---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '9663'
abstract:
- lang: eng
text: 'Molecular dynamics simulations of small Cu nanoparticles using three different
interatomic potentials at rising temperature indicate that small nanoparticles
can undergo solid-solid structural transitions through a direct geometrical conversion
route. The direct geometrical conversion can happen for cuboctahedral nanoparticles,
which turn into an icosahedra shape: one diagonal of the square faces contracts,
and the faces are folded along the diagonal to give rise to two equilateral triangles.
The transition is a kinetic process that cannot be fully explained through an
energetic point of view. It has low activation energy and fast reaction time in
the simulations. The transition mechanism is via the transmission of shear waves
initiated from the particle surface and does not involve dislocation activity.'
article_number: '164314'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H. W.
full_name: Ngan, Alfonso H. W.
last_name: Ngan
citation:
ama: Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper
nanoparticles through direct geometrical conversion. The Journal of Chemical
Physics. 2013;138(16). doi:10.1063/1.4802025
apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural
transition of copper nanoparticles through direct geometrical conversion. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025
chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid
Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.”
The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025.
ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion,” The Journal
of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013.
ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition
of copper nanoparticles through direct geometrical conversion. The Journal of
Chemical Physics. 138(16), 164314.
mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural
Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The
Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013,
doi:10.1063/1.4802025.
short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).
date_created: 2021-07-15T09:27:58Z
date_published: 2013-04-28T00:00:00Z
date_updated: 2021-08-09T12:35:34Z
day: '28'
doi: 10.1063/1.4802025
extern: '1'
external_id:
pmid:
- '23635145'
intvolume: ' 138'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pubmed.ncbi.nlm.nih.gov/23635145/
month: '04'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermally induced solid-solid structural transition of copper nanoparticles
through direct geometrical conversion
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 138
year: '2013'
...
---
_id: '9674'
abstract:
- lang: eng
text: The coalescence of nano-crystals during sintering is often found to result
in interesting crystalline structures such as multi-fold twins, and yet the plasticity
mechanism accompanying their formation is unclear. In this work, the sintering
behavior of two unsupported copper nanoparticles initially at room temperature
is investigated by molecular dynamics simulations under the constant-energy ensemble.
The results reveal that once the two nanoparticles are brought into contact, they
often go through drastic structural changes with the inter-particle grain boundary
quickly eliminated, and single- and multi-fold twinning occurs frequently in the
coalesced product. Whereas the formation of single twins is found to be via the
more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation
of fivefold twins, however, takes place via a novel dislocation-free mechanism
involving a series of shear and rigid-body rotation processes caused by elastic
waves with amplitudes not corresponding to any allowable Burgers vector in the
fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never
been reported before.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles:
A molecular dynamics study. International Journal of Plasticity. 2013;47:65-79.
doi:10.1016/j.ijplas.2013.01.006'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). The crystal structures of sintered
copper nanoparticles: A molecular dynamics study. International Journal of
Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2013.01.006'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered
Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of
Plasticity. Elsevier, 2013. https://doi.org/10.1016/j.ijplas.2013.01.006.'
ieee: 'B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles:
A molecular dynamics study,” International Journal of Plasticity, vol.
47. Elsevier, pp. 65–79, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles:
A molecular dynamics study. International Journal of Plasticity. 47, 65–79.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered
Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of
Plasticity, vol. 47, Elsevier, 2013, pp. 65–79, doi:10.1016/j.ijplas.2013.01.006.'
short: B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79.
date_created: 2021-07-15T14:27:44Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2023-02-23T14:04:30Z
day: '01'
doi: 10.1016/j.ijplas.2013.01.006
extern: '1'
intvolume: ' 47'
language:
- iso: eng
month: '08'
oa_version: None
page: 65-79
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The crystal structures of sintered copper nanoparticles: A molecular dynamics
study'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 47
year: '2013'
...
