer
publist_id: '5932'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative monitor automata
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9837
year: '2016'
...
---
_id: '1344'
abstract:
- lang: eng
text: Despite being composed of immobile cells, plants reorient along directional
stimuli. The hormone auxin is redistributed in stimulated organs leading to differential
growth and bending. Auxin application triggers rapid cell wall acidification and
elongation of aerial organs of plants, but the molecular players mediating these
effects are still controversial. Here we use genetically-encoded pH and auxin
signaling sensors, pharmacological and genetic manipulations available for Arabidopsis
etiolated hypocotyls to clarify how auxin is perceived and the downstream growth
executed. We show that auxin-induced acidification occurs by local activation
of H+-ATPases, which in the context of gravity response is restricted to the lower
organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA
nuclear auxin perception. In addition, auxin-induced gene transcription and specifically
SAUR proteins are crucial downstream mediators of this growth. Our study provides
strong experimental support for the acid growth theory and clarified the contribution
of the upstream auxin perception mechanisms.
acknowledgement: "The authors express their gratitude to Veronika Bierbaum, Robert
Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay.
We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser,
Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas
and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch
leading to these results has received funding from the People Programme (Marie Curie\r\nActions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement
n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP)."
article_number: e19048
author:
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jeffrey
full_name: Leung, Jeffrey
last_name: Leung
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid
cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5.
doi:10.7554/eLife.19048
apa: Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception
mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.19048
chicago: Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin
Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.”
ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048.
ieee: M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates
rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife,
vol. 5. eLife Sciences Publications, 2016.
ista: Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates
rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5,
e19048.
mla: Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid
Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol.
5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.
short: M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).
date_created: 2018-12-11T11:51:29Z
date_published: 2016-09-14T00:00:00Z
date_updated: 2021-01-12T06:50:01Z
day: '14'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.7554/eLife.19048
ec_funded: 1
file:
- access_level: open_access
checksum: 9209541fbba00f24daad21a5d568540d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:24Z
date_updated: 2020-07-14T12:44:45Z
file_id: '4748'
file_name: IST-2016-693-v1+1_e19048-download.pdf
file_size: 5666343
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5908'
pubrep_id: '654'
quality_controlled: '1'
scopus_import: 1
status: public
title: TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and
growth of Arabidopsis hypocotyls
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: 5
year: '2016'
...
---
_id: '1343'
abstract:
- lang: eng
text: "The Fermi-Hubbard model is one of the key models of condensed matter physics,
which holds a\r\n\r\npotential for explaining the mystery of high-temperature
superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices
has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools
of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations
plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate
laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF)
and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat
using the machinery of dissipative quantum state engineering, one can observe
the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions
in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser
scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe
driven-dissipative dynamics. The proposed controlled dissipation channels described
in this work\r\n\r\nare straightforward to add to already existing experimental
setups."
acknowledgement: "We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco,
Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza,
and Martin Zwierlein. The work was supported by the People Programme (Marie Curie
Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within
SFB 1227 (DQ-mat)."
article_number: '093042'
author:
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Hendrik
full_name: Weimer, Hendrik
last_name: Weimer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic
order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042
apa: Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation
of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics.
IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042
chicago: Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation
of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics.
IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042.
ieee: J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic
order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no.
9. IOP Publishing Ltd., 2016.
ista: Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic
order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042.
mla: Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order
in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042,
IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042.
short: J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016).
date_created: 2018-12-11T11:51:29Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2021-01-12T06:50:01Z
day: '22'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/18/9/093042
ec_funded: 1
file:
- access_level: open_access
checksum: 2a43e235222755e31ffbd369882c61de
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:52Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5309'
file_name: IST-2016-655-v1+1_njp_18_9_093042.pdf
file_size: 1076029
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5909'
pubrep_id: '655'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model
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: 18
year: '2016'
...
---
_id: '1340'
abstract:
- lang: eng
text: We study repeated games with absorbing states, a type of two-player, zero-sum
concurrent mean-payoff games with the prototypical example being the Big Match
of Gillete (1957). These games may not allow optimal strategies but they always
have ε-optimal strategies. In this paper we design ε-optimal strategies for Player
1 in these games that use only O(log log T) space. Furthermore, we construct strategies
for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing
function s, and which guarantee an ε-optimal value for Player 1 in the limit superior
sense. The previously known strategies use space Ω(log T) and it was known that
no strategy can use constant space if it is ε-optimal even in the limit superior
sense. We also give a complementary lower bound. Furthermore, we also show that
no Markov strategy, even extended with finite memory, can ensure value greater
than 0 in the Big Match, answering a question posed by Neyman [11].
alternative_title:
- LNCS
author:
- first_name: Kristoffer
full_name: Hansen, Kristoffer
last_name: Hansen
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Michal
full_name: Koucký, Michal
last_name: Koucký
citation:
ama: 'Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol
9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6'
apa: 'Hansen, K., Ibsen-Jensen, R., & Koucký, M. (2016). The big match in small
space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic
Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_6'
chicago: Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match
in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6.
ieee: 'K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,”
presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United
Kingdom, 2016, vol. 9928, pp. 64–76.'
ista: 'Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT:
Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76.'
mla: Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928,
Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6.
short: K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76.
conference:
end_date: 2016-09-21
location: Liverpool, United Kingdom
name: 'SAGT: Symposium on Algorithmic Game Theory'
start_date: 2016-09-19
date_created: 2018-12-11T11:51:28Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T06:50:00Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-53354-3_6
ec_funded: 1
intvolume: ' 9928'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.07634
month: '09'
oa: 1
oa_version: Preprint
page: 64 - 76
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '5927'
quality_controlled: '1'
scopus_import: 1
status: public
title: The big match in small space
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9928
year: '2016'
...
