---
_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: '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: '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: '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
license: https://creativecommons.org/licenses/by/4.0/
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: '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: '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: '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: '8241'
abstract:
- lang: eng
text: 'Background: Anticancer vaccines could represent a valuable complementary
strategy to established therapies, especially in settings of early stage and minimal
residual disease. HER-2 is an important target for immunotherapy and addressed
by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope
peptides from phage display libraries. The synthesized peptides were coupled to
carriers and applied for epitope-specific induction of trastuzumab-like IgG. For
simplification and to avoid methodological limitations of synthesis and coupling
chemistry, we herewith present a novel and optimized approach by using adeno-associated
viruses (AAV) as effective and high-density mimotope-display system, which can
be directly used for vaccination. Methods: An AAV capsid display library was constructed
by genetically incorporating random peptides in a plasmid encoding the wild-type
AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to
trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human
HER-2 were determined, and the isotype composition and functional properties of
these were tested. Finally, prophylactically immunized mice were challenged with
human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines
induced antibodies specific to human HER-2. Two clones were selected for immunization
of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones
delayed the growth of tumors significantly, as compared to controls. Conclusion:
In this study, a novel mimotope AAV-based platform was created allowing the isolation
of mimotopes, which can be directly used as anticancer vaccines. The example of
trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to
establish active immunotherapy for breast-cancer patients.'
article_number: e1171446
article_processing_charge: No
article_type: original
author:
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Kathrin
full_name: Thell, Kathrin
last_name: Thell
- first_name: Anna
full_name: Bentley-Lukschal, Anna
last_name: Bentley-Lukschal
- first_name: Caroline
full_name: Stremnitzer, Caroline
last_name: Stremnitzer
- first_name: Franziska
full_name: Roth-Walter, Franziska
last_name: Roth-Walter
- first_name: Margit
full_name: Weghofer, Margit
last_name: Weghofer
- first_name: Mirko
full_name: Ritter, Mirko
last_name: Ritter
- first_name: Kerstin
full_name: Pino Tossi, Kerstin
last_name: Pino Tossi
- first_name: Markus
full_name: Hörer, Markus
last_name: Hörer
- first_name: Uwe
full_name: Michaelis, Uwe
last_name: Michaelis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Singer J, Manzano-Szalai K, Singer J, et al. Proof of concept study with an
HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform.
OncoImmunology. 2016;5(7). doi:10.1080/2162402x.2016.1171446
apa: Singer, J., Manzano-Szalai, K., Singer, J., Thell, K., Bentley-Lukschal, A.,
Stremnitzer, C., … Jensen-Jarolim, E. (2016). Proof of concept study with an HER-2
mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform.
OncoImmunology. Taylor & Francis. https://doi.org/10.1080/2162402x.2016.1171446
chicago: Singer, Josef, Krisztina Manzano-Szalai, Judit Singer, Kathrin Thell, Anna
Bentley-Lukschal, Caroline Stremnitzer, Franziska Roth-Walter, et al. “Proof of
Concept Study with an HER-2 Mimotope Anticancer Vaccine Deduced from a Novel AAV-Mimotope
Library Platform.” OncoImmunology. Taylor & Francis, 2016. https://doi.org/10.1080/2162402x.2016.1171446.
ieee: J. Singer et al., “Proof of concept study with an HER-2 mimotope anticancer
vaccine deduced from a novel AAV-mimotope library platform,” OncoImmunology,
vol. 5, no. 7. Taylor & Francis, 2016.
ista: Singer J, Manzano-Szalai K, Singer J, Thell K, Bentley-Lukschal A, Stremnitzer
C, Roth-Walter F, Weghofer M, Ritter M, Pino Tossi K, Hörer M, Michaelis U, Jensen-Jarolim
E. 2016. Proof of concept study with an HER-2 mimotope anticancer vaccine deduced
from a novel AAV-mimotope library platform. OncoImmunology. 5(7), e1171446.
mla: Singer, Josef, et al. “Proof of Concept Study with an HER-2 Mimotope Anticancer
Vaccine Deduced from a Novel AAV-Mimotope Library Platform.” OncoImmunology,
vol. 5, no. 7, e1171446, Taylor & Francis, 2016, doi:10.1080/2162402x.2016.1171446.
short: J. Singer, K. Manzano-Szalai, J. Singer, K. Thell, A. Bentley-Lukschal, C.
Stremnitzer, F. Roth-Walter, M. Weghofer, M. Ritter, K. Pino Tossi, M. Hörer,
U. Michaelis, E. Jensen-Jarolim, OncoImmunology 5 (2016).
date_created: 2020-08-10T11:54:03Z
date_published: 2016-06-30T00:00:00Z
date_updated: 2021-01-12T08:17:41Z
day: '30'
doi: 10.1080/2162402x.2016.1171446
extern: '1'
intvolume: ' 5'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/2162402X.2016.1171446
month: '06'
oa: 1
oa_version: Published Version
publication: OncoImmunology
publication_identifier:
issn:
- 2162-402X
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
status: public
title: Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from
a novel AAV-mimotope library platform
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '8302'
abstract:
- lang: eng
text: While showing great promise, Bitcoin requires users to wait tens of minutes
for transactions to commit, and even then, offering only probabilistic guarantees.
This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages
scalable collective signing to commit Bitcoin transactions irreversibly within
seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open
membership by dynamically forming hash power-proportionate consensus groups that
represent recently-successful block miners. ByzCoin employs communication trees
to optimize transaction commitment and verification under normal operation while
guaranteeing safety and liveness under Byzantine faults, up to a near-optimal
tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double
spending and selfish mining attacks by producing collectively signed transaction
blocks within one minute of transaction submission. Tree-structured communication
further reduces this latency to less than 30 seconds. Due to these optimizations,
ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation
latency of 15-20 seconds.
article_processing_charge: No
arxiv: 1
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ismail
full_name: Khoffi, Ismail
last_name: Khoffi
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. Enhancing
bitcoin security and performance with strong consistency via collective signing.