---
_id: '9676'
abstract:
- lang: eng
text: Despite its relevance to a range of technological applications including nanocrystalline
material fabrication, the sintering mechanisms of nanoparticles have not been
well understood. It has been recognized that extrapolation from understanding
of macro-particle sintering is unreliable for the nano-particle size regime. In
this work, the sintering behaviour of copper nanoparticles under periodic boundary
conditions at different temperatures and pressures was investigated by Molecular
Dynamics simulations. It was found that smaller particle sizes, higher temperature
and higher external pressure facilitate densification. Through a comparison with
a two-sphere model, the governing mechanisms for many nanoparticles sintered at
low temperature (T⩽900K) were identified to be a variety of plasticity processes
including dislocation, twinning and even amorphization at the contact neck regions,
due to the presence of high stresses.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. The sintering and densification behaviour of many copper
nanoparticles: A molecular dynamics study. Computational Materials Science.
2013;74:1-11. doi:10.1016/j.commatsci.2013.03.014'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). The sintering and densification behaviour
of many copper nanoparticles: A molecular dynamics study. Computational Materials
Science. Elsevier. https://doi.org/10.1016/j.commatsci.2013.03.014'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification
Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational
Materials Science. Elsevier, 2013. https://doi.org/10.1016/j.commatsci.2013.03.014.'
ieee: 'B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of
many copper nanoparticles: A molecular dynamics study,” Computational Materials
Science, vol. 74. Elsevier, pp. 1–11, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many
copper nanoparticles: A molecular dynamics study. Computational Materials Science.
74, 1–11.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification
Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational
Materials Science, vol. 74, Elsevier, 2013, pp. 1–11, doi:10.1016/j.commatsci.2013.03.014.'
short: B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11.
date_created: 2021-07-16T06:46:38Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2023-02-23T14:04:35Z
day: '01'
doi: 10.1016/j.commatsci.2013.03.014
extern: '1'
intvolume: ' 74'
language:
- iso: eng
month: '06'
oa_version: None
page: 1-11
publication: Computational Materials Science
publication_identifier:
issn:
- 0927-0256
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The sintering and densification behaviour of many copper nanoparticles: A
molecular dynamics study'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 74
year: '2013'
...
---
_id: '9682'
abstract:
- lang: eng
text: In this work, we simulate the response of two Cu nanoparticles colliding at
different approaching rates at room temperature by MD. For small nanospheres,
the formation of single twins is favored at high approach rates, whereas larger
nanospheres mainly deform by dislocation slip. For small nanocubes with large
{100} flat surfaces, however, a dislocation-free direct geometrical conversion
process that leads to five-fold twinning dominates except at highly retarded approaching
rates. For larger nanocubes, single twin formation is the governing plasticity
mechanism. The probability for plastic deformation by dislocation slip or twinning
is attributed to the abundance of surface steps, which act as sites for dislocation
nucleation.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alfonso H.W.
full_name: Ngan, Alfonso H.W.
last_name: Ngan
citation:
ama: 'Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision.
Materials Science and Engineering: A. 2013;585:326-334. doi:10.1016/j.msea.2013.07.065'
apa: 'Cheng, B., & Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals
during collision. Materials Science and Engineering: A. Elsevier. https://doi.org/10.1016/j.msea.2013.07.065'
chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals
during Collision.” Materials Science and Engineering: A. Elsevier, 2013.
https://doi.org/10.1016/j.msea.2013.07.065.'
ieee: 'B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during
collision,” Materials Science and Engineering: A, vol. 585. Elsevier, pp.
326–334, 2013.'
ista: 'Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision.
Materials Science and Engineering: A. 585, 326–334.'
mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals
during Collision.” Materials Science and Engineering: A, vol. 585, Elsevier,
2013, pp. 326–34, doi:10.1016/j.msea.2013.07.065.'
short: 'B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.'
date_created: 2021-07-19T09:04:36Z
date_published: 2013-11-15T00:00:00Z
date_updated: 2023-02-23T14:04:51Z
day: '15'
doi: 10.1016/j.msea.2013.07.065
extern: '1'
intvolume: ' 585'
language:
- iso: eng
month: '11'
oa_version: None
page: 326-334
publication: 'Materials Science and Engineering: A'
publication_identifier:
issn:
- 0921-5093
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crystal plasticity of Cu nanocrystals during collision
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 585
year: '2013'
...
