---
_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: '1181'
abstract:
- lang: eng
text: 'This review accompanies a 2016 SFN mini-symposium presenting examples of
current studies that address a central question: How do neural stem cells (NSCs)
divide in different ways to produce heterogeneous daughter types at the right
time and in proper numbers to build a cerebral cortex with the appropriate size
and structure? We will focus on four aspects of corticogenesis: cytokinesis events
that follow apical mitoses of NSCs; coordinating abscission with delamination
from the apical membrane; timing of neurogenesis and its indirect regulation through
emergence of intermediate progenitors; and capacity of single NSCs to generate
the correct number and laminar fate of cortical neurons. Defects in these mechanisms
can cause microcephaly and other brain malformations, and understanding them is
critical to designing diagnostic tools and preventive and corrective therapies.'
acknowledgement: This work was supported by National Institutes of Health Grants R01NS089795
and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777
to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444
and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from
the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent
to L.N. The authors apologize to colleagues whose work could not be cited due to
space limitations.
author:
- first_name: Noelle
full_name: Dwyer, Noelle
last_name: Dwyer
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Shen
full_name: Chou, Shen
last_name: Chou
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Laurent
full_name: Nguyen, Laurent
last_name: Nguyen
- first_name: Troy
full_name: Ghashghaei, Troy
last_name: Ghashghaei
citation:
ama: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem
cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and
productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016'
apa: 'Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei,
T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating
progenitor behavior and productivity. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016'
chicago: 'Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen,
and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience.
Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.'
ieee: 'N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei,
“Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society
for Neuroscience, pp. 11394–11401, 2016.'
ista: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural
stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior
and productivity. Journal of Neuroscience. 36(45), 11394–11401.'
mla: 'Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience,
vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.'
short: N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal
of Neuroscience 36 (2016) 11394–11401.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2021-01-12T06:48:54Z
day: '09'
department:
- _id: SiHi
doi: 10.1523/JNEUROSCI.2359-16.2016
intvolume: ' 36'
issue: '45'
language:
- iso: eng
month: '11'
oa_version: None
page: 11394 - 11401
project:
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '6172'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 36
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: '1185'
abstract:
- lang: eng
text: The developmental programme of the pistil is under the control of both auxin
and cytokinin. Crosstalk between these factors converges on regulation of the
auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription
factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length
and ovule number were reduced. PIN1 expression was also lower in the triple mutant
and the phenotypes could not be rescued by exogenous cytokinin application. pin1
complementation studies using genomic PIN1 constructs showed that the pistil phenotypes
were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without
this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating
the pivotal role of CRFs in auxin-cytokinin crosstalk.
acknowledgement: M.C. was funded by a PhD fellowship from the Università degli Studi
di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca
(MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would
like to thank Andrew MacCabe and Edward Kiegle for editing the paper.
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Andrea
full_name: Guazzotti, Andrea
last_name: Guazzotti
- first_name: Nadia
full_name: Quadrelli, Nadia
last_name: Quadrelli
- first_name: Marta
full_name: Mendes, Marta
last_name: Mendes
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate
auxin and cytokinin pathways for female reproductive organ development. Development.
2016;143(23):4419-4424. doi:10.1242/dev.143545
apa: Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková,
E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin
pathways for female reproductive organ development. Development. Company
of Biologists. https://doi.org/10.1242/dev.143545
chicago: Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta
Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate
Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development.
Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.
ieee: M. Cucinotta et al., “Cytokinin response factors integrate auxin and
cytokinin pathways for female reproductive organ development,” Development,
vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.
ista: Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo
L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for
female reproductive organ development. Development. 143(23), 4419–4424.
mla: Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin
Pathways for Female Reproductive Organ Development.” Development, vol.
143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.
short: M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková,
L. Colombo, Development 143 (2016) 4419–4424.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '01'
department:
- _id: EvBe
doi: 10.1242/dev.143545
intvolume: ' 143'
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 4419 - 4424
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6168'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin response factors integrate auxin and cytokinin pathways for female
reproductive organ development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
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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file_size: 295274
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checksum: e13171843283774404c936c581b4543e
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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
file_id: '5225'
file_name: IST-2017-770-v1+3_Fig2.pdf
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creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5226'
file_name: IST-2017-770-v1+4_Fig3.pdf
file_size: 1172194
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checksum: e47b2a0c32142f423b3100150c0294f8
content_type: application/pdf
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
- access_level: open_access
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: '1201'
abstract:
- lang: eng
text: In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear
actin cytoskeleton that protects the nucleus and its genomic content of migrating
cells squeezing through small spaces.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Sixt MK. Formin’ a nuclear protection. Cell. 2016;167(6):1448-1449.
doi:10.1016/j.cell.2016.11.024
apa: Renkawitz, J., & Sixt, M. K. (2016). Formin’ a nuclear protection. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2016.11.024
chicago: Renkawitz, Jörg, and Michael K Sixt. “Formin’ a Nuclear Protection.” Cell.
Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.024.
ieee: J. Renkawitz and M. K. Sixt, “Formin’ a nuclear protection,” Cell,
vol. 167, no. 6. Cell Press, pp. 1448–1449, 2016.
ista: Renkawitz J, Sixt MK. 2016. Formin’ a nuclear protection. Cell. 167(6), 1448–1449.
mla: Renkawitz, Jörg, and Michael K. Sixt. “Formin’ a Nuclear Protection.” Cell,
vol. 167, no. 6, Cell Press, 2016, pp. 1448–49, doi:10.1016/j.cell.2016.11.024.
short: J. Renkawitz, M.K. Sixt, Cell 167 (2016) 1448–1449.
date_created: 2018-12-11T11:50:41Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.cell.2016.11.024
intvolume: ' 167'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 1448 - 1449
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '6149'
quality_controlled: '1'
scopus_import: 1
status: public
title: Formin’ a nuclear protection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 167
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: '1210'
abstract:
- lang: eng
text: Mechanisms for cell protection are essential for survival of multicellular
organisms. In plants, the apical hook, which is transiently formed in darkness
when the germinating seedling penetrates towards the soil surface, plays such
protective role and shields the vitally important shoot apical meristem and cotyledons
from damage. The apical hook is formed by bending of the upper hypocotyl soon
after germination, and it is maintained in a closed stage while the hypocotyl
continues to penetrate through the soil and rapidly opens when exposed to light
in proximity of the soil surface. To uncover the complex molecular network orchestrating
this spatiotemporally tightly coordinated process, monitoring of the apical hook
development in real time is indispensable. Here we describe an imaging platform
that enables high-resolution kinetic analysis of this dynamic developmental process.