In: Proceedings of the 25th USENIX Conference on Security Symposium. USENIX
Association; 2016:279–296.'
apa: 'Kokoris Kogias, E., Jovanovic, P., Gailly, N., Khoffi, I., Gasser, L., &
Ford, B. (2016). Enhancing bitcoin security and performance with strong consistency
via collective signing. In Proceedings of the 25th USENIX Conference on Security
Symposium (pp. 279–296). Austin, TX, United States: USENIX Association.'
chicago: Kokoris Kogias, Eleftherios, Philipp Jovanovic, Nicolas Gailly, Ismail
Khoffi, Linus Gasser, and Bryan Ford. “Enhancing Bitcoin Security and Performance
with Strong Consistency via Collective Signing.” In Proceedings of the 25th
USENIX Conference on Security Symposium, 279–296. USENIX Association, 2016.
ieee: E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, and B. Ford,
“Enhancing bitcoin security and performance with strong consistency via collective
signing,” in Proceedings of the 25th USENIX Conference on Security Symposium,
Austin, TX, United States, 2016, pp. 279–296.
ista: 'Kokoris Kogias E, Jovanovic P, Gailly N, Khoffi I, Gasser L, Ford B. 2016.
Enhancing bitcoin security and performance with strong consistency via collective
signing. Proceedings of the 25th USENIX Conference on Security Symposium. SEC:
Security Symposium, 279–296.'
mla: Kokoris Kogias, Eleftherios, et al. “Enhancing Bitcoin Security and Performance
with Strong Consistency via Collective Signing.” Proceedings of the 25th USENIX
Conference on Security Symposium, USENIX Association, 2016, pp. 279–296.
short: E. Kokoris Kogias, P. Jovanovic, N. Gailly, I. Khoffi, L. Gasser, B. Ford,
in:, Proceedings of the 25th USENIX Conference on Security Symposium, USENIX Association,
2016, pp. 279–296.
conference:
end_date: 2016-08-12
location: Austin, TX, United States
name: 'SEC: Security Symposium'
start_date: 2016-08-10
date_created: 2020-08-26T12:08:35Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:18:00Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1602.06997'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.06997
month: '09'
oa: 1
oa_version: Published Version
page: 279–296
publication: Proceedings of the 25th USENIX Conference on Security Symposium
publication_identifier:
isbn:
- '9781931971324'
publication_status: published
publisher: USENIX Association
quality_controlled: '1'
status: public
title: Enhancing bitcoin security and performance with strong consistency via collective
signing
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '9019'
abstract:
- lang: eng
text: Targeting protein–protein interactions has long been considered as a very
difficult if impossible task, but over the past decade, front lines have moved.
The number of successful examples is exponentially growing. This review presents
a rapid overview of recent advances in this field considering the strengths and
weaknesses of the small molecule approaches and alternative strategies such as
the selection or design of artificial antibodies, peptides or peptidomimetics.
- lang: fre
text: Cibler les interactions protéine–protéine a longtemps été considéré comme
une tâche très difficile, voire impossible, mais, depuis les dix dernières années,
les lignes ont bougé. Le nombre d’exemples de réussites s’accroît exponentiellement.
Cette revue présente un rapide panorama des avancées récentes dans ce domaine,
considérant les forces et les faiblesses de l’approche « petite molécule » ainsi
que des stratégies alternatives comme la sélection ou le design d’anticorps artificiels,
de peptides ou de peptidomimétiques.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Francoise
full_name: Ochsenbein, Francoise
last_name: Ochsenbein
citation:
ama: Bakail MM, Ochsenbein F. Targeting protein–protein interactions, a wide open
field for drug design. Comptes Rendus Chimie. 2016;19(1-2):19-27. doi:10.1016/j.crci.2015.12.004
apa: Bakail, M. M., & Ochsenbein, F. (2016). Targeting protein–protein interactions,
a wide open field for drug design. Comptes Rendus Chimie. Elsevier. https://doi.org/10.1016/j.crci.2015.12.004
chicago: Bakail, May M, and Francoise Ochsenbein. “Targeting Protein–Protein Interactions,
a Wide Open Field for Drug Design.” Comptes Rendus Chimie. Elsevier, 2016.
https://doi.org/10.1016/j.crci.2015.12.004.
ieee: M. M. Bakail and F. Ochsenbein, “Targeting protein–protein interactions, a
wide open field for drug design,” Comptes Rendus Chimie, vol. 19, no. 1–2.
Elsevier, pp. 19–27, 2016.
ista: Bakail MM, Ochsenbein F. 2016. Targeting protein–protein interactions, a wide
open field for drug design. Comptes Rendus Chimie. 19(1–2), 19–27.
mla: Bakail, May M., and Francoise Ochsenbein. “Targeting Protein–Protein Interactions,
a Wide Open Field for Drug Design.” Comptes Rendus Chimie, vol. 19, no.