---
_id: '1345'
abstract:
- lang: eng
text: The electrostatic charge at the inner surface of the plasma membrane is strongly
negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate
plays a critical role in establishing plasma membrane surface charge in Arabidopsis,
which regulates the correct localization of signalling components.
article_number: '16102'
author:
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature
Plants. 2016;2. doi:10.1038/nplants.2016.102'
apa: 'Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative
attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102'
chicago: 'Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative
Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.'
ieee: 'G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,”
Nature Plants, vol. 2. Nature Publishing Group, 2016.'
ista: 'Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction.
Nature Plants. 2, 16102.'
mla: 'Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature
Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.'
short: G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).
date_created: 2018-12-11T11:51:30Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:02Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/nplants.2016.102
file:
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checksum: 9ba65f558563b287f875f48fa9f30fb2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:36Z
date_updated: 2020-07-14T12:44:45Z
file_id: '4954'
file_name: IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf
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relation: main_file
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checksum: 550d252be808d8ca2b43e83dddb4212f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:37Z
date_updated: 2020-07-14T12:44:45Z
file_id: '4955'
file_name: IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf
file_size: 430556
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5907'
pubrep_id: '1007'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Plasma membrane: Negative attraction'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2016'
...
---
_id: '1342'
abstract:
- lang: eng
text: A key aspect of bacterial survival is the ability to evolve while migrating
across spatially varying environmental challenges. Laboratory experiments, however,
often study evolution in well-mixed systems. Here, we introduce an experimental
device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria
spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that
allowed visual observation of mutation and selection in a migrating bacterial
front.While resistance increased consistently, multiple coexisting lineages diversified
both phenotypically and genotypically. Analyzing mutants at and behind the propagating
front,we found that evolution is not always led by the most resistant mutants;
highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate
provides a versatile platformfor studying microbial adaption and directly visualizing
evolutionary dynamics.
author:
- first_name: Michael
full_name: Baym, Michael
last_name: Baym
- first_name: Tami
full_name: Lieberman, Tami
last_name: Lieberman
- first_name: Eric
full_name: Kelsic, Eric
last_name: Kelsic
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Rotem
full_name: Gross, Rotem
last_name: Gross
- first_name: Idan
full_name: Yelin, Idan
last_name: Yelin
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on
antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822
apa: Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., &
Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822
chicago: Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross,
Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic
Landscapes.” Science. American Association for the Advancement of Science,
2016. https://doi.org/10.1126/science.aag0822.
ieee: M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,”
Science, vol. 353, no. 6304. American Association for the Advancement of
Science, pp. 1147–1151, 2016.
ista: Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016.
Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304),
1147–1151.
mla: Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.”
Science, vol. 353, no. 6304, American Association for the Advancement of
Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822.
short: M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony,
Science 353 (2016) 1147–1151.
date_created: 2018-12-11T11:51:29Z
date_published: 2016-09-09T00:00:00Z
date_updated: 2021-01-12T06:50:01Z
day: '09'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.aag0822
intvolume: ' 353'
issue: '6304'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/
month: '09'
oa: 1
oa_version: Preprint
page: 1147 - 1151
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5911'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spatiotemporal microbial evolution on antibiotic landscapes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 353
year: '2016'
...
---
_id: '1339'
abstract:
- lang: eng
text: "We present a microelectromechanical system, in which a silicon beam is attached
to a comb-drive\r\nactuator, which is used to tune the tension in the silicon
beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies
of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave
as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5
MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate
(10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant
of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally,
we show that the comb-drive actuator\r\ncan be used to switch between different
coupling rates with a frequency of at least 10 kHz.\r\n"
acknowledgement: We acknowledge the support from the Helmholtz Nanoelectronic Facility
(HNF) and funding from the ERC (GA-Nr. 280140).
article_number: '143507'
author:
- first_name: Gerard
full_name: Verbiest, Gerard
last_name: Verbiest
- first_name: Duo
full_name: Xu, Duo
id: 3454D55E-F248-11E8-B48F-1D18A9856A87
last_name: Xu
- first_name: Matthias
full_name: Goldsche, Matthias
last_name: Goldsche
- first_name: Timofiy
full_name: Khodkov, Timofiy
last_name: Khodkov
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Nils
full_name: Von Den Driesch, Nils
last_name: Von Den Driesch
- first_name: Dan
full_name: Buca, Dan
last_name: Buca
- first_name: Christoph
full_name: Stampfer, Christoph
last_name: Stampfer
citation:
ama: Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven
microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122
apa: Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch,
N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical
resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122
chicago: Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh,
Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling
between Driven Microelectromechanical Resonators.” Applied Physics Letter.