© Springer Science+Business Media New York 2017.
acknowledgement: "We thank Herman \r\nHöfte \r\n, Todor Asenov, Robert Hauschield,
and \r\nMarcal Gallemi for help with the establishment of the real-time
\ \r\nimaging platform and technical support. This work was supported \r\nby the
Czech Science Foundation (GA13-39982S) to Eva Benková. \r\nDominique Van Der
\ Straeten acknowledges the Research \r\nFoundation Flanders for fi\r\n
\ nancial support (G.0656.13N). Dajo \r\nSmet holds a PhD fellowship of the
Research Foundation Flanders. "
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Dajo
full_name: Smet, Dajo
last_name: Smet
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: 'Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. Real time analysis
of the apical hook development. In: Plant Hormones. Vol 1497. Humana Press;
2016:1-8. doi:10.1007/978-1-4939-6469-7_1'
apa: Zhu, Q., Žádníková, P., Smet, D., Van Der Straeten, D., & Benková, E. (2016).
Real time analysis of the apical hook development. In Plant Hormones (Vol.
1497, pp. 1–8). Humana Press. https://doi.org/10.1007/978-1-4939-6469-7_1
chicago: Zhu, Qiang, Petra Žádníková, Dajo Smet, Dominique Van Der Straeten, and
Eva Benková. “Real Time Analysis of the Apical Hook Development.” In Plant
Hormones, 1497:1–8. Humana Press, 2016. https://doi.org/10.1007/978-1-4939-6469-7_1.
ieee: Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, and E. Benková, “Real
time analysis of the apical hook development,” in Plant Hormones, vol.
1497, Humana Press, 2016, pp. 1–8.
ista: 'Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. 2016.Real time
analysis of the apical hook development. In: Plant Hormones. Methods in Molecular
Biology, vol. 1497, 1–8.'
mla: Zhu, Qiang, et al. “Real Time Analysis of the Apical Hook Development.” Plant
Hormones, vol. 1497, Humana Press, 2016, pp. 1–8, doi:10.1007/978-1-4939-6469-7_1.
short: Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, E. Benková, in:, Plant
Hormones, Humana Press, 2016, pp. 1–8.
date_created: 2018-12-11T11:50:44Z
date_published: 2016-11-19T00:00:00Z
date_updated: 2021-01-12T06:49:07Z
day: '19'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6469-7_1
intvolume: ' 1497'
language:
- iso: eng
month: '11'
oa_version: None
page: 1 - 8
publication: Plant Hormones
publication_status: published
publisher: Humana Press
publist_id: '6135'
quality_controlled: '1'
scopus_import: 1
status: public
title: Real time analysis of the apical hook development
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1497
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: '1214'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. While very successful with classical robots, these methods run into
severe difficulties when applied to soft robots, a new field of robotics with
large interest for human-robot interaction. We claim that a novel controller paradigm
opens new perspective for this field. This paper applies a recently developed
neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon
driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we
observe a vast variety of self-organized behavior patterns: when left alone, the
arm realizes pseudo-random sequences of different poses. By applying physical
forces, the system can be entrained into definite motion patterns like wiping
a table. Most interestingly, after attaching an object, the controller gets in
a functional resonance with the object''s internal dynamics, starting to shake
spontaneously bottles half-filled with water or sensitively driving an attached
pendulum into a circular mode. When attached to the crank of a wheel the neural
system independently develops to rotate it. In this way, the robot discovers affordances
of objects its body is interacting with.'
acknowledgement: RD thanks for the hospitality at the Max-Planck-Institute and for
helpful discussions with Nihat Ay and Keyan Zahedi.
article_number: '7759138'
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Raphael
full_name: Hostettler, Raphael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots:
Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November.
IEEE; 2016. doi:10.1109/IROS.2016.7759138'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant
control for soft robots: Emergent behavior of a tendon driven anthropomorphic
arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on
Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138'
chicago: 'Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant
Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic
Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138.'
ieee: 'G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for
soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented
at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS
, Daejeon, Korea, 2016, vol. 2016–November.'
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft
robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International
Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.'
mla: 'Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior
of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE,
2016, doi:10.1109/IROS.2016.7759138.'
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.
conference:
end_date: 2016-09-14
location: Daejeon, Korea
name: 'IEEE RSJ International Conference on Intelligent Robots and Systems IROS '
start_date: 2016-09-09
date_created: 2018-12-11T11:50:45Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2021-01-12T06:49:08Z
day: '28'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1109/IROS.2016.7759138
language:
- iso: eng
month: '11'
oa_version: None
publication_status: published
publisher: IEEE
publist_id: '6121'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic
arm'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016-November
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: '1217'
abstract:
- lang: eng
text: Understanding the regulation of T-cell responses during inflammation and auto-immunity
is fundamental for designing efficient therapeutic strategies against immune diseases.
In this regard, prostaglandin E 2 (PGE 2) is mostly considered a myeloid-derived
immunosuppressive molecule. We describe for the first time that T cells secrete
PGE 2 during T-cell receptor stimulation. In addition, we show that autocrine
PGE 2 signaling through EP receptors is essential for optimal CD4 + T-cell activation
in vitro and in vivo, and for T helper 1 (Th1) and regulatory T cell differentiation.
PGE 2 was found to provide additive co-stimulatory signaling through AKT activation.
Intravital multiphoton microscopy showed that triggering EP receptors in T cells
is also essential for the stability of T cell-dendritic cell (DC) interactions
and Th-cell accumulation in draining lymph nodes (LNs) during inflammation. We
further demonstrated that blocking EP receptors in T cells during the initial
phase of collagen-induced arthritis in mice resulted in a reduction of clinical
arthritis. This could be attributable to defective T-cell activation, accompanied
by a decline in activated and interferon-γ-producing CD4 + Th1 cells in draining
LNs. In conclusion, we prove that T lymphocytes secret picomolar concentrations
of PGE 2, which in turn provide additive co-stimulatory signaling, enabling T
cells to attain a favorable activation threshold. PGE 2 signaling in T cells is
also required for maintaining long and stable interactions with DCs within LNs.
Blockade of EP receptors in vivo impairs T-cell activation and development of
T cell-mediated inflammatory responses. This may have implications in various
pathophysiological settings.
acknowledgement: This manuscript has been supported by grants SAF2007-61716 and S-SAL-0159/2006
awarded by the Spanish Ministry of Science and Education and the Community of Madrid
to Dr M Fresno.
author:
- first_name: Vinatha
full_name: Sreeramkumar, Vinatha
last_name: Sreeramkumar
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Carmen
full_name: Punzón, Carmen
last_name: Punzón
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
- first_name: David
full_name: Sancho, David
last_name: Sancho
- first_name: Manuel
full_name: Fresno Forcelledo, Manuel
last_name: Fresno Forcelledo
- first_name: Natalia
full_name: Cuesta, Natalia
last_name: Cuesta
citation:
ama: Sreeramkumar V, Hons M, Punzón C, et al. Efficient T-cell priming and activation
requires signaling through prostaglandin E2 (EP) receptors. Immunology and
Cell Biology. 2016;94(1):39-51. doi:10.1038/icb.2015.62
apa: Sreeramkumar, V., Hons, M., Punzón, C., Stein, J., Sancho, D., Fresno Forcelledo,
M., & Cuesta, N. (2016). Efficient T-cell priming and activation requires
signaling through prostaglandin E2 (EP) receptors. Immunology and Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/icb.2015.62
chicago: Sreeramkumar, Vinatha, Miroslav Hons, Carmen Punzón, Jens Stein, David
Sancho, Manuel Fresno Forcelledo, and Natalia Cuesta. “Efficient T-Cell Priming
and Activation Requires Signaling through Prostaglandin E2 (EP) Receptors.” Immunology
and Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/icb.2015.62.