1–2, Elsevier, 2016, pp. 19–27, doi:10.1016/j.crci.2015.12.004.
short: M.M. Bakail, F. Ochsenbein, Comptes Rendus Chimie 19 (2016) 19–27.
date_created: 2021-01-19T11:11:54Z
date_published: 2016-02-06T00:00:00Z
date_updated: 2023-02-23T13:46:55Z
day: '06'
ddc:
- '570'
doi: 10.1016/j.crci.2015.12.004
extern: '1'
file:
- access_level: open_access
checksum: c262814ffdbfe95900256ab9ff42cdf5
content_type: application/pdf
creator: dernst
date_created: 2021-01-22T12:36:52Z
date_updated: 2021-01-22T12:36:52Z
file_id: '9035'
file_name: 2016_ComptesRendueChimie_Bakail.pdf
file_size: 2045260
relation: main_file
success: 1
file_date_updated: 2021-01-22T12:36:52Z
has_accepted_license: '1'
intvolume: ' 19'
issue: 1-2
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 19-27
publication: Comptes Rendus Chimie
publication_identifier:
issn:
- 1631-0748
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Targeting protein–protein interactions, a wide open field for drug design
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: 19
year: '2016'
...
---
_id: '9051'
abstract:
- lang: eng
text: 'Biological systems often involve the self-assembly of basic components into
complex and functioning structures. Artificial systems that mimic such processes
can provide a well-controlled setting to explore the principles involved and also
synthesize useful micromachines. Our experiments show that immotile, but active,
components self-assemble into two types of structure that exhibit the fundamental
forms of motility: translation and rotation. Specifically, micron-scale metallic
rods are designed to induce extensile surface flows in the presence of a chemical
fuel; these rods interact with each other and pair up to form either a swimmer
or a rotor. Such pairs can transition reversibly between these two configurations,
leading to kinetics reminiscent of bacterial run-and-tumble motion.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Megan S.
full_name: Davies Wykes, Megan S.
last_name: Davies Wykes
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Takuji
full_name: Adachi, Takuji
last_name: Adachi
- first_name: Leif
full_name: Ristroph, Leif
last_name: Ristroph
- first_name: Xiao
full_name: Zhong, Xiao
last_name: Zhong
- first_name: Michael D.
full_name: Ward, Michael D.
last_name: Ward
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
citation:
ama: Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale
rotors and swimmers. Soft Matter. 2016;12(20):4584-4589. doi:10.1039/c5sm03127c
apa: Davies Wykes, M. S., Palacci, J. A., Adachi, T., Ristroph, L., Zhong, X., Ward,
M. D., … Shelley, M. J. (2016). Dynamic self-assembly of microscale rotors and
swimmers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c5sm03127c
chicago: Davies Wykes, Megan S., Jérémie A Palacci, Takuji Adachi, Leif Ristroph,
Xiao Zhong, Michael D. Ward, Jun Zhang, and Michael J. Shelley. “Dynamic Self-Assembly
of Microscale Rotors and Swimmers.” Soft Matter. Royal Society of Chemistry,
2016. https://doi.org/10.1039/c5sm03127c.
ieee: M. S. Davies Wykes et al., “Dynamic self-assembly of microscale rotors
and swimmers,” Soft Matter, vol. 12, no. 20. Royal Society of Chemistry,
pp. 4584–4589, 2016.
ista: Davies Wykes MS, Palacci JA, Adachi T, Ristroph L, Zhong X, Ward MD, Zhang
J, Shelley MJ. 2016. Dynamic self-assembly of microscale rotors and swimmers.
Soft Matter. 12(20), 4584–4589.
mla: Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors
and Swimmers.” Soft Matter, vol. 12, no. 20, Royal Society of Chemistry,
2016, pp. 4584–89, doi:10.1039/c5sm03127c.
short: M.S. Davies Wykes, J.A. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward,
J. Zhang, M.J. Shelley, Soft Matter 12 (2016) 4584–4589.
date_created: 2021-02-01T13:44:00Z
date_published: 2016-05-28T00:00:00Z
date_updated: 2023-02-23T13:47:38Z
day: '28'
doi: 10.1039/c5sm03127c
extern: '1'
external_id:
arxiv:
- '1509.06330'
pmid:
- '27121100'
intvolume: ' 12'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.06330
month: '05'
oa: 1
oa_version: Preprint
page: 4584-4589
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic self-assembly of microscale rotors and swimmers
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12
year: '2016'
...
---
_id: '9052'
abstract:
- lang: eng
text: We describe colloidal Janus particles with metallic and dielectric faces that
swim vigorously when illuminated by defocused optical tweezers without consuming
any chemical fuel. Rather than wandering randomly, these optically-activated colloidal
swimmers circulate back and forth through the beam of light, tracing out sinuous
rosette patterns. We propose a model for this mode of light-activated transport
that accounts for the observed behavior through a combination of self-thermophoresis
and optically-induced torque. In the deterministic limit, this model yields trajectories
that resemble rosette curves known as hypotrochoids.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Henrique
full_name: Moyses, Henrique
last_name: Moyses
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: David G.
full_name: Grier, David G.
last_name: Grier
citation:
ama: Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled
Janus particles in a diverging laser beam. Soft Matter. 2016;12(30):6357-6364.
doi:10.1039/c6sm01163b
apa: Moyses, H., Palacci, J. A., Sacanna, S., & Grier, D. G. (2016). Trochoidal
trajectories of self-propelled Janus particles in a diverging laser beam. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c6sm01163b
chicago: Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier.
“Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser
Beam.” Soft Matter. Royal Society of Chemistry , 2016. https://doi.org/10.1039/c6sm01163b.
ieee: H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories
of self-propelled Janus particles in a diverging laser beam,” Soft Matter,
vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016.
ista: Moyses H, Palacci JA, Sacanna S, Grier DG. 2016. Trochoidal trajectories of
self-propelled Janus particles in a diverging laser beam. Soft Matter. 12(30),
6357–6364.
mla: Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles
in a Diverging Laser Beam.” Soft Matter, vol. 12, no. 30, Royal Society
of Chemistry , 2016, pp. 6357–64, doi:10.1039/c6sm01163b.
short: H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364.
date_created: 2021-02-01T13:44:15Z
date_published: 2016-08-14T00:00:00Z
date_updated: 2023-02-23T13:47:40Z
day: '14'
doi: 10.1039/c6sm01163b
extern: '1'
external_id:
arxiv:
- '1609.01497'
pmid:
- '27338294'
intvolume: ' 12'
issue: '30'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01497
month: '08'
oa: 1
oa_version: Preprint
page: 6357-6364
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Trochoidal trajectories of self-propelled Janus particles in a diverging laser
beam
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12
year: '2016'
...