American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122.
ieee: G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical
resonators,” Applied Physics Letter, vol. 109. American Institute of Physics,
2016.
ista: Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca
D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical
resonators. Applied Physics Letter. 109, 143507.
mla: Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical
Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute
of Physics, 2016, doi:10.1063/1.4964122.
short: G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch,
D. Buca, C. Stampfer, Applied Physics Letter 109 (2016).
date_created: 2018-12-11T11:51:28Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2023-02-21T10:35:06Z
day: '04'
department:
- _id: JoFi
doi: 10.1063/1.4964122
intvolume: ' 109'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.04406
month: '10'
oa: 1
oa_version: Preprint
publication: Applied Physics Letter
publication_status: published
publisher: American Institute of Physics
publist_id: '5928'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tunable mechanical coupling between driven microelectromechanical resonators
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2016'
...
---
_id: '1349'
abstract:
- lang: eng
text: Crossing fitness valleys is one of the major obstacles to function optimization.
In this paper we investigate how the structure of the fitness valley, namely its
depth d and length ℓ, influence the runtime of different strategies for crossing
these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist
nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis
algorithm. While the (1+1) EA has to jump across the valley to a point of higher
fitness because it does not accept decreasing moves, the non-elitist algorithms
may cross the valley by accepting worsening moves. We show that while the runtime
of the (1+1) EA algorithm depends critically on the length of the valley, the
runtimes of the non-elitist algorithms depend crucially only on the depth of the
valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial
in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of
small length. Moreover, we show that both SSWM and Metropolis can also efficiently
optimize a rugged function consisting of consecutive valleys.
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms
elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary
Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909'
apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016).
When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings
of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170).
Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909'
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora
Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.”
In Proceedings of the Genetic and Evolutionary Computation Conference 2016
, 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism
outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic
and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp.
1163–1170.
ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism
outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and
Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation
conference, 1163–1170.'
mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing
Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference
2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.
short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings
of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.
conference:
end_date: 2016-07-24
location: Denver, CO, USA
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2016-07-20
date_created: 2018-12-11T11:51:31Z
date_published: 2016-07-20T00:00:00Z
date_updated: 2021-01-12T06:50:03Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2908812.2908909
ec_funded: 1
file:
- access_level: open_access
checksum: a1896e39e4113f2711e46b435d5f3e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:27Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5214'
file_name: IST-2016-650-v1+1_p1163-oliveto.pdf
file_size: 979026
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1163 - 1170
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 '
publication_status: published
publisher: ACM
publist_id: '5900'
pubrep_id: '650'
quality_controlled: '1'
scopus_import: 1
status: public
title: When non-elitism outperforms elitism for crossing fitness valleys
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1350'
abstract:
- lang: eng
text: "The hippocampal CA3 region plays a key role in learning and memory. Recurrent
CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion.
However, the\r\nsynaptic mechanisms of this network computation remain enigmatic.
To investigate these mechanisms, we combined functional connectivity analysis
with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal
neurons revealed that connectivity was sparse, spatially uniform, and highly enriched
in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary
connections were composed of one or two synaptic contacts, suggesting efficient
use of postsynaptic space. Real-size modeling indicated that CA3 networks with
sparse connectivity, disynaptic motifs, and single-contact connections robustly
generated pattern completion.Thus, macro- and microconnectivity contribute to
efficient\r\nmemory storage and retrieval in hippocampal networks."
acknowledged_ssus:
- _id: ScienComp
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern
completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123.
doi:10.1126/science.aaf1836
apa: Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic
mechanisms of pattern completion in the hippocampal CA3 network. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836
chicago: Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic
Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836.
ieee: J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms
of pattern completion in the hippocampal CA3 network,” Science, vol. 353,
no. 6304. American Association for the Advancement of Science, pp. 1117–1123,
2016.
ista: Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern
completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.
mla: Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal
CA3 Network.” Science, vol. 353, no. 6304, American Association for the
Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836.
short: J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.
date_created: 2018-12-11T11:51:31Z
date_published: 2016-09-09T00:00:00Z
date_updated: 2021-01-12T06:50:04Z
day: '09'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.1126/science.aaf1836
ec_funded: 1
file:
- access_level: open_access
checksum: 89caefa4e181424cbf0aecc835fcc5ec
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:27Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4945'
file_name: IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf
file_size: 19408143
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 353'
issue: '6304'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 1117 - 1123
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5899'
pubrep_id: '823'
quality_controlled: '1'
scopus_import: 1
status: public
title: Synaptic mechanisms of pattern completion in the hippocampal CA3 network
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 353
year: '2016'
...
---
_id: '1347'
abstract:
- lang: eng
text: 'During the past 70 years, the quantum theory of angular momentum has been
successfully applied to describing the properties of nuclei, atoms, and molecules,
and their interactions with each other as well as with external fields. Because
of the properties of quantum rotations, the angular-momentum algebra can be of
tremendous complexity even for a few interacting particles, such as valence electrons
of an atom, not to mention larger many-particle systems. In this work, we study
an example of the latter: A rotating quantum impurity coupled to a many-body bosonic
bath. In the regime of strong impurity-bath couplings, the problem involves the
addition of an infinite number of angular momenta, which renders it intractable
using currently available techniques. Here, we introduce a novel canonical transformation
that allows us to eliminate the complex angular-momentum algebra from such a class
of many-body problems. In addition, the transformation exposes the problem''s
constants of motion, and renders it solvable exactly in the limit of a slowly
rotating impurity. We exemplify the technique by showing that there exists a critical
rotational speed at which the impurity suddenly acquires one quantum of angular
momentum from the many-particle bath. Such an instability is accompanied by the
deformation of the phonon density in the frame rotating along with the impurity.'