ieee: V. Sreeramkumar et al., “Efficient T-cell priming and activation requires
signaling through prostaglandin E2 (EP) receptors,” Immunology and Cell Biology,
vol. 94, no. 1. Nature Publishing Group, pp. 39–51, 2016.
ista: Sreeramkumar V, Hons M, Punzón C, Stein J, Sancho D, Fresno Forcelledo M,
Cuesta N. 2016. Efficient T-cell priming and activation requires signaling through
prostaglandin E2 (EP) receptors. Immunology and Cell Biology. 94(1), 39–51.
mla: Sreeramkumar, Vinatha, et al. “Efficient T-Cell Priming and Activation Requires
Signaling through Prostaglandin E2 (EP) Receptors.” Immunology and Cell Biology,
vol. 94, no. 1, Nature Publishing Group, 2016, pp. 39–51, doi:10.1038/icb.2015.62.
short: V. Sreeramkumar, M. Hons, C. Punzón, J. Stein, D. Sancho, M. Fresno Forcelledo,
N. Cuesta, Immunology and Cell Biology 94 (2016) 39–51.
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: MiSi
doi: 10.1038/icb.2015.62
intvolume: ' 94'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 39 - 51
publication: Immunology and Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6116'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient T-cell priming and activation requires signaling through prostaglandin
E2 (EP) receptors
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
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: '1224'
abstract:
- lang: eng
text: Sexual dimorphism in resource allocation is expected to change during the
life cycle of dioecious plants because of temporal differences between the sexes
in reproductive investment. Given the potential for sex-specific differences in
reproductive costs, resource availability may contribute to variation in reproductive
allocation in females and males. Here, we used Rumex hastatulus, a dioecious,
wind-pollinated annual plant, to investigate whether sexual dimorphism varies
with life-history stage and nutrient availability, and determine whether allocation
patterns differ depending on reproductive commitment. To examine if the costs
of reproduction varied between the sexes, reproduction was either allowed or prevented
through bud removal, and biomass allocation was measured at maturity. In a second
experiment to assess variation in sexual dimorphism across the life cycle, and
whether this varied with resource availability, plants were grown in high and
low nutrients and allocation to roots, aboveground vegetative growth and reproduction
were measured at three developmental stages. Males prevented from reproducing
compensated with increased above- and belowground allocation to a much larger
degree than females, suggesting that male reproductive costs reduce vegetative
growth. The proportional allocation to roots, reproductive structures and aboveground
vegetative growth varied between the sexes and among life-cycle stages, but not
with nutrient treatment. Females allocated proportionally more resources to roots
than males at peak flowering, but this pattern was reversed at reproductive maturity
under low-nutrient conditions. Our study illustrates the importance of temporal
dynamics in sex-specific resource allocation and provides support for high male
reproductive costs in wind-pollinated plants.
author:
- first_name: Zachary
full_name: Teitel, Zachary
last_name: Teitel
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation
and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant.
Plant Biology. 2016;18(1):98-103. doi:10.1111/plb.12336
apa: Teitel, Z., Pickup, M., Field, D., & Barrett, S. (2016). The dynamics of
resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated
dioecious plant. Plant Biology. Wiley-Blackwell. https://doi.org/10.1111/plb.12336
chicago: Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The
Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic,
Wind-Pollinated Dioecious Plant.” Plant Biology. Wiley-Blackwell, 2016.
https://doi.org/10.1111/plb.12336.
ieee: Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource
allocation and costs of reproduction in a sexually dimorphic, wind-pollinated
dioecious plant,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103,
2016.
ista: Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation
and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant.
Plant Biology. 18(1), 98–103.
mla: Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction
in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology,
vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.
short: Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.
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: NiBa
doi: 10.1111/plb.12336
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 98 - 103
publication: Plant Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6110'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dynamics of resource allocation and costs of reproduction in a sexually
dimorphic, wind-pollinated dioecious plant
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
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: '1232'
abstract:
- lang: eng
text: Mitochondrial electron transport chain complexes are organized into supercomplexes
responsible for carrying out cellular respiration. Here we present three architectures
of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We
identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome)
- a major 'tight' form and a minor 'loose' form (resolved at the resolution of
5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex
assembly or disassembly. We have also determined an architecture of supercomplex
CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known
80 subunits of the individual complexes, including 132 transmembrane helices.
The individual complexes form tight interactions that vary between the architectures,
with complex IV subunit COX7a switching contact from complex III to complex I.
The arrangement of active sites within the supercomplex may help control reactive
oxygen species production. To our knowledge, these are the first complete architectures
of the dominant, physiologically relevant state of the electron transport chain.
acknowledgement: We thank the MRC LMB Cambridge for the use of the Titan Krios microscope.
Data processing was performed using the IST high-performance computer cluster. J.A.L.
holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD
fellowship.
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes.
Nature. 2016;537(7622):644-648. doi:10.1038/nature19774
apa: Letts, J. A., Fiedorczuk, K., & Sazanov, L. A. (2016). The architecture
of respiratory supercomplexes. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19774
chicago: Letts, James A, Karol Fiedorczuk, and Leonid A Sazanov. “The Architecture
of Respiratory Supercomplexes.” Nature. Nature Publishing Group, 2016.
https://doi.org/10.1038/nature19774.
ieee: J. A. Letts, K. Fiedorczuk, and L. A. Sazanov, “The architecture of respiratory
supercomplexes,” Nature, vol. 537, no. 7622. Nature Publishing Group, pp.
644–648, 2016.
ista: Letts JA, Fiedorczuk K, Sazanov LA. 2016. The architecture of respiratory
supercomplexes. Nature. 537(7622), 644–648.
mla: Letts, James A., et al. “The Architecture of Respiratory Supercomplexes.” Nature,
vol. 537, no. 7622, Nature Publishing Group, 2016, pp. 644–48, doi:10.1038/nature19774.
short: J.A. Letts, K. Fiedorczuk, L.A. Sazanov, Nature 537 (2016) 644–648.
date_created: 2018-12-11T11:50:51Z
date_published: 2016-09-29T00:00:00Z
date_updated: 2021-01-12T06:49:16Z
day: '29'
department:
- _id: LeSa
doi: 10.1038/nature19774
intvolume: ' 537'
issue: '7622'
language:
- iso: eng
month: '09'
oa_version: None
page: 644 - 648
project:
- _id: 2593EBD6-B435-11E9-9278-68D0E5697425
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(FEBS)
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6102'
quality_controlled: '1'
scopus_import: 1
status: public
title: The architecture of respiratory supercomplexes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 537
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: '1237'
abstract:
- lang: eng
text: 'Bitmap images of arbitrary dimension may be formally perceived as unions
of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology
and homology groups are well known topological invariants of such sets. Cohomological
operations, such as the cup product, provide higher-order algebraic topological
invariants, especially important for digital images of dimension higher than 3.