---
_id: '9140'
abstract:
- lang: eng
text: 'Expected changes to future extreme precipitation remain a key uncertainty
associated with anthropogenic climate change. Extreme precipitation has been proposed
to scale with the precipitable water content in the atmosphere. Assuming constant
relative humidity, this implies an increase of precipitation extremes at a rate
of about 7% °C−1 globally as indicated by the Clausius‐Clapeyron relationship.
Increases faster and slower than Clausius‐Clapeyron have also been reported. In
this work, we examine the scaling between precipitation extremes and temperature
in the present climate using simulations and measurements from surface weather
stations collected in the frame of the HyMeX and MED‐CORDEX programs in Southern
France. Of particular interest are departures from the Clausius‐Clapeyron thermodynamic
expectation, their spatial and temporal distribution, and their origin. Looking
at the scaling of precipitation extreme with temperature, two regimes emerge which
form a hook shape: one at low temperatures (cooler than around 15°C) with rates
of increase close to the Clausius‐Clapeyron rate and one at high temperatures
(warmer than about 15°C) with sub‐Clausius‐Clapeyron rates and most often negative
rates. On average, the region of focus does not seem to exhibit super Clausius‐Clapeyron
behavior except at some stations, in contrast to earlier studies. Many factors
can contribute to departure from Clausius‐Clapeyron scaling: time and spatial
averaging, choice of scaling temperature (surface versus condensation level),
and precipitation efficiency and vertical velocity in updrafts that are not necessarily
constant with temperature. But most importantly, the dynamical contribution of
orography to precipitation in the fall over this area during the so‐called “Cevenoles”
events, explains the hook shape of the scaling of precipitation extremes.'
article_processing_charge: No
article_type: original
author:
- first_name: P.
full_name: Drobinski, P.
last_name: Drobinski
- first_name: B.
full_name: Alonzo, B.
last_name: Alonzo
- first_name: S.
full_name: Bastin, S.
last_name: Bastin
- first_name: N. Da
full_name: Silva, N. Da
last_name: Silva
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: 'Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. Scaling of precipitation
extremes with temperature in the French Mediterranean region: What explains the
hook shape? Journal of Geophysical Research: Atmospheres. 2016;121(7):3100-3119.
doi:10.1002/2015jd023497'
apa: 'Drobinski, P., Alonzo, B., Bastin, S., Silva, N. D., & Muller, C. J. (2016).
Scaling of precipitation extremes with temperature in the French Mediterranean
region: What explains the hook shape? Journal of Geophysical Research: Atmospheres.
American Geophysical Union. https://doi.org/10.1002/2015jd023497'
chicago: 'Drobinski, P., B. Alonzo, S. Bastin, N. Da Silva, and Caroline J Muller.
“Scaling of Precipitation Extremes with Temperature in the French Mediterranean
Region: What Explains the Hook Shape?” Journal of Geophysical Research: Atmospheres.
American Geophysical Union, 2016. https://doi.org/10.1002/2015jd023497.'
ieee: 'P. Drobinski, B. Alonzo, S. Bastin, N. D. Silva, and C. J. Muller, “Scaling
of precipitation extremes with temperature in the French Mediterranean region:
What explains the hook shape?,” Journal of Geophysical Research: Atmospheres,
vol. 121, no. 7. American Geophysical Union, pp. 3100–3119, 2016.'
ista: 'Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. 2016. Scaling of precipitation
extremes with temperature in the French Mediterranean region: What explains the
hook shape? Journal of Geophysical Research: Atmospheres. 121(7), 3100–3119.'
mla: 'Drobinski, P., et al. “Scaling of Precipitation Extremes with Temperature
in the French Mediterranean Region: What Explains the Hook Shape?” Journal
of Geophysical Research: Atmospheres, vol. 121, no. 7, American Geophysical
Union, 2016, pp. 3100–19, doi:10.1002/2015jd023497.'
short: 'P. Drobinski, B. Alonzo, S. Bastin, N.D. Silva, C.J. Muller, Journal of
Geophysical Research: Atmospheres 121 (2016) 3100–3119.'
date_created: 2021-02-15T14:21:16Z
date_published: 2016-03-16T00:00:00Z
date_updated: 2022-01-24T13:41:02Z
day: '16'
doi: 10.1002/2015jd023497
extern: '1'
intvolume: ' 121'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2015JD023497
month: '03'
oa: 1
oa_version: Published Version
page: 3100-3119
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 2169-897X
- 2169-8996
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: 'Scaling of precipitation extremes with temperature in the French Mediterranean
region: What explains the hook shape?'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 121
year: '2016'
...
---
_id: '7068'
abstract:
- lang: eng
text: Electrons in materials with linear dispersion behave as massless Weyl- or
Dirac-quasiparticles, and continue to intrigue due to their close resemblance
to elusive ultra-relativistic particles as well as their potential for future
electronics. Yet the experimental signatures of Weyl-fermions are often subtle
and indirect, in particular if they coexist with conventional, massive quasiparticles.
Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal
NbAs upon entering the quantum limit state in high magnetic fields. The torque
changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy
that can be directly attributed to the topological nature of the Weyl electrons.