acknowledgement: We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari,
and Hendrik Weimer for insightful discussions. The work was supported by the NSF
through a grant for the Institute for Theoretical Atomic, Molecular, and Optical
Physics at Harvard University and Smithsonian Astrophysical Observatory.
article_number: '011012'
author:
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating
impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012
apa: Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle
system by a rotating impurity. Physical Review X. American Physical Society.
https://doi.org/10.1103/PhysRevX.6.011012
chicago: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle
System by a Rotating Impurity.” Physical Review X. American Physical Society,
2016. https://doi.org/10.1103/PhysRevX.6.011012.
ieee: R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system
by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical
Society, 2016.
ista: Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system
by a rotating impurity. Physical Review X. 6(1), 011012.
mla: Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle
System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012,
American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012.
short: R. Schmidt, M. Lemeshko, Physical Review X 6 (2016).
date_created: 2018-12-11T11:51:30Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:03Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevX.6.011012
file:
- access_level: open_access
checksum: 6757a164d3c38905e05b2b5a188cb8ff
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:59Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5183'
file_name: IST-2016-652-v1+1_PhysRevX.6.011012.pdf
file_size: 1165869
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '5902'
pubrep_id: '652'
quality_controlled: '1'
scopus_import: 1
status: public
title: Deformation of a quantum many-particle system by a rotating impurity
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: '1348'
abstract:
- lang: eng
text: 'A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function
γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii)
γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where
x(.) denotes the projection to the xaxis.We prove a characterization of isotopy
classes of embeddings of connected graphs equipped with γ in the plane containing
an x-bounded embedding.Then we present an efficient algorithm, which relies on
our result, for testing the existence of an x-bounded embedding if the given graph
is a forest.This partially answers a question raised recently by Angelini et al.and
Chang et al., and proves that c-planarity testing of flat clustered graphs with
three clusters is tractable when the underlying abstract graph is a forest.'
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. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer;
2016:31-42. doi:10.1007/978-3-319-44543-4_3'
apa: 'Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp.
31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms,
Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3'
chicago: Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42.
Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3.
ieee: 'R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA:
International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol.
9843, pp. 31–42.'
ista: 'Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International
Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.'
mla: Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843,
Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3.
short: R. Fulek, in:, Springer, 2016, pp. 31–42.
conference:
end_date: 2018-08-19
location: Helsinki, Finland
name: 'IWOCA: International Workshop on Combinatorial Algorithms'
start_date: 2016-08-17
date_created: 2018-12-11T11:51:31Z
date_published: 2016-08-09T00:00:00Z
date_updated: 2021-01-12T06:50:03Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/978-3-319-44543-4_3
ec_funded: 1
intvolume: ' 9843'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.07144
month: '08'
oa: 1
oa_version: Preprint
page: 31 - 42
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: '5901'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bounded embeddings of graphs in the plane
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9843
year: '2016'
...
---
_id: '1355'
abstract:
- lang: eng
text: Radiation pressure has recently been used to effectively couple the quantum
motion of mechanical elements to the fields of optical or microwave light. Integration
of all three degrees of freedom—mechanical, optical and microwave—would enable
a quantum interconnect between microwave and optical quantum systems. We present
a platform based on silicon nitride nanomembranes for integrating superconducting
microwave circuits with planar acoustic and optical devices such as phononic and
photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral
inductor coils of micron pitch we realize microwave resonant circuits with large
electromechanical coupling to planar acoustic structures of nanoscale dimensions
and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate
microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam
to an occupancy as low as 0.32. These results indicate the viability of silicon
nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical
experiments.
acknowledgement: This work was supported by the DARPA MESO programme, the Institute
for Quantum Information and Matter, an NSF Physics Frontiers Center with support
of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at
Caltech. A.P. was supported by a Marie Curie International Outgoing Fellowship within
the 7th European Community Framework Programme, NEMO (GA 298861). Certain commercial
equipment and software are identified in this documentation to describe the subject
adequately. Such identification does not imply recommendation or endorsement by
the NIST, nor does it imply that the equipment identified is necessarily the best
available for the purpose.
article_number: '12396'
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Mahmoud
full_name: Kalaee, Mahmoud
last_name: Kalaee
- first_name: Alessandro
full_name: Pitanti, Alessandro
last_name: Pitanti
- first_name: Richard
full_name: Norte, Richard
last_name: Norte
- first_name: Lukas
full_name: Heinzle, Lukas
last_name: Heinzle
- first_name: Marcelo
full_name: Davanço, Marcelo
last_name: Davanço
- first_name: Kartik
full_name: Srinivasan, Kartik
last_name: Srinivasan
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
citation:
ama: Fink JM, Kalaee M, Pitanti A, et al. Quantum electromechanics on silicon nitride
nanomembranes. Nature Communications. 2016;7. doi:10.1038/ncomms12396
apa: Fink, J. M., Kalaee, M., Pitanti, A., Norte, R., Heinzle, L., Davanço, M.,
… Painter, O. (2016). Quantum electromechanics on silicon nitride nanomembranes.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12396
chicago: Fink, Johannes M, Mahmoud Kalaee, Alessandro Pitanti, Richard Norte, Lukas
Heinzle, Marcelo Davanço, Kartik Srinivasan, and Oskar Painter. “Quantum Electromechanics
on Silicon Nitride Nanomembranes.” Nature Communications. Nature Publishing
Group, 2016. https://doi.org/10.1038/ncomms12396.