---
_id: '970'
abstract:
- lang: eng
text: 'Recently a new high-mobility Dirac material, trilayer graphene, was realized
experimentally. The band structure of ABA-stacked trilayer graphene consists of
a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties
of ABA-stacked trilayer graphene biased by a perpendicular electric field. We
find that the combination of the bias and trigonal warping gives rise to a set
of new Dirac points: In each valley, seven species of Dirac fermions with small
masses of order of a few meV emerge. The positions and masses of the emergent
Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless
at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity
at the neutrality point is expected to show nonmonotonic behavior, becoming of
the order of a few e2/h when some Dirac masses vanish. Further, we analyze the
evolution of the Landau level spectrum as a function of bias. The emergence of
new Dirac points in the band structure translates into new threefold-degenerate
groups of Landau levels. This leads to an anomalous quantum Hall effect, in which
some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies
of all Landau levels get lifted, and in this regime all quantum Hall plateaus
are spaced by e2/h. Finally, we show that the pattern of Landau level crossings
is very sensitive to certain band structure parameters, and can therefore provide
a useful tool for determining their precise values.'
acknowledgement: We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat
for attracting our attention to the problem of biased trilayer graphene, and for
many helpful discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in
biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422
apa: Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level
crossings in biased trilayer graphene. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422
chicago: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau
Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422.
ieee: M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings
in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials
Physics, vol. 87, no. 11. American Physical Society, 2013.
ista: Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings
in biased trilayer graphene. Physical Review B - Condensed Matter and Materials
Physics. 87(11).
mla: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level
Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422.
short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-03-18T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '18'
doi: 10.1103/PhysRevB.87.115422
extern: 1
intvolume: ' 87'
issue: '11'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.6251
month: '03'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6428'
quality_controlled: 0
status: public
title: New Dirac points and multiple Landau level crossings in biased trilayer graphene
type: journal_article
volume: 87
year: '2013'
...
---
_id: '971'
abstract:
- lang: eng
text: We study the stability of the normal state in a mesoscopic NSN junction biased
by a constant voltage V with respect to the formation of the superconducting order.
Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature
dependence of the instability line, V inst(T), where nucleation of superconductivity
takes place. For sufficiently low biases, a stationary symmetric superconducting
state emerges below the instability line. For higher biases, the normal phase
is destroyed by the formation of a nonstationary bimodal state with two superconducting
nuclei localized near the opposite terminals. The low-temperature and large-voltage
behavior of the instability line is highly sensitive to the details of the inelastic
relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T)
in NSN junctions may be used as an effective tool to access the parameters of
the inelastic relaxation in the normal state.
acknowledgement: We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk,
J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail
full_name: Skvortsov, Mikhail A
last_name: Skvortsov
citation:
ama: Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge. Physical Review B - Condensed Matter and Materials Physics.
2013;87(2). doi:10.1103/PhysRevB.87.020501
apa: Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501
chicago: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a
Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2013.
https://doi.org/10.1103/PhysRevB.87.020501.
ieee: M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2. American Physical Society, 2013.
ista: Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased
normal-superconducting-normal microbridge. Physical Review B - Condensed Matter
and Materials Physics. 87(2).
mla: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased
Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter
and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501.
short: M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials
Physics 87 (2013).
date_created: 2018-12-11T11:49:28Z
date_published: 2013-01-02T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '02'
doi: 10.1103/PhysRevB.87.020501
extern: 1
intvolume: ' 87'
issue: '2'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1208.6004
month: '01'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6429'
quality_controlled: 0
status: public
title: Onset of superconductivity in a voltage-biased normal-superconducting-normal
microbridge
type: journal_article
volume: 87
year: '2013'
...