Our results establish that anomalous quantum limit torque measurements provide
a direct experimental method to identify and distinguish Weyl and Dirac systems.
article_number: '12492'
article_processing_charge: No
article_type: original
author:
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: Andrew C.
full_name: Potter, Andrew C.
last_name: Potter
- first_name: Nityan L.
full_name: Nair, Nityan L.
last_name: Nair
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Scott
full_name: Riggs, Scott
last_name: Riggs
- first_name: Bin
full_name: Zeng, Bin
last_name: Zeng
- first_name: Nirmal J.
full_name: Ghimire, Nirmal J.
last_name: Ghimire
- first_name: Eric D.
full_name: Bauer, Eric D.
last_name: Bauer
- first_name: Robert
full_name: Kealhofer, Robert
last_name: Kealhofer
- first_name: Filip
full_name: Ronning, Filip
last_name: Ronning
- first_name: James G.
full_name: Analytis, James G.
last_name: Analytis
citation:
ama: Moll PJW, Potter AC, Nair NL, et al. Magnetic torque anomaly in the quantum
limit of Weyl semimetals. Nature Communications. 2016;7. doi:10.1038/ncomms12492
apa: Moll, P. J. W., Potter, A. C., Nair, N. L., Ramshaw, B. J., Modic, K. A., Riggs,
S., … Analytis, J. G. (2016). Magnetic torque anomaly in the quantum limit of
Weyl semimetals. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms12492
chicago: Moll, Philip J. W., Andrew C. Potter, Nityan L. Nair, B. J. Ramshaw, Kimberly
A Modic, Scott Riggs, Bin Zeng, et al. “Magnetic Torque Anomaly in the Quantum
Limit of Weyl Semimetals.” Nature Communications. Springer Nature, 2016.
https://doi.org/10.1038/ncomms12492.
ieee: P. J. W. Moll et al., “Magnetic torque anomaly in the quantum limit
of Weyl semimetals,” Nature Communications, vol. 7. Springer Nature, 2016.
ista: Moll PJW, Potter AC, Nair NL, Ramshaw BJ, Modic KA, Riggs S, Zeng B, Ghimire
NJ, Bauer ED, Kealhofer R, Ronning F, Analytis JG. 2016. Magnetic torque anomaly
in the quantum limit of Weyl semimetals. Nature Communications. 7, 12492.
mla: Moll, Philip J. W., et al. “Magnetic Torque Anomaly in the Quantum Limit of
Weyl Semimetals.” Nature Communications, vol. 7, 12492, Springer Nature,
2016, doi:10.1038/ncomms12492.
short: P.J.W. Moll, A.C. Potter, N.L. Nair, B.J. Ramshaw, K.A. Modic, S. Riggs,
B. Zeng, N.J. Ghimire, E.D. Bauer, R. Kealhofer, F. Ronning, J.G. Analytis, Nature
Communications 7 (2016).
date_created: 2019-11-19T13:20:53Z
date_published: 2016-08-22T00:00:00Z
date_updated: 2021-01-12T08:11:40Z
day: '22'
ddc:
- '530'
doi: 10.1038/ncomms12492
extern: '1'
file:
- access_level: open_access
checksum: e3272ed18d22187406b30be48a56e7b2
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T12:52:19Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7114'
file_name: 2016_NatureComm_Moll.pdf
file_size: 663911
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Magnetic torque anomaly in the quantum limit of Weyl semimetals
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: 7
year: '2016'
...
---
_id: '7279'
abstract:
- lang: eng
text: Kinetics of electrochemical reactions are several orders of magnitude slower
in solids than in liquids as a result of the much lower ion diffusivity. Yet,
the solid state maximizes the density of redox species, which is at least two
orders of magnitude lower in liquids because of solubility limitations. With regard
to electrochemical energy storage devices, this leads to high-energy batteries
with limited power and high-power supercapacitors with a well-known energy deficiency.
For such devices the ideal system should endow the liquid state with a density
of redox species close to the solid state. Here we report an approach based on
biredox ionic liquids to achieve bulk-like redox density at liquid-like fast kinetics.
The cation and anion of these biredox ionic liquids bear moieties that undergo
very fast reversible redox reactions. As a first demonstration of their potential
for high-capacity/high-rate charge storage, we used them in redox supercapacitors.
These ionic liquids are able to decouple charge storage from an ion-accessible
electrode surface, by storing significant charge in the pores of the electrodes,
to minimize self-discharge and leakage current as a result of retaining the redox
species in the pores, and to raise working voltage due to their wide electrochemical
window.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Laura
full_name: Coustan, Laura
last_name: Coustan
- first_name: Pierre
full_name: Lannelongue, Pierre
last_name: Lannelongue
- first_name: Dodzi
full_name: Zigah, Dodzi
last_name: Zigah
- first_name: Ahmad
full_name: Mehdi, Ahmad
last_name: Mehdi
- first_name: André
full_name: Vioux, André
last_name: Vioux
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Frédéric
full_name: Favier, Frédéric
last_name: Favier
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
citation:
ama: Mourad E, Coustan L, Lannelongue P, et al. Biredox ionic liquids with solid-like
redox density in the liquid state for high-energy supercapacitors. Nature Materials.