If such an operation is determined at the level of simplicial chains [see e.g.
González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively
computable. However, decomposing a cubical complex into a simplicial one deleteriously
affects the efficiency of such an approach. In order to avoid this overhead, a
direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015,
253-275] for the cup product in cohomology, and implemented in the ChainCon software
package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for
the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series,
1947, 290-320] directly at the level of cubical chains, and we prove the correctness
of this formula. An implementation of this formula is programmed in C++ within
the ChainCon software framework. We provide a few examples and discuss the effectiveness
of this approach. One specific application follows from the fact that Steenrod
squares yield tests for the topological extension problem: Can a given map A →
Sd to a sphere Sd be extended to a given super-complex X of A? In particular,
the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value
r > 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the
extension problem.'
acknowledgement: The research conducted by both authors has received funding from
the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and
no. 622033 (for P. P.).
alternative_title:
- LNCS
author:
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: 'Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667.
Springer; 2016:140-151. doi:10.1007/978-3-319-39441-1_13'
apa: 'Krcál, M., & Pilarczyk, P. (2016). Computation of cubical Steenrod squares
(Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image
Context, Marseille, France: Springer. https://doi.org/10.1007/978-3-319-39441-1_13'
chicago: Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,”
9667:140–51. Springer, 2016. https://doi.org/10.1007/978-3-319-39441-1_13.
ieee: 'M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented
at the CTIC: Computational Topology in Image Context, Marseille, France, 2016,
vol. 9667, pp. 140–151.'
ista: 'Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC:
Computational Topology in Image Context, LNCS, vol. 9667, 140–151.'
mla: Krcál, Marek, and Pawel Pilarczyk. Computation of Cubical Steenrod Squares.
Vol. 9667, Springer, 2016, pp. 140–51, doi:10.1007/978-3-319-39441-1_13.
short: M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151.
conference:
end_date: 2016-06-17
location: Marseille, France
name: 'CTIC: Computational Topology in Image Context'
start_date: 2016-06-15
date_created: 2018-12-11T11:50:52Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2021-01-12T06:49:18Z
day: '02'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/978-3-319-39441-1_13
ec_funded: 1
intvolume: ' 9667'
language:
- iso: eng
month: '06'
oa_version: None
page: 140 - 151
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication_status: published
publisher: Springer
publist_id: '6096'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computation of cubical Steenrod squares
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9667
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: '1239'
abstract:
- lang: eng
text: Nonadherent polarized cells have been observed to have a pearlike, elongated
shape. Using a minimal model that describes the cell cortex as a thin layer of
contractile active gel, we show that the anisotropy of active stresses, controlled
by cortical viscosity and filament ordering, can account for this morphology.
The predicted shapes can be determined from the flow pattern only; they prove
to be independent of the mechanism at the origin of the cortical flow, and are
only weakly sensitive to the cytoplasmic rheology. In the case of actin flows
resulting from a contractile instability, we propose a phase diagram of three-dimensional
cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate
shapes, all of which have been observed in experiment.
acknowledgement: 'V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant
No. T560-B17).'
article_number: '028102'
author:
- first_name: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- 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: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical
flow-driven shapes of nonadherent cells. Physical Review Letters. 2016;116(2).
doi:10.1103/PhysRevLett.116.028102
apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez,
R. (2016). Cortical flow-driven shapes of nonadherent cells. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.116.028102
chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg,
and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical
Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.116.028102.
ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez,
“Cortical flow-driven shapes of nonadherent cells,” Physical Review Letters,
vol. 116, no. 2. American Physical Society, 2016.
ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016.
Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2),
028102.
mla: Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.”
Physical Review Letters, vol. 116, no. 2, 028102, American Physical Society,
2016, doi:10.1103/PhysRevLett.116.028102.
short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez,
Physical Review Letters 116 (2016).
date_created: 2018-12-11T11:50:53Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T06:49:19Z
day: '15'
department:
- _id: CaHe
doi: 10.1103/PhysRevLett.116.028102
intvolume: ' 116'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
project:
- _id: 2529486C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T 560-B17
name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6095'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cortical flow-driven shapes of nonadherent cells
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 116
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: '1245'
abstract:
- lang: eng
text: 'To facilitate collaboration in massive online classrooms, instructors must
make many decisions. For instance, the following parameters need to be decided
when designing a peer-feedback system where students review each others'' essays:
the number of students each student must provide feedback to, an algorithm to
map feedback providers to receivers, constraints that ensure students do not become
free-riders (receiving feedback but not providing it), the best times to receive
feedback to improve learning etc. While instructors can answer these questions
by running experiments or invoking past experience, game-theoretic models with
data from online learning platforms can identify better initial designs for further
improvements. As an example, we explore the design space of a peer feedback system
by modeling it using game theory. Our simulations show that incentivizing students
to provide feedback requires the value obtained from receiving a feedback to exceed
the cost of providing it by a large factor (greater than 7). Furthermore, hiding
feedback from low-effort students incentivizes them to provide more feedback.'
acknowledgement: 'ERC Start Grant Graph Games 279307 supported this research. '
author:
- first_name: Vineet
full_name: Pandey, Vineet
last_name: Pandey
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Pandey V, Chatterjee K. Game-theoretic models identify useful principles for
peer collaboration in online learning platforms. In: Proceedings of the ACM
Conference on Computer Supported Cooperative Work. Vol 26. ACM; 2016:365-368.
doi:10.1145/2818052.2869122'
apa: 'Pandey, V., & Chatterjee, K. (2016). Game-theoretic models identify useful
principles for peer collaboration in online learning platforms. In Proceedings
of the ACM Conference on Computer Supported Cooperative Work (Vol. 26, pp.
365–368). San Francisco, CA, USA: ACM. https://doi.org/10.1145/2818052.2869122'
chicago: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” In Proceedings
of the ACM Conference on Computer Supported Cooperative Work, 26:365–68. ACM,
2016. https://doi.org/10.1145/2818052.2869122.
ieee: V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles
for peer collaboration in online learning platforms,” in Proceedings of the
ACM Conference on Computer Supported Cooperative Work, San Francisco, CA,
USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.
ista: 'Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles
for peer collaboration in online learning platforms. Proceedings of the ACM Conference
on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work
and Social Computing vol. 26, 365–368.'
mla: Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify
Useful Principles for Peer Collaboration in Online Learning Platforms.” Proceedings
of the ACM Conference on Computer Supported Cooperative Work, vol. 26, no.