---
_id: '972'
abstract:
- lang: eng
text: In topological crystalline insulators (TCIs), topology and crystal symmetry
intertwine to create surface states with distinct characteristics. The breaking
of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac
fermions. Here, we report high-resolution scanning tunneling microscopy studies
of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected
by crystal symmetry with massive Dirac fermions consistent with crystal symmetry
breaking. In addition, we show two distinct regimes of the Fermi surface topology
separated by a Van-Hove singularity at the Lifshitz transition point. Our work
paves the way for engineering the Dirac band gap and realizing interaction-driven
topological quantum phenomena in TCIs.
arxiv: 1
author:
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Chetan
full_name: Dhital, Chetan
last_name: Dhital
- first_name: Madhab
full_name: Neupane, Madhab
last_name: Neupane
- first_name: Suyang
full_name: Xu, Suyang
last_name: Xu
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Md
full_name: Hasan, Md
last_name: Hasan
- first_name: Stephen
full_name: Wilson, Stephen
last_name: Wilson
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass
acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499.
doi:10.1126/science.1239451
apa: Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan,
V. (2013). Observation of dirac node formation and mass acquisition in a topological
crystalline insulator. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1239451
chicago: Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou,
Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and
Mass Acquisition in a Topological Crystalline Insulator.” Science. American
Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451.
ieee: Y. Okada et al., “Observation of dirac node formation and mass acquisition
in a topological crystalline insulator,” Science, vol. 341, no. 6153. American
Association for the Advancement of Science, pp. 1496–1499, 2013.
ista: Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang
Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation
of dirac node formation and mass acquisition in a topological crystalline insulator.
Science. 341(6153), 1496–1499.
mla: Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition
in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American
Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451.
short: Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S.
Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan,
Science 341 (2013) 1496–1499.
date_created: 2018-12-11T11:49:29Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:20Z
day: '01'
doi: 10.1126/science.1239451
extern: '1'
external_id:
arxiv:
- '1305.2823'
intvolume: ' 341'
issue: '6153'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.2823
month: '01'
oa: 1
oa_version: Preprint
page: 1496 - 1499
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6430'
quality_controlled: '1'
status: public
title: Observation of dirac node formation and mass acquisition in a topological crystalline
insulator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 341
year: '2013'
...
---
_id: '973'
abstract:
- lang: eng
text: We construct a complete set of local integrals of motion that characterize
the many-body localized (MBL) phase. Our approach relies on the assumption that
local perturbations act locally on the eigenstates in the MBL phase, which is
supported by numerical simulations of the random-field XXZ spin chain. We describe
the structure of the eigenstates in the MBL phase and discuss the implications
of local conservation laws for its nonequilibrium quantum dynamics. We argue that
the many-body localization can be used to protect coherence in the system by suppressing
relaxation between eigenstates with different local integrals of motion.
acknowledgement: We thank J. Moore for useful discussions. Research at Perimeter Institute
is supported by the Government of Canada through Industry Canada and by the Province
of Ontario through the Ministry of Economic Development & Innovation. Z. P. was
supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science
Foundation under Grant No. DMR-1104498. The simulations presented in this article
were performed on computational resources supported by the High Performance Computing
Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Local conservation laws and the structure of the
many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and
the structure of the many body localized states. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws
and the Structure of the Many Body Localized States.” Physical Review Letters.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure
of the many body localized states,” Physical Review Letters, vol. 111,
no. 12. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure
of the many body localized states. Physical Review Letters. 111(12).
mla: Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many
Body Localized States.” Physical Review Letters, vol. 111, no. 12, American
Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-09-17T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '17'
doi: 10.1103/PhysRevLett.111.127201
extern: 1
intvolume: ' 111'
issue: '12'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1305.5554
month: '09'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6424'
quality_controlled: 0
status: public
title: Local conservation laws and the structure of the many body localized states
type: journal_article
volume: 111
year: '2013'
...
---
_id: '974'
abstract:
- lang: eng
text: We propose a possible realization of the overscreened Kondo impurity problem
by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid
with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid
behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid
fixed point in the overscreened Kondo problem. Using a large-N expansion together
with an expansion in the dynamical exponent of the gauge field, we find that the
coupling to the gauge field leads to weak but observable changes in the physical
properties of the system at the overscreened Kondo fixed point. We discuss the
extrapolation of this result to a physical case and argue that the realization
of overscreened Kondo physics could lead to observations of effects due to gauge
fields.
arxiv: 1
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Todadri
full_name: Senthil, Todadri
last_name: Senthil
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid.