2016;16(4):446-453. doi:10.1038/nmat4808
apa: Mourad, E., Coustan, L., Lannelongue, P., Zigah, D., Mehdi, A., Vioux, A.,
… Fontaine, O. (2016). Biredox ionic liquids with solid-like redox density in
the liquid state for high-energy supercapacitors. Nature Materials. Springer
Nature. https://doi.org/10.1038/nmat4808
chicago: Mourad, Eléonore, Laura Coustan, Pierre Lannelongue, Dodzi Zigah, Ahmad
Mehdi, André Vioux, Stefan Alexander Freunberger, Frédéric Favier, and Olivier
Fontaine. “Biredox Ionic Liquids with Solid-like Redox Density in the Liquid State
for High-Energy Supercapacitors.” Nature Materials. Springer Nature, 2016.
https://doi.org/10.1038/nmat4808.
ieee: E. Mourad et al., “Biredox ionic liquids with solid-like redox density
in the liquid state for high-energy supercapacitors,” Nature Materials,
vol. 16, no. 4. Springer Nature, pp. 446–453, 2016.
ista: Mourad E, Coustan L, Lannelongue P, Zigah D, Mehdi A, Vioux A, Freunberger
SA, Favier F, Fontaine O. 2016. Biredox ionic liquids with solid-like redox density
in the liquid state for high-energy supercapacitors. Nature Materials. 16(4),
446–453.
mla: Mourad, Eléonore, et al. “Biredox Ionic Liquids with Solid-like Redox Density
in the Liquid State for High-Energy Supercapacitors.” Nature Materials,
vol. 16, no. 4, Springer Nature, 2016, pp. 446–53, doi:10.1038/nmat4808.
short: E. Mourad, L. Coustan, P. Lannelongue, D. Zigah, A. Mehdi, A. Vioux, S.A.
Freunberger, F. Favier, O. Fontaine, Nature Materials 16 (2016) 446–453.
date_created: 2020-01-15T07:27:54Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2021-01-12T08:12:43Z
day: '28'
doi: 10.1038/nmat4808
extern: '1'
external_id:
arxiv:
- '1711.11518'
intvolume: ' 16'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.11518
month: '11'
oa: 1
oa_version: Preprint
page: 446-453
publication: Nature Materials
publication_identifier:
issn:
- 1476-1122
- 1476-4660
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Biredox ionic liquids with solid-like redox density in the liquid state for
high-energy supercapacitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '7297'
abstract:
- lang: eng
text: Redox mediators facilitate the oxidation of the highly insulating discharge
product in metal–oxygen batteries during recharge and offer opportunities to achieve
high reversible capacities. Now a design principle for selecting redox mediators
that can recharge the batteries more efficiently is suggested.
article_number: '16074'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: 'Freunberger SA. Batteries: Charging ahead rationally. Nature Energy.
2016;1(6). doi:10.1038/nenergy.2016.74'
apa: 'Freunberger, S. A. (2016). Batteries: Charging ahead rationally. Nature
Energy. Springer Nature. https://doi.org/10.1038/nenergy.2016.74'
chicago: 'Freunberger, Stefan Alexander. “Batteries: Charging Ahead Rationally.”
Nature Energy. Springer Nature, 2016. https://doi.org/10.1038/nenergy.2016.74.'
ieee: 'S. A. Freunberger, “Batteries: Charging ahead rationally,” Nature Energy,
vol. 1, no. 6. Springer Nature, 2016.'
ista: 'Freunberger SA. 2016. Batteries: Charging ahead rationally. Nature Energy.
1(6), 16074.'
mla: 'Freunberger, Stefan Alexander. “Batteries: Charging Ahead Rationally.” Nature
Energy, vol. 1, no. 6, 16074, Springer Nature, 2016, doi:10.1038/nenergy.2016.74.'
short: S.A. Freunberger, Nature Energy 1 (2016).
date_created: 2020-01-15T12:16:40Z
date_published: 2016-05-23T00:00:00Z
date_updated: 2021-01-12T08:12:51Z
day: '23'
ddc:
- '540'
- '541'
- '547'
- '546'
doi: 10.1038/nenergy.2016.74
extern: '1'
file:
- access_level: open_access
checksum: d90d675947262f7437b483b251918df2
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T13:41:56Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8047'
file_name: N&V Freunberger final.pdf
file_size: 197375
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '6'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
publication: Nature Energy
publication_identifier:
issn:
- 2058-7546
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Batteries: Charging ahead rationally'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2016'
...
---
_id: '7599'
abstract:
- lang: eng
text: Normal leaf margin development is important for leaf morphogenesis and contributes
to diverse leaf shapes in higher plants. We here show the crucial roles of an
atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin
development. PI4Kγ5 presents a dynamics expression pattern along with leaf development
and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is
resulted from the accelerated cell division and increased auxin concentration
at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates
a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated
that membrane-bound transcription factors regulate gene transcription by undergoing
proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis
by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis
indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced
in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078.
This is consistent with the subcellular localization observation showing that
fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in
pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal,
driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1.
Further analysis showed that ANAC078 suppresses the auxin synthesis by directly
binding and regulating the expression of auxin synthesis-related genes. These
results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin
synthesis and hence influences cell proliferation and leaf development, providing
informative clues for the regulation of in situ auxin synthesis and cell division,
as well as the cleavage and functional mechanism of membrane-bound transcription
factors.
article_number: e1006252
article_processing_charge: No
article_type: original
author:
- first_name: Yong
full_name: Tang, Yong
last_name: Tang
- first_name: Chun-Yan
full_name: Zhao, Chun-Yan
last_name: Zhao
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
citation:
ama: Tang Y, Zhao C-Y, Tan S, Xue H-W. Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078. PLOS Genetics.
2016;12(8). doi:10.1371/journal.pgen.1006252
apa: Tang, Y., Zhao, C.-Y., Tan, S., & Xue, H.-W. (2016). Arabidopsis type II
phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin
development through interacting with membrane-bound transcription factor ANAC078.
PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1006252
chicago: Tang, Yong, Chun-Yan Zhao, Shutang Tan, and Hong-Wei Xue. “Arabidopsis
Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and
Leaf Margin Development through Interacting with Membrane-Bound Transcription
Factor ANAC078.” PLOS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1006252.
ieee: Y. Tang, C.-Y. Zhao, S. Tan, and H.-W. Xue, “Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078,” PLOS Genetics,
vol. 12, no. 8. Public Library of Science, 2016.
ista: Tang Y, Zhao C-Y, Tan S, Xue H-W. 2016. Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078. PLOS Genetics. 12(8),
e1006252.
mla: Tang, Yong, et al. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5
Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with
Membrane-Bound Transcription Factor ANAC078.” PLOS Genetics, vol. 12, no.
8, e1006252, Public Library of Science, 2016, doi:10.1371/journal.pgen.1006252.
short: Y. Tang, C.-Y. Zhao, S. Tan, H.-W. Xue, PLOS Genetics 12 (2016).
date_created: 2020-03-21T16:08:33Z
date_published: 2016-08-16T00:00:00Z
date_updated: 2021-01-12T08:14:25Z
day: '16'
ddc:
- '580'
doi: 10.1371/journal.pgen.1006252
extern: '1'
file:
- access_level: open_access
checksum: ff0ab9a6bed11cda800a6e59820866a0
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T12:15:31Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7612'
file_name: 2016_PlosGenetics_Tang.PDF
file_size: 3266119
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis
and leaf margin development through interacting with membrane-bound transcription
factor ANAC078
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: 12
year: '2016'
...
---
_id: '7737'
abstract:
- lang: eng
text: Genome-wide association studies (GWAS) have identified thousands of genetic
variants associated with human complex traits. However, the genes or functional
DNA elements through which these variants exert their effects on the traits are
often unknown. We propose a method (called SMR) that integrates summary-level
data from GWAS with data from expression quantitative trait locus (eQTL) studies
to identify genes whose expression levels are associated with a complex trait
because of pleiotropy. We apply the method to five human complex traits using
GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and
we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis
and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates;
77 genes are not the nearest annotated gene to the top associated GWAS SNP. These
genes provide important leads to design future functional studies to understand
the mechanism whereby DNA variation leads to complex trait variation.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Futao
full_name: Zhang, Futao
last_name: Zhang
- first_name: Han
full_name: Hu, Han
last_name: Hu
- first_name: Andrew
full_name: Bakshi, Andrew
last_name: Bakshi
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Joseph E
full_name: Powell, Joseph E
last_name: Powell
- first_name: Grant W
full_name: Montgomery, Grant W
last_name: Montgomery
- first_name: Michael E
full_name: Goddard, Michael E
last_name: Goddard
- first_name: Naomi R
full_name: Wray, Naomi R
last_name: Wray
- first_name: Peter M
full_name: Visscher, Peter M
last_name: Visscher
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
citation:
ama: Zhu Z, Zhang F, Hu H, et al. Integration of summary data from GWAS and eQTL
studies predicts complex trait gene targets. Nature Genetics. 2016;48(5):481-487.
doi:10.1038/ng.3538
apa: Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., … Yang,
J. (2016). Integration of summary data from GWAS and eQTL studies predicts complex
trait gene targets. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3538
chicago: Zhu, Zhihong, Futao Zhang, Han Hu, Andrew Bakshi, Matthew Richard Robinson,
Joseph E Powell, Grant W Montgomery, et al. “Integration of Summary Data from
GWAS and EQTL Studies Predicts Complex Trait Gene Targets.” Nature Genetics.
Springer Nature, 2016. https://doi.org/10.1038/ng.3538.
ieee: Z. Zhu et al., “Integration of summary data from GWAS and eQTL studies
predicts complex trait gene targets,” Nature Genetics, vol. 48, no. 5.
Springer Nature, pp. 481–487, 2016.
ista: Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, Montgomery GW, Goddard
ME, Wray NR, Visscher PM, Yang J. 2016. Integration of summary data from GWAS
and eQTL studies predicts complex trait gene targets. Nature Genetics. 48(5),
481–487.
mla: Zhu, Zhihong, et al. “Integration of Summary Data from GWAS and EQTL Studies
Predicts Complex Trait Gene Targets.” Nature Genetics, vol. 48, no. 5,
Springer Nature, 2016, pp. 481–87, doi:10.1038/ng.3538.
short: Z. Zhu, F. Zhang, H. Hu, A. Bakshi, M.R. Robinson, J.E. Powell, G.W. Montgomery,
M.E. Goddard, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 48 (2016) 481–487.
date_created: 2020-04-30T10:50:26Z
date_published: 2016-03-28T00:00:00Z
date_updated: 2021-01-12T08:15:11Z
day: '28'
doi: 10.1038/ng.3538
extern: '1'
intvolume: ' 48'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ng.3538
month: '03'
oa: 1
oa_version: Published Version
page: 481-487
publication: Nature Genetics
publication_identifier:
issn:
- 1061-4036
- 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Integration of summary data from GWAS and eQTL studies predicts complex trait
gene targets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2016'
...
---
_id: '786'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers prefer to treat
concurrent code as if it were wait-free, guaranteeing that all operations always
make progress. Unfortunately, designing wait-free algorithms is generally a very
complex task, and the resulting algorithms are not always efficient. Although
obtaining efficient wait-free algorithms has been a long-time goal for the theory
community, most nonblocking commercial code is only lock-free. This article suggests
a simple solution to this problem.We show that for a large class of lock-free
algorithms, under scheduling conditions that approximate those found in commercial
hardware architectures, lock-free algorithms behave as if they are wait-free.
In other words, programmers can continue to design simple lock-free algorithms
instead of complex wait-free ones, and in practice, they will get wait-free progress.