Februar-2016, ACM, 2016, pp. 365–68, doi:10.1145/2818052.2869122.
short: V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer
Supported Cooperative Work, ACM, 2016, pp. 365–368.
conference:
end_date: 2016-03-02
location: San Francisco, CA, USA
name: 'CSCW: Computer Supported Cooperative Work and Social Computing'
start_date: 2016-02-26
date_created: 2018-12-11T11:50:55Z
date_published: 2016-02-27T00:00:00Z
date_updated: 2021-01-12T06:49:22Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/2818052.2869122
ec_funded: 1
intvolume: ' 26'
issue: Februar-2016
language:
- iso: eng
month: '02'
oa_version: None
page: 365 - 368
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM Conference on Computer Supported Cooperative Work
publication_status: published
publisher: ACM
publist_id: '6083'
quality_controlled: '1'
scopus_import: 1
status: public
title: Game-theoretic models identify useful principles for peer collaboration in
online learning platforms
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
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: '1258'
abstract:
- lang: eng
text: When plants grow in close proximity basic resources such as light can become
limiting. Under such conditions plants respond to anticipate and/or adapt to the
light shortage, a process known as the shade avoidance syndrome (SAS). Following
genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC),
we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian
nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together
with other nucleoporins, participates positively in the control of the hypocotyl
elongation response to plant proximity, a role that can be considered dependent
on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent).
In addition, our results reveal a specific role for DRA2 in controlling shade-induced
gene expression. We suggest that this novel regulatory role of DRA2 is transport
independent and that it might rely on its dynamic localization within and outside
of the NPC. These results provide mechanistic insights in to how SAS responses
are rapidly established by light conditions. They also indicate that nucleoporins
have an active role in plant signaling.
acknowledgement: M.G. received an FPI fellowship from the Spanish Ministerio de Economía
y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish
Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió
D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received
a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V.
received initially an FPI fellowship from the Spanish MINECO and later a Beatriu
de Pinós contract from AGAUR. Our research is supported by grants from the Spanish
MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat
de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112,
PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish
MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533].
We thank the CRAG greenhouse service for plant care; Chus Burillo for technical
help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle
(UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG,
Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing
DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP,
Valencia, Spain) for comments on the manuscript.
author:
- first_name: Marcal
full_name: Gallemi Rovira, Marcal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi Rovira
- first_name: Anahit
full_name: Galstyan, Anahit
last_name: Galstyan
- first_name: Sandi
full_name: Paulišić, Sandi
last_name: Paulišić
- first_name: Christiane
full_name: Then, Christiane
last_name: Then
- first_name: Almudena
full_name: Ferrández Ayela, Almudena
last_name: Ferrández Ayela
- first_name: Laura
full_name: Lorenzo Orts, Laura
last_name: Lorenzo Orts
- first_name: Irma
full_name: Roig Villanova, Irma
last_name: Roig Villanova
- first_name: Xuewen
full_name: Wang, Xuewen
last_name: Wang
- first_name: José
full_name: Micol, José
last_name: Micol
- first_name: Maria
full_name: Ponce, Maria
last_name: Ponce
- first_name: Paul
full_name: Devlin, Paul
last_name: Devlin
- first_name: Jaime
full_name: Martínez García, Jaime
last_name: Martínez García
citation:
ama: Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin
with a role in regulating the shade avoidance syndrome in Arabidopsis. Development.
2016;143(9):1623-1631. doi:10.1242/dev.130211
apa: Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo
Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with
a role in regulating the shade avoidance syndrome in Arabidopsis. Development.
Company of Biologists. https://doi.org/10.1242/dev.130211
chicago: Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena
Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is
a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in
Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211.
ieee: M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in
regulating the shade avoidance syndrome in Arabidopsis,” Development, vol.
143, no. 9. Company of Biologists, pp. 1623–1631, 2016.
ista: Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts
L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016.
DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance
syndrome in Arabidopsis. Development. 143(9), 1623–1631.
mla: Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating
the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no.
9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211.
short: M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo
Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García,
Development 143 (2016) 1623–1631.
date_created: 2018-12-11T11:50:59Z
date_published: 2016-05-03T00:00:00Z
date_updated: 2021-01-12T06:49:27Z
day: '03'
department:
- _id: EvBe
doi: 10.1242/dev.130211
intvolume: ' 143'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 1623 - 1631
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6068'
quality_controlled: '1'
scopus_import: 1
status: public
title: DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance
syndrome in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
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: '1265'
abstract:
- lang: eng
text: Extracellular matrices (ECMs) are central to the advent of multicellular life,
and their mechanical propertiesare modulated by and impinge on intracellular signaling
pathways that regulate vital cellular functions. High spatial-resolution mapping
of mechanical properties in live cells is, however, extremely challenging. Thus,
our understanding of how signaling pathways process physiological signals to generate
appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin
scattering imaging (FBi), a method for the parallel and all-optical measurements
of mechanical properties and fluorescence at the submicrometer scale in living
organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and
cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We
further established that the measured "stiffness" of plant ECMs is symmetrically
patternedin hypocotyl cells undergoing directional growth. Finally, application
of this method to Arabidopsis thaliana with photoreceptor mutants revealed that
red and far-red light signals are essential modulators of ECM viscoelasticity.
By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor
the organism-wide applicability of FBi for measuring the mechanical outputs of
intracellular signaling pathways. As such, our work has implications for investigations
of mechanosignaling pathways and developmental biology.
article_number: rs5
author:
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Stephanie
full_name: Werner, Stephanie
last_name: Werner
- first_name: Marcal
full_name: Gallemi Rovira, Marcal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi Rovira
- first_name: Jixiang
full_name: Kong, Jixiang
last_name: Kong
- first_name: Edmundo
full_name: Guajardo, Edmundo
last_name: Guajardo
- first_name: Lijuan
full_name: Zhang, Lijuan
last_name: Zhang
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Thomas
full_name: Greb, Thomas
last_name: Greb
- first_name: Youssef
full_name: Belkhadir, Youssef
last_name: Belkhadir
citation:
ama: Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties
of live cells in tissues with fluorescence emission-Brillouin imaging. Science
Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326
apa: Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., …
Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells
in tissues with fluorescence emission-Brillouin imaging. Science Signaling.
American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326
chicago: Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo
Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping
the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence
Emission-Brillouin Imaging.” Science Signaling. American Association for
the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326.
ieee: K. Elsayad et al., “Mapping the subcellular mechanical properties of
live cells in tissues with fluorescence emission-Brillouin imaging,” Science
Signaling, vol. 9, no. 435. American Association for the Advancement of Science,
2016.
ista: Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb
T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells
in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435),
rs5.
mla: Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live
Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling,
vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016,
doi:10.1126/scisignal.aaf6326.
short: K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais,
T. Greb, Y. Belkhadir, Science Signaling 9 (2016).
date_created: 2018-12-11T11:51:02Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:49:29Z
day: '05'
department:
- _id: EvBe
doi: 10.1126/scisignal.aaf6326
intvolume: ' 9'
issue: '435'
language:
- iso: eng
month: '07'
oa_version: None
publication: Science Signaling
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6057'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping the subcellular mechanical properties of live cells in tissues with
fluorescence emission-Brillouin imaging
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
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: '1268'
acknowledgement: We would like to thank Mihai Netea for inviting us to contribute
to this Theme Issue.
author:
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: Milutinovic B, Kurtz J. Immune memory in invertebrates. Seminars in Immunology.