ieee: J. M. Fink et al., “Quantum electromechanics on silicon nitride nanomembranes,”
Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Fink JM, Kalaee M, Pitanti A, Norte R, Heinzle L, Davanço M, Srinivasan K,
Painter O. 2016. Quantum electromechanics on silicon nitride nanomembranes. Nature
Communications. 7, 12396.
mla: Fink, Johannes M., et al. “Quantum Electromechanics on Silicon Nitride Nanomembranes.”
Nature Communications, vol. 7, 12396, Nature Publishing Group, 2016, doi:10.1038/ncomms12396.
short: J.M. Fink, M. Kalaee, A. Pitanti, R. Norte, L. Heinzle, M. Davanço, K. Srinivasan,
O. Painter, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:33Z
date_published: 2016-08-03T00:00:00Z
date_updated: 2021-01-12T06:50:06Z
day: '03'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/ncomms12396
file:
- access_level: open_access
checksum: 25513bd59d5bda495efa8f5920e91b22
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:30Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5014'
file_name: IST-2016-629-v1+1_ncomms12396.pdf
file_size: 2139802
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5891'
pubrep_id: '629'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantum electromechanics on silicon nitride nanomembranes
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: 7
year: '2016'
...
---
_id: '1359'
abstract:
- lang: eng
text: "The role of gene interactions in the evolutionary process has long\r\nbeen
controversial. Although some argue that they are not of\r\nimportance, because
most variation is additive, others claim that\r\ntheir effect in the long term
can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions
under directional\r\nselection assuming no mutation or dominance, and that epistasis
is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can
be increased by selection and analyze two extreme\r\nregimes, in which either
drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios,
epistatic interactions affect\r\nthe long-term response to selection by modulating
the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson
A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument
to show that, for any form of epistasis, the total response\r\nof a haploid population
is proportional to the initial total genotypic\r\nvariance. In contrast, the total
response of a diploid population is\r\nincreased by epistasis, for a given initial
genotypic variance. When\r\nselection dominates, we show that the total selection
response can\r\nonly be increased by epistasis when s\r\nome initially deleterious
alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple
approximation for this effect and show that, in this regime, it is\r\nthe structure
of the genotype - phenotype map that matters and not\r\nthe variance components
of the population."
article_processing_charge: No
article_type: original
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Paixao T, Barton NH. The effect of gene interactions on the long-term response
to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
apa: Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on
the long-term response to selection. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1518830113
chicago: Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions
on the Long-Term Response to Selection.” PNAS. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1518830113.
ieee: T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term
response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences,
pp. 4422–4427, 2016.
ista: Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term
response to selection. PNAS. 113(16), 4422–4427.
mla: Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on
the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National
Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.
short: T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.
date_created: 2018-12-11T11:51:34Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2021-01-12T06:50:08Z
day: '19'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1073/pnas.1518830113
ec_funded: 1
external_id:
pmid:
- '27044080'
intvolume: ' 113'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/
month: '04'
oa: 1
oa_version: Published Version
page: 4422 - 4427
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5886'
quality_controlled: '1'
scopus_import: 1
status: public
title: The effect of gene interactions on the long-term response to selection
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1352'
abstract:
- lang: eng
text: We study the interplay of nematic and superconducting order in the two-dimensional
Hubbard model and show that they can coexist, especially when superconductivity
is not the energetically dominant phase. Due to a breaking of the C4 symmetry,
the coexisting phase inherently contains admixture of the s-wave pairing components.
As a result, the superconducting gap exhibits nonstandard features including changed
nodal directions. Our results also show that in the optimally doped regime the
pure superconducting phase is typically unstable towards developing nematicity
(breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors,
for which in this regime the so-called intertwined orders have recently been observed.
Namely, the coexisting phase may be viewed as a precursor to such more involved
patterns of symmetry breaking.
acknowledgement: The authors are grateful to Florian Gebhard and Mikhail Lemeshko
for discussions and critical reading of the manuscript. The work was supported by
the Ministry of Science and Higher Education in Poland through the Iuventus Plus
Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant
Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in
Hannover where a large part of the work was performed.
article_number: '085152'
author:
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Tobias
full_name: Schickling, Tobias
last_name: Schickling
- first_name: Jörg
full_name: Bünemann, Jörg
last_name: Bünemann
citation:
ama: Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity
in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics.