Our main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes to the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1 but that in
fact a general subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes. To the best
of our knowledge, this is the first attempt to analyze progress conditions, typically
stated in relation to a worst-case adversary, in a stochastic model capturing
their expected asymptotic behavior.
acknowledgement: Part of this work was performed while the first author was a postdoctoral
associate at MIT CSAIL, where he was supported by the SNF Postdoctoral Fellows Program,
NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the
Oracle and Intel corporations. The second author was supported in part by ISF grant
1696/14. The third author was supported in part by NSF grants CCF-1217921, CCF-1301926,
IIS-1447786, and CCF-1561807, and the U.S. Department of Energy under grant DE-SC0008923,
and by equipment grants from Intel Corporation.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: Alistarh D-A, Censor Hillel K, Shavit N. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 2016;63(4). doi:10.1145/2903136
apa: Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2016). Are lock free
concurrent algorithms practically wait free . Journal of the ACM. ACM.
https://doi.org/10.1145/2903136
chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock Free
Concurrent Algorithms Practically Wait Free .” Journal of the ACM. ACM,
2016. https://doi.org/10.1145/2903136.
ieee: D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock free concurrent
algorithms practically wait free ,” Journal of the ACM, vol. 63, no. 4.
ACM, 2016.
ista: Alistarh D-A, Censor Hillel K, Shavit N. 2016. Are lock free concurrent algorithms
practically wait free . Journal of the ACM. 63(4).
mla: Alistarh, Dan-Adrian, et al. “Are Lock Free Concurrent Algorithms Practically
Wait Free .” Journal of the ACM, vol. 63, no. 4, ACM, 2016, doi:10.1145/2903136.
short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, Journal of the ACM 63 (2016).
date_created: 2018-12-11T11:48:29Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-02-23T13:19:04Z
day: '01'
doi: 10.1145/2903136
extern: '1'
external_id:
arxiv:
- '1311.3200'
intvolume: ' 63'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3200
month: '09'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '6870'
quality_controlled: '1'
status: public
title: 'Are lock free concurrent algorithms practically wait free '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2016'
...
---
_id: '8020'
abstract:
- lang: eng
text: Balance of cortical excitation and inhibition (EI) is thought to be disrupted
in several neuropsychiatric conditions, yet it is not clear how it is maintained
in the healthy human brain. When EI balance is disturbed during learning and memory
in animal models, it can be restabilized via formation of inhibitory replicas
of newly formed excitatory connections. Here we assess evidence for such selective
inhibitory rebalancing in humans. Using fMRI repetition suppression we measure
newly formed cortical associations in the human brain. We show that expression
of these associations reduces over time despite persistence in behavior, consistent
with inhibitory rebalancing. To test this, we modulated excitation/inhibition
balance with transcranial direct current stimulation (tDCS). Using ultra-high-field
(7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations
to be re-expressed. This suggests that in humans associative memories are stored
in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory
connections are unmasked.
article_processing_charge: No
article_type: original
author:
- first_name: H.C.
full_name: Barron, H.C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: U.E.
full_name: Emir, U.E.
last_name: Emir
- first_name: T.R.
full_name: Makin, T.R.
last_name: Makin
- first_name: J.
full_name: O’Shea, J.
last_name: O’Shea
- first_name: S.
full_name: Clare, S.
last_name: Clare
- first_name: S.
full_name: Jbabdi, S.
last_name: Jbabdi
- first_name: R.J.
full_name: Dolan, R.J.
last_name: Dolan
- first_name: T.E.J.
full_name: Behrens, T.E.J.
last_name: Behrens
citation:
ama: Barron HC, Vogels TP, Emir UE, et al. Unmasking latent inhibitory connections
in human cortex to reveal dormant cortical memories. Neuron. 2016;90(1):191-203.
doi:10.1016/j.neuron.2016.02.031
apa: Barron, H. C., Vogels, T. P., Emir, U. E., Makin, T. R., O’Shea, J., Clare,
S., … Behrens, T. E. J. (2016). Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.02.031
chicago: Barron, H.C., Tim P Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare,
S. Jbabdi, R.J. Dolan, and T.E.J. Behrens. “Unmasking Latent Inhibitory Connections
in Human Cortex to Reveal Dormant Cortical Memories.” Neuron. Elsevier,
2016. https://doi.org/10.1016/j.neuron.2016.02.031.
ieee: H. C. Barron et al., “Unmasking latent inhibitory connections in human
cortex to reveal dormant cortical memories,” Neuron, vol. 90, no. 1. Elsevier,
pp. 191–203, 2016.
ista: Barron HC, Vogels TP, Emir UE, Makin TR, O’Shea J, Clare S, Jbabdi S, Dolan
RJ, Behrens TEJ. 2016. Unmasking latent inhibitory connections in human cortex
to reveal dormant cortical memories. Neuron. 90(1), 191–203.
mla: Barron, H. C., et al. “Unmasking Latent Inhibitory Connections in Human Cortex
to Reveal Dormant Cortical Memories.” Neuron, vol. 90, no. 1, Elsevier,
2016, pp. 191–203, doi:10.1016/j.neuron.2016.02.031.
short: H.C. Barron, T.P. Vogels, U.E. Emir, T.R. Makin, J. O’Shea, S. Clare, S.
Jbabdi, R.J. Dolan, T.E.J. Behrens, Neuron 90 (2016) 191–203.
date_created: 2020-06-25T13:05:33Z
date_published: 2016-04-06T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '06'
ddc:
- '570'
doi: 10.1016/j.neuron.2016.02.031
extern: '1'
external_id:
pmid:
- '26996082'
file:
- access_level: open_access
checksum: 9ce7a1c64986dce0435c070285a7ef9b
content_type: application/pdf
creator: cziletti
date_created: 2020-07-09T09:57:04Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8104'
file_name: 2016_Neuron_Barron.pdf
file_size: 5334136
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 90'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 191-203
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Unmasking latent inhibitory connections in human cortex to reveal dormant cortical
memories
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 90
year: '2016'
...