2016;28(4):328-342. doi:10.1016/j.smim.2016.05.004
apa: Milutinovic, B., & Kurtz, J. (2016). Immune memory in invertebrates. Seminars
in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2016.05.004
chicago: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.”
Seminars in Immunology. Academic Press, 2016. https://doi.org/10.1016/j.smim.2016.05.004.
ieee: B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” Seminars
in Immunology, vol. 28, no. 4. Academic Press, pp. 328–342, 2016.
ista: Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in
Immunology. 28(4), 328–342.
mla: Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.”
Seminars in Immunology, vol. 28, no. 4, Academic Press, 2016, pp. 328–42,
doi:10.1016/j.smim.2016.05.004.
short: B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342.
date_created: 2018-12-11T11:51:03Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:49:30Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.smim.2016.05.004
intvolume: ' 28'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 328 - 342
publication: Seminars in Immunology
publication_status: published
publisher: Academic Press
publist_id: '6053'
quality_controlled: '1'
scopus_import: 1
status: public
title: Immune memory in invertebrates
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 28
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: '1275'
article_number: '139802'
author:
- first_name: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- 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: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
citation:
ama: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones
et al. Reply. Physical Review Letters. 2016;117(13). doi:10.1103/PhysRevLett.117.139802
apa: Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez,
R. (2016). Callan-Jones et al. Reply. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.117.139802
chicago: Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg,
and Raphaël Voituriez. “Callan-Jones et Al. Reply.” Physical Review Letters.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.139802.
ieee: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez,
“Callan-Jones et al. Reply,” Physical Review Letters, vol. 117, no. 13.
American Physical Society, 2016.
ista: Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016.
Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802.
mla: Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” Physical Review
Letters, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.139802.
short: A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez,
Physical Review Letters 117 (2016).
date_created: 2018-12-11T11:51:05Z
date_published: 2016-09-22T00:00:00Z
date_updated: 2021-01-12T06:49:33Z
day: '22'
department:
- _id: CaHe
doi: 10.1103/PhysRevLett.117.139802
intvolume: ' 117'
issue: '13'
language:
- iso: eng
month: '09'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6041'
quality_controlled: '1'
scopus_import: 1
status: public
title: Callan-Jones et al. Reply
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...
---
_id: '1283'
abstract:
- lang: eng
text: The impact of the plant hormone ethylene on seedling development has long
been recognized; however, its ecophysiological relevance is unexplored. Three
recent studies demonstrate that ethylene is a critical endogenous integrator of
various environmental signals including mechanical stress, light, and oxygen availability
during seedling germination and growth through the soil.
acknowledgement: "This work was supported by the Austrian Science Fund (FWF01_I1774S)
to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the
Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of
Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript."
article_type: original
author:
- first_name: Qiang
full_name: Zhu, Qiang
id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87
last_name: Zhu
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. Trends
in Plant Science. 2016;21(10):809-811. doi:10.1016/j.tplants.2016.08.003
apa: Zhu, Q., & Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier.
Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2016.08.003
chicago: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.”
Trends in Plant Science. Cell Press, 2016. https://doi.org/10.1016/j.tplants.2016.08.003.
ieee: Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” Trends
in Plant Science, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.
ista: Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends
in Plant Science. 21(10), 809–811.
mla: Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.”
Trends in Plant Science, vol. 21, no. 10, Cell Press, 2016, pp. 809–11,
doi:10.1016/j.tplants.2016.08.003.
short: Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.
date_created: 2018-12-11T11:51:08Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:36Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.tplants.2016.08.003
file:
- access_level: local
checksum: 4d569977fad7a7f22b7e3424003d2ab1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:19Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4679'
file_name: IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf
file_size: 229094
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 21'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: Submitted Version
page: 809 - 811
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '6033'
pubrep_id: '1018'
quality_controlled: '1'
scopus_import: 1
status: public
title: Seedlings’ strategy to overcome a soil barrier
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
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: '1285'
abstract:
- lang: eng
text: Cell migration is central to a multitude of physiological processes, including
embryonic development, immune surveillance, and wound healing, and deregulated
migration is key to cancer dissemination. Decades of investigations have uncovered
many of the molecular and physical mechanisms underlying cell migration. Together
with protrusion extension and cell body retraction, adhesion to the substrate
via specific focal adhesion points has long been considered an essential step
in cell migration. Although this is true for cells moving on two-dimensional substrates,
recent studies have demonstrated that focal adhesions are not required for cells
moving in three dimensions, in which confinement is sufficient to maintain a cell
in contact with its substrate. Here, we review the investigations that have led
to challenging the requirement of specific adhesions for migration, discuss the
physical mechanisms proposed for cell body translocation during focal adhesion-independent
migration, and highlight the remaining open questions for the future.
acknowledgement: We would like to thank Dani Bodor for critical comments on the manuscript
and Guillaume Salbreux for discussions. The authors are supported by the United
Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the
MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC
GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian
Science Foundation (M.S.).
author:
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Irene
full_name: Aspalter, Irene
last_name: Aspalter
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. Annual
Review of Cell and Developmental Biology. 2016;32:469-490. doi:10.1146/annurev-cellbio-111315-125341
apa: Paluch, E., Aspalter, I., & Sixt, M. K. (2016). Focal adhesion-independent
cell migration. Annual Review of Cell and Developmental Biology. Annual
Reviews. https://doi.org/10.1146/annurev-cellbio-111315-125341
chicago: Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent
Cell Migration.” Annual Review of Cell and Developmental Biology. Annual
Reviews, 2016. https://doi.org/10.1146/annurev-cellbio-111315-125341.
ieee: E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,”
Annual Review of Cell and Developmental Biology, vol. 32. Annual Reviews,
pp. 469–490, 2016.
ista: Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration.
Annual Review of Cell and Developmental Biology. 32, 469–490.
mla: Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” Annual
Review of Cell and Developmental Biology, vol. 32, Annual Reviews, 2016, pp.
469–90, doi:10.1146/annurev-cellbio-111315-125341.
short: E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental
Biology 32 (2016) 469–490.
date_created: 2018-12-11T11:51:08Z
date_published: 2016-10-06T00:00:00Z
date_updated: 2021-01-12T06:49:37Z
day: '06'
department:
- _id: MiSi
doi: 10.1146/annurev-cellbio-111315-125341
ec_funded: 1
intvolume: ' 32'
language:
- iso: eng
month: '10'
oa_version: None
page: 469 - 490
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: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '6031'
quality_controlled: '1'
scopus_import: 1
status: public
title: Focal adhesion-independent cell migration
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2016'
...