2016;94(8). doi:10.1103/PhysRevB.94.085152
apa: Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2016). Coexistence of
nematic order and superconductivity in the Hubbard model. Physical Review B
- Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.085152
chicago: Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of
Nematic Order and Superconductivity in the Hubbard Model.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2016.
https://doi.org/10.1103/PhysRevB.94.085152.
ieee: J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order
and superconductivity in the Hubbard model,” Physical Review B - Condensed
Matter and Materials Physics, vol. 94, no. 8. American Physical Society, 2016.
ista: Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order
and superconductivity in the Hubbard model. Physical Review B - Condensed Matter
and Materials Physics. 94(8), 085152.
mla: Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity
in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics,
vol. 94, no. 8, 085152, American Physical Society, 2016, doi:10.1103/PhysRevB.94.085152.
short: J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed
Matter and Materials Physics 94 (2016).
date_created: 2018-12-11T11:51:32Z
date_published: 2016-08-30T00:00:00Z
date_updated: 2021-01-12T06:50:05Z
day: '30'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.94.085152
ec_funded: 1
intvolume: ' 94'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1512.06688
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5897'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coexistence of nematic order and superconductivity in the Hubbard model
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2016'
...
---
_id: '1354'
abstract:
- lang: eng
text: Fabrication processes involving anhydrous hydrofluoric vapor etching are developed
to create high-Q aluminum superconducting microwave resonators on free-standing
silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication
process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with
a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave
spectroscopy and radiation pressure backaction are used to characterize the coupled
system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding
a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical
resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical
resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being
realized at an elevated fridge temperature of Tf=211 mK.
article_number: '014013'
author:
- first_name: Paul
full_name: Dieterle, Paul
last_name: Dieterle
- first_name: Mahmoud
full_name: Kalaee, Mahmoud
last_name: Kalaee
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
citation:
ama: Dieterle P, Kalaee M, Fink JM, Painter O. Superconducting cavity electromechanics
on a silicon-on-insulator platform. Physical Review Applied. 2016;6(1).
doi:10.1103/PhysRevApplied.6.014013
apa: Dieterle, P., Kalaee, M., Fink, J. M., & Painter, O. (2016). Superconducting
cavity electromechanics on a silicon-on-insulator platform. Physical Review
Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.6.014013
chicago: Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting
Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review
Applied. American Physical Society, 2016. https://doi.org/10.1103/PhysRevApplied.6.014013.
ieee: P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity
electromechanics on a silicon-on-insulator platform,” Physical Review Applied,
vol. 6, no. 1. American Physical Society, 2016.
ista: Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics
on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013.
mla: Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator
Platform.” Physical Review Applied, vol. 6, no. 1, 014013, American Physical
Society, 2016, doi:10.1103/PhysRevApplied.6.014013.
short: P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6
(2016).
date_created: 2018-12-11T11:51:32Z
date_published: 2016-07-22T00:00:00Z
date_updated: 2021-01-12T06:50:06Z
day: '22'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.6.014013
intvolume: ' 6'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1601.04019
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_status: published
publisher: American Physical Society
publist_id: '5892'
quality_controlled: '1'
scopus_import: 1
status: public
title: Superconducting cavity electromechanics on a silicon-on-insulator platform
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1356'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting
Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796
apa: Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and
the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796
chicago: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations
and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016.
https://doi.org/10.1534/genetics.115.184796.
ieee: N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the
‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America,
pp. 3–4, 2016.
ista: Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the
“Shifting Balance”. Genetics. 202(1), 3–4.
mla: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and
the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of
America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.
short: N.H. Barton, Genetics 202 (2016) 3–4.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-01-05T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1534/genetics.115.184796
file:
- access_level: open_access
checksum: 3562b89c821a4be84edf2b6ebd870cf5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:26Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4687'
file_name: IST-2017-769-v1+1_SewallWright1931.pdf
file_size: 112674
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 3 - 4
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5889'
pubrep_id: '769'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1357'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics.
2016;202(3):865-866. doi:10.1534/genetics.116.187542
apa: Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542
chicago: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent
Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.
ieee: N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,”
Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.
ista: Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. 202(3), 865–866.
mla: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.”
Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66,
doi:10.1534/genetics.116.187542.
short: N.H. Barton, Genetics 202 (2016) 865–866.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.187542
file:
- access_level: open_access
checksum: b2174bab2de1d1142900062a150f35c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:09Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5127'
file_name: IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf
file_size: 130779
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 865 - 866
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5888'
pubrep_id: '768'
quality_controlled: '1'
scopus_import: 1
status: public
title: Richard Hudson and Norman Kaplan on the coalescent process
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1353'
abstract:
- lang: eng
text: We characterize absorption in finite idempotent algebras by means of Jónsson
absorption and cube term blockers. As an application we show that it is decidable
whether a given subset is an absorbing subuniverse of an algebra given by the
tables of its basic operations.
acknowledgement: 'Libor Barto and Alexandr Kazda were supported by the the Grant Agency
of the Czech Republic, grant GACR 13-01832S. '
author:
- first_name: Libor
full_name: Barto, Libor
last_name: Barto
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
citation:
ama: Barto L, Kazda A. Deciding absorption. International Journal of Algebra
and Computation. 2016;26(5):1033-1060. doi:10.1142/S0218196716500430
apa: Barto, L., & Kazda, A. (2016). Deciding absorption. International Journal
of Algebra and Computation. World Scientific Publishing. https://doi.org/10.1142/S0218196716500430
chicago: Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International
Journal of Algebra and Computation. World Scientific Publishing, 2016. https://doi.org/10.1142/S0218196716500430.
ieee: L. Barto and A. Kazda, “Deciding absorption,” International Journal of
Algebra and Computation, vol. 26, no. 5. World Scientific Publishing, pp.