---
_id: '1288'
abstract:
- lang: eng
text: Respiratory complex I transfers electrons from NADH to quinone, utilizing
the reaction energy to translocate protons across the membrane. It is a key enzyme
of the respiratory chain of many prokaryotic and most eukaryotic organisms. The
reversible NADH oxidation reaction is facilitated in complex I by non-covalently
bound flavin mononucleotide (FMN). Here we report that the catalytic activity
of E. coli complex I with artificial electron acceptors potassium ferricyanide
(FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced
by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation
of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar
range in oxidized complex I to the nanomolar range in the NADH reduced enzyme,
with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex
I, rather than that of FMN, proved critical to the dissociation. Such dissociation
is not observed with the T. thermophilus enzyme and our analysis suggests that
the difference may be due to the unusually high redox potential of Fe-S cluster
N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo
by releasing FMN under highly reducing conditions.
acknowledgement: This work was funded by the UK Medical Research Council.
author:
- first_name: Peter
full_name: Holt, Peter
last_name: Holt
- first_name: Rouslan
full_name: Efremov, Rouslan
last_name: Efremov
- first_name: Eiko
full_name: Nakamaru Ogiso, Eiko
last_name: Nakamaru Ogiso
- 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: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation
from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta
- Bioenergetics. 2016;1857(11):1777-1785. doi:10.1016/j.bbabio.2016.08.008
apa: Holt, P., Efremov, R., Nakamaru Ogiso, E., & Sazanov, L. A. (2016). Reversible
FMN dissociation from Escherichia coli respiratory complex I. Biochimica et
Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.08.008
chicago: Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov.
“Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica
et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.08.008.
ieee: P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN
dissociation from Escherichia coli respiratory complex I,” Biochimica et Biophysica
Acta - Bioenergetics, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016.
ista: Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation
from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics.
1857(11), 1777–1785.
mla: Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory
Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no.
11, Elsevier, 2016, pp. 1777–85, doi:10.1016/j.bbabio.2016.08.008.
short: P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica
Acta - Bioenergetics 1857 (2016) 1777–1785.
date_created: 2018-12-11T11:51:09Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T06:49:38Z
day: '01'
department:
- _id: LeSa
doi: 10.1016/j.bbabio.2016.08.008
intvolume: ' 1857'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1777 - 1785
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '6028'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reversible FMN dissociation from Escherichia coli respiratory complex I
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1857
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: '1295'
abstract:
- lang: eng
text: Voronoi diagrams and Delaunay triangulations have been extensively used to
represent and compute geometric features of point configurations. We introduce
a generalization to poset diagrams and poset complexes, which contain order-k
and degree-k Voronoi diagrams and their duals as special cases. Extending a result
of Aurenhammer from 1990, we show how to construct poset diagrams as weighted
Voronoi diagrams of average balls.
acknowledgement: This work is partially supported by the Toposys project FP7-ICT-318493-STREP,
and by ESF under the ACAT Research Network Programme.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages.
Electronic Notes in Discrete Mathematics. 2016;54:169-174. doi:10.1016/j.endm.2016.09.030'
apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2016). Multiple covers with balls
II: Weighted averages. Electronic Notes in Discrete Mathematics. Elsevier.
https://doi.org/10.1016/j.endm.2016.09.030'
chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
II: Weighted Averages.” Electronic Notes in Discrete Mathematics. Elsevier,
2016. https://doi.org/10.1016/j.endm.2016.09.030.'
ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted
averages,” Electronic Notes in Discrete Mathematics, vol. 54. Elsevier,
pp. 169–174, 2016.'
ista: 'Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted
averages. Electronic Notes in Discrete Mathematics. 54, 169–174.'
mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
II: Weighted Averages.” Electronic Notes in Discrete Mathematics, vol.
54, Elsevier, 2016, pp. 169–74, doi:10.1016/j.endm.2016.09.030.'
short: H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics
54 (2016) 169–174.
date_created: 2018-12-11T11:51:12Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:41Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.endm.2016.09.030
ec_funded: 1
intvolume: ' 54'
language:
- iso: eng
month: '10'
oa_version: None
page: 169 - 174
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Electronic Notes in Discrete Mathematics
publication_status: published
publisher: Elsevier
publist_id: '5976'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Multiple covers with balls II: Weighted averages'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
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: '1319'
abstract:
- lang: eng
text: We present a novel optimization-based algorithm for the design and fabrication
of customized, deformable input devices, capable of continuously sensing their
deformation. We propose to embed piezoresistive sensing elements into flexible
3D printed objects. These sensing elements are then utilized to recover rich and
natural user interactions at runtime. Designing such objects is a challenging
and hard problem if attempted manually for all but the simplest geometries and
deformations. Our method simultaneously optimizes the internal routing of the
sensing elements and computes a mapping from low-level sensor readings to user-specified
outputs in order to minimize reconstruction error. We demonstrate the power and
flexibility of the approach by designing and fabricating a set of flexible input
devices. Our results indicate that the optimization-based design greatly outperforms
manual routings in terms of reconstruction accuracy and thus interaction fidelity.
acknowledgement: "We thank Damian Karrer, Rocco Ghielmini and Jemin\r\nHwangbo
for their help in our initial explorations. We would\r\nlike to thank Christian
Schumacher for creating the video and\r\nC\r\n ́\r\necile Edwards-Rietmann for providing
the voiceover. Mau-\r\nrizio Nitti helped us in designing our 3D characters. We
thank\r\nChiara Daraio for insightful discussions on material proper-\r\nties and
3D printing. We also thank the CHI reviewers for\r\ntheir feedback and guidance.
Fabrizio Pece was supported by\r\nan ETH/Marie Curie fellowship (FEL-3314-1)."
author:
- first_name: Moritz
full_name: Bächer, Moritz
last_name: Bächer
- first_name: Benjamin
full_name: Hepp, Benjamin
last_name: Hepp
- first_name: Fabrizio
full_name: Pece, Fabrizio
last_name: Pece
- first_name: Paul
full_name: Kry, Paul
last_name: Kry
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: Otmar
full_name: Hilliges, Otmar
last_name: Hilliges
citation:
ama: 'Bächer M, Hepp B, Pece F, et al. DefSense: computational design of customized
deformable input devices. In: ACM; 2016:3806-3816. doi:10.1145/2858036.2858354'
apa: 'Bächer, M., Hepp, B., Pece, F., Kry, P., Bickel, B., Thomaszewski, B., &
Hilliges, O. (2016). DefSense: computational design of customized deformable input
devices (pp. 3806–3816). Presented at the CHI: Conference on Human Factors in
Computing Systems, San Jose, California, USA: ACM. https://doi.org/10.1145/2858036.2858354'
chicago: 'Bächer, Moritz, Benjamin Hepp, Fabrizio Pece, Paul Kry, Bernd Bickel,
Bernhard Thomaszewski, and Otmar Hilliges. “DefSense: Computational Design of
Customized Deformable Input Devices,” 3806–16. ACM, 2016. https://doi.org/10.1145/2858036.2858354.'
ieee: 'M. Bächer et al., “DefSense: computational design of customized deformable
input devices,” presented at the CHI: Conference on Human Factors in Computing
Systems, San Jose, California, USA, 2016, pp. 3806–3816.'
ista: 'Bächer M, Hepp B, Pece F, Kry P, Bickel B, Thomaszewski B, Hilliges O. 2016.
DefSense: computational design of customized deformable input devices. CHI: Conference
on Human Factors in Computing Systems, 3806–3816.'
mla: 'Bächer, Moritz, et al. DefSense: Computational Design of Customized Deformable
Input Devices. ACM, 2016, pp. 3806–16, doi:10.1145/2858036.2858354.'
short: M. Bächer, B. Hepp, F. Pece, P. Kry, B. Bickel, B. Thomaszewski, O. Hilliges,
in:, ACM, 2016, pp. 3806–3816.
conference:
end_date: 2016-05-12
location: San Jose, California, USA
name: 'CHI: Conference on Human Factors in Computing Systems'
start_date: 2016-05-07
date_created: 2018-12-11T11:51:21Z
date_published: 2016-05-07T00:00:00Z
date_updated: 2021-01-12T06:49:51Z
day: '07'
department:
- _id: BeBi
doi: 10.1145/2858036.2858354
language:
- iso: eng
month: '05'
oa_version: None
page: 3806 - 3816
publication_status: published
publisher: ACM
publist_id: '5951'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DefSense: computational design of customized deformable input devices'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
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: '1320'
abstract:
- lang: eng
text: 'In recent years, several biomolecular systems have been shown to be scale-invariant
(SI), i.e. to show the same output dynamics when exposed to geometrically scaled
input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant
inputs. In this article, we show that SI systems-as well as systems invariant
with respect to other input transformations-can realize nonlinear differential
operators: when excited by inputs obeying functional forms characteristic for
a given class of invariant systems, the systems'' outputs converge to constant
values directly quantifying the speed of the input.'
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]. Work supported
in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473.
article_number: '7526722'
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Eduardo
full_name: Sontag, Eduardo
last_name: Sontag
citation:
ama: 'Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators.
In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722'
apa: 'Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear
differential operators (Vol. 2016–July). Presented at the ACC: American Control
Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722'
chicago: Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear
Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.
ieee: 'M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential
operators,” presented at the ACC: American Control Conference, Boston, MA, USA,
2016, vol. 2016–July.'
ista: 'Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential
operators. ACC: American Control Conference vol. 2016–July, 7526722.'
mla: Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear
Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722.
short: M. Lang, E. Sontag, in:, IEEE, 2016.
conference:
end_date: 2016-07-08
location: Boston, MA, USA
name: 'ACC: American Control Conference'
start_date: 2016-07-06
date_created: 2018-12-11T11:51:21Z
date_published: 2016-07-28T00:00:00Z
date_updated: 2021-01-12T06:49:51Z
day: '28'
ddc:
- '003'
- '621'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1109/ACC.2016.7526722
ec_funded: 1
file:
- access_level: local
checksum: 7219432b43defc62a0d45f48d4ce6a19
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:17Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5203'
file_name: IST-2017-810-v1+1_root.pdf
file_size: 539166
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: IEEE
publist_id: '5950'
pubrep_id: '810'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scale-invariant systems realize nonlinear differential operators
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016-July
year: '2016'
...
---
_id: '1324'
abstract:
- lang: eng
text: 'DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate
in an uncertain environment independently to achieve a joint objective. DEC-POMDPs
have been studied with finite-horizon and infinite-horizon discounted-sum objectives,
and there exist solvers both for exact and approximate solutions. In this work
we consider Goal-DEC-POMDPs, where given a set of target states, the objective
is to ensure that the target set is reached with minimal cost. We consider the
indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum,
where absorbing goal states have zero-cost) problem. We present a new and novel
method to solve the problem that extends methods for finite-horizon DEC-POMDPs
and the RTDP-Bel approach for POMDPs. We present experimental results on several
examples, and show that our approach presents promising results. Copyright '
author:
- 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
citation:
ama: 'Chatterjee K, Chmelik M. Indefinite-horizon reachability in Goal-DEC-POMDPs.
In: Proceedings of the Twenty-Sixth International Conference on International
Conference on Automated Planning and Scheduling. Vol 2016-January. AAAI Press;
2016:88-96.'
apa: 'Chatterjee, K., & Chmelik, M. (2016). Indefinite-horizon reachability
in Goal-DEC-POMDPs. In Proceedings of the Twenty-Sixth International Conference
on International Conference on Automated Planning and Scheduling (Vol. 2016–January,
pp. 88–96). London, United Kingdom: AAAI Press.'
chicago: Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability
in Goal-DEC-POMDPs.” In Proceedings of the Twenty-Sixth International Conference
on International Conference on Automated Planning and Scheduling, 2016–January:88–96.
AAAI Press, 2016.
ieee: K. Chatterjee and M. Chmelik, “Indefinite-horizon reachability in Goal-DEC-POMDPs,”
in Proceedings of the Twenty-Sixth International Conference on International
Conference on Automated Planning and Scheduling, London, United Kingdom, 2016,
vol. 2016–January, pp. 88–96.
ista: 'Chatterjee K, Chmelik M. 2016. Indefinite-horizon reachability in Goal-DEC-POMDPs.
Proceedings of the Twenty-Sixth International Conference on International Conference
on Automated Planning and Scheduling. ICAPS: International Conference on Automated
Planning and Scheduling vol. 2016–January, 88–96.'
mla: Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability
in Goal-DEC-POMDPs.” Proceedings of the Twenty-Sixth International Conference
on International Conference on Automated Planning and Scheduling, vol. 2016–January,
AAAI Press, 2016, pp. 88–96.
short: K. Chatterjee, M. Chmelik, in:, Proceedings of the Twenty-Sixth International
Conference on International Conference on Automated Planning and Scheduling, AAAI
Press, 2016, pp. 88–96.
conference:
end_date: 2016-06-17
location: London, United Kingdom
name: 'ICAPS: International Conference on Automated Planning and Scheduling'
start_date: 2016-06-12
date_created: 2018-12-11T11:51:22Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:53Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
language:
- iso: eng
main_file_link:
- url: http://www.aaai.org/ocs/index.php/ICAPS/ICAPS16/paper/view/12999
month: '01'
oa_version: None
page: 88 - 96
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the Twenty-Sixth International Conference on International
Conference on Automated Planning and Scheduling
publication_status: published
publisher: AAAI Press
publist_id: '5946'
quality_controlled: '1'
scopus_import: 1
status: public
title: Indefinite-horizon reachability in Goal-DEC-POMDPs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016-January
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
license: https://creativecommons.org/licenses/by-nc/4.0/
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:
- access_level: open_access
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
file_size: 127781
relation: main_file
- access_level: open_access
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'
...