1033–1060, 2016.
ista: Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra
and Computation. 26(5), 1033–1060.
mla: Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal
of Algebra and Computation, vol. 26, no. 5, World Scientific Publishing, 2016,
pp. 1033–60, doi:10.1142/S0218196716500430.
short: L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016)
1033–1060.
date_created: 2018-12-11T11:51:32Z
date_published: 2016-07-20T00:00:00Z
date_updated: 2021-01-12T06:50:06Z
day: '20'
department:
- _id: VlKo
doi: 10.1142/S0218196716500430
intvolume: ' 26'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1512.07009
month: '07'
oa: 1
oa_version: Preprint
page: 1033 - 1060
publication: International Journal of Algebra and Computation
publication_status: published
publisher: World Scientific Publishing
publist_id: '5893'
quality_controlled: '1'
scopus_import: 1
status: public
title: Deciding absorption
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1363'
abstract:
- lang: eng
text: When aiming to seamlessly integrate a fluid simulation into a larger scenario
(like an open ocean), careful attention must be paid to boundary conditions. In
particular, one must implement special "non-reflecting" boundary conditions,
which dissipate out-going waves as they exit the simulation. Unfortunately, the
state of the art in non-reflecting boundary conditions (perfectly-matched layers,
or PMLs) only permits trivially simple inflow/outflow conditions, so there is
no reliable way to integrate a fluid simulation into a more complicated environment
like a stormy ocean or a turbulent river. This paper introduces the first method
for combining nonreflecting boundary conditions based on PMLs with inflow/outflow
boundary conditions that vary arbitrarily throughout space and time. Our algorithm
is a generalization of stateof- the-art mean-flow boundary conditions in the computational
fluid dynamics literature, and it allows for seamless integration of a fluid simulation
into much more complicated environments. Our method also opens the door for previously-unseen
postprocess effects like retroactively changing the location of solid obstacles,
and locally increasing the visual detail of a pre-existing simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'We thank the IST Austria Visual Computing group for helpful feedback
throughout the project. '
alternative_title:
- ACM Transactions on Graphics
article_number: '96'
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid
re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963'
apa: 'Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries
for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA,
USA: ACM. https://doi.org/10.1145/2897824.2925963'
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963.
ieee: M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for
fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol.
35, no. 4.
ista: Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for
fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.
short: M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-11T00:00:00Z
date_updated: 2023-02-21T10:36:12Z
day: '11'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925963
ec_funded: 1
file:
- access_level: open_access
checksum: 140b5532f0a2a006a0149cab7c73c17c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:00Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4981'
file_name: IST-2016-631-v1+2_a96-bojsen-hansen.pdf
file_size: 12422760
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5879'
pubrep_id: '631'
quality_controlled: '1'
status: public
title: Generalized non-reflecting boundaries for fluid re-simulation
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1364'
abstract:
- lang: eng
text: We present a computational method for designing wire sculptures consisting
of interlocking wires. Our method allows the computation of aesthetically pleasing
structures that are structurally stable, efficiently fabricatable with a 2D wire
bending machine, and assemblable without the need of additional connectors. Starting
from a set of planar contours provided by the user, our method automatically tests
for the feasibility of a design, determines a discrete ordering of wires at intersection
points, and optimizes for the rest shape of the individual wires to maximize structural
stability under frictional contact. In addition to their application to art, wire
sculptures present an extremely efficient and fast alternative for low-fidelity
rapid prototyping because manufacturing time and required material linearly scales
with the physical size of objects. We demonstrate the effectiveness of our approach
on a varied set of examples, all of which we fabricated.
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under grant agreement No 645599.
alternative_title:
- ACM Transactions on Graphics
article_number: '86'
author:
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
- first_name: Mathias
full_name: Lepoutre, Mathias
last_name: Lepoutre
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod
structures. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925978'
apa: 'Miguel Villalba, E., Lepoutre, M., & Bickel, B. (2016). Computational
design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH,
Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925978'
chicago: Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational
Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925978.
ieee: E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable
planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016,
vol. 35, no. 4.
ista: Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable
planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86.
mla: Miguel Villalba, Eder, et al. Computational Design of Stable Planar-Rod
Structures. Vol. 35, no. 4, 86, ACM, 2016, doi:10.1145/2897824.2925978.
short: E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:36Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:10Z
day: '01'
ddc:
- '006'
department:
- _id: BeBi
doi: 10.1145/2897824.2925978
ec_funded: 1
file:
- access_level: open_access
checksum: d00c2664a43d945df8876ea0193734e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:01Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4853'
file_name: IST-2017-763-v1+1_wirebending.pdf
file_size: 44766392
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
publication_status: published
publisher: ACM
publist_id: '5878'
pubrep_id: '763'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computational design of stable planar-rod structures
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1361'
abstract:
- lang: eng
text: We propose a novel surface-only technique for simulating incompressible, inviscid
and uniform-density liquids with surface tension in three dimensions. The liquid
surface is captured by a triangle mesh on which a Lagrangian velocity field is
stored. Because advection of the velocity field may violate the incompressibility
condition, we devise an orthogonal projection technique to remove the divergence
while requiring the evaluation of only two boundary integrals. The forces of surface
tension, gravity, and solid contact are all treated by a boundary element solve,
allowing us to perform detailed simulations of a wide range of liquid phenomena,
including waterbells, droplet and jet collisions, fluid chains, and crown splashes.
alternative_title:
- ACM Transactions on Graphics
article_number: a78
author:
- first_name: Fang
full_name: Da, Fang
last_name: Da
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher
full_name: Batty, Christopher
last_name: Batty
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Eitan
full_name: Grinspun, Eitan
last_name: Grinspun
citation:
ama: 'Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol
35. ACM; 2016. doi:10.1145/2897824.2925899'
apa: 'Da, F., Hahn, D., Batty, C., Wojtan, C., & Grinspun, E. (2016). Surface
only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM.
https://doi.org/10.1145/2897824.2925899'
chicago: Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun.
“Surface Only Liquids,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925899.
ieee: F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,”
presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.
ista: Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM
SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.
mla: Da, Fang, et al. Surface Only Liquids. Vol. 35, no. 4, a78, ACM, 2016,
doi:10.1145/2897824.2925899.
short: F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-11T00:00:00Z
date_updated: 2023-02-21T10:36:07Z
day: '11'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925899
ec_funded: 1
file:
- access_level: open_access
checksum: 6d662893bd447d4f575b4961a2247811
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4660'
file_name: IST-2016-637-v1+1_2016_Da_SOL.pdf
file_size: 10561865
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5881'
pubrep_id: '637'
quality_controlled: '1'
scopus_import: 1
status: public
title: Surface only liquids
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1365'
abstract:
- lang: eng
text: A memory-hard function (MHF) f is equipped with a space cost σ and time cost
τ parameter such that repeatedly computing fσ,τ on an application specific integrated
circuit (ASIC) is not economically advantageous relative to a general purpose
computer. Technically we would like that any (generalized) circuit for evaluating
an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent
MHF (iMHF) has the added property that it can be computed with almost optimal
memory and time complexity by an algorithm which accesses memory in a pattern
independent of the input value. Such functions can be specified by fixing a directed
acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph.
In this work we develop new tools for analyzing iMHFs. First we define and motivate
a new complexity measure capturing the amount of energy (i.e. electricity) required
to compute a function. We argue that, in practice, this measure is at least as
important as the more traditional AT-complexity. Next we describe an algorithm
A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound
both its energy and AT complexities per instance evaluated in terms of a certain
combinatorial property of G. Next we instantiate our attack for several general
classes of DAGs which include those underlying many of the most important iMHF
candidates in the literature. In particular, we obtain the following results which
hold for all choices of parameters σ and τ (and thread-count) such that n = σ
∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities
O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67).
-The Double-Buffer and the Linear functions of [CGBS16] both have complexities
in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing
Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function
of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm
with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1
this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ )
is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness
of any DAG which may prove to be of independent interest.
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
citation:
ama: 'Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions.
In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9'
apa: 'Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent
memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International
Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9'
chicago: Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent
Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9.
ieee: 'J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard
functions,” presented at the CRYPTO: International Cryptology Conference, Santa
Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.'
ista: 'Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard
functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.'
mla: Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent
Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9.
short: J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.
conference:
end_date: 2016-08-18
location: Santa Barbara, CA, USA
name: 'CRYPTO: International Cryptology Conference'
start_date: 2016-08-14
date_created: 2018-12-11T11:51:36Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:50:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53008-5_9
intvolume: ' 9815'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2016/115
month: '08'
oa: 1
oa_version: Preprint
page: 241 - 271
publication_status: published
publisher: Springer
publist_id: '5876'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficiently computing data-independent memory-hard functions
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9815
year: '2016'
...
---
_id: '1366'
abstract:
- lang: eng
text: 'We study the problem of devising provably secure PRNGs with input based on
the sponge paradigm. Such constructions are very appealing, as efficient software/hardware
implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box
way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES
2010), fails to achieve the security notion of robustness recently considered
by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic,
and thus there are high-entropy input distributions on which the construction
fails to extract random bits, and (2) The construction is not forward secure,
and presented solutions aiming at restoring forward security have not been rigorously
analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which
we prove secure in the sense of robustness, delivering in particular concrete
security bounds. On the way, we make what we believe to be an important conceptual
contribution, developing a variant of the security framework of Dodis et al. tailored
at the ideal permutation model that captures PRNG security in settings where the
weakly random inputs are provided from a large class of possible adversarial samplers
which are also allowed to query the random permutation. As a further application
of our techniques, we also present an efficient sponge-based key-derivation function
(which can be instantiated from SHA-3 in a black-box fashion), which we also prove
secure when fed with samples from permutation-dependent distributions.'
alternative_title:
- LNCS
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665.
Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4'
apa: 'Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and
KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4'
chicago: Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and
KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4.
ieee: 'P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented
at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna,
Austria, 2016, vol. 9665, pp. 87–116.'
ista: 'Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT:
Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.'
mla: Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and
KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4.
short: P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.
conference:
end_date: 2016-05-12
location: Vienna, Austria
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2016-05-08
date_created: 2018-12-11T11:51:36Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-662-49890-3_4
ec_funded: 1
intvolume: ' 9665'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/169/20160219:201940
month: '05'
oa: 1
oa_version: Preprint
page: 87 - 116
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5872'
quality_controlled: '1'
scopus_import: 1
status: public
title: Provably robust sponge-based PRNGs and KDFs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9665
year: '2016'
...