Physical Review B - Condensed Matter and Materials Physics. 2013;88(2).
doi:10.1103/PhysRevB.88.024419
apa: Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point
in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419
chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed
Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419.
ieee: M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1
spin liquid,” Physical Review B - Condensed Matter and Materials Physics,
vol. 88, no. 2. American Physical Society, 2013.
ista: Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin
liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2).
mla: Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.”
Physical Review B - Condensed Matter and Materials Physics, vol. 88, no.
2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419.
short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials
Physics 88 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-07-19T00:00:00Z
date_updated: 2021-01-12T08:22:21Z
day: '19'
doi: 10.1103/PhysRevB.88.024419
extern: '1'
external_id:
arxiv:
- '1212.5179'
intvolume: ' 88'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1212.5179
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6425'
quality_controlled: '1'
status: public
title: Overscreened Kondo fixed point in S=1 spin liquid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2013'
...
---
_id: '9749'
abstract:
- lang: eng
text: Cooperative behavior, where one individual incurs a cost to help another,
is a wide spread phenomenon. Here we study direct reciprocity in the context of
the alternating Prisoner's Dilemma. We consider all strategies that can be implemented
by one and two-state automata. We calculate the payoff matrix of all pairwise
encounters in the presence of noise. We explore deterministic selection dynamics
with and without mutation. Using different error rates and payoff values, we observe
convergence to a small number of distinct equilibria. Two of them are uncooperative
strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium
is mixed and represents a cooperative alliance of several strategies, dominated
by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent
has cooperated; it defects once when the opponent has defected, but subsequently
Forgiver attempts to re-establish cooperation even if the opponent has defected
again. Forgiver is not an evolutionarily stable strategy, but the alliance, which
it rules, is asymptotically stable. For a wide range of parameter values the most
commonly observed outcome is convergence to the mixed equilibrium, dominated by
Forgiver. Our results show that although forgiving might incur a short-term loss
it can lead to a long-term gain. Forgiveness facilitates stable cooperation in
the presence of exploitation and noise.
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Zagorsky, Benjamin
last_name: Zagorsky
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- 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: Nowak, Martin
last_name: Nowak
citation:
ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating
prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001
apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver
triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001
chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin
Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library
of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001.
ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in
alternating prisoner’s dilemma .” Public Library of Science, 2013.
ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating
prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001.
mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma
. Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001.
short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).
date_created: 2021-07-28T15:45:07Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2025-09-29T14:30:03Z
day: '12'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0080814.s001
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2247'
relation: used_in_publication
status: public
status: public
title: 'Forgiver triumphs in alternating prisoner''s dilemma '
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '975'
abstract:
- lang: eng
text: Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic
in time, growth of the entanglement entropy for initial product states in a putative
many-body localized phase. We show that this surprising phenomenon results from
the dephasing due to exponentially small interaction-induced corrections to the
eigenenergies of different states. For weak interactions, we find that the entanglement
entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the
single-particle localization length. The saturated value of the entanglement entropy
at long times is determined by the participation ratios of the initial state over
the eigenstates of the subsystem. Our work shows that the logarithmic entanglement
growth is a universal phenomenon characteristic of the many-body localized phase
in any number of spatial dimensions, and reveals a broad hierarchy of dephasing
time scales present in such a phase.
acknowledgement: We would like to thank E. Altman and J. Moore for useful comments
on the manuscript. This research was supported in part by Perimeter Institute for
Theoretical Physics. Research at Perimeter Institute is supported by the Government
of Canada through Industry Canada and by the Province of Ontario through the Ministry
of Economic Development & Innovation. Z. P. was supported by DOE Grant No. DE-SC0002140.
The simulations presented in this article were performed on computational resources
supported by the High Performance Computing Center (PICSciE) at Princeton University.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Universal slow growth of entanglement in interacting
strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601
apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement
in interacting strongly disordered systems. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth
of Entanglement in Interacting Strongly Disordered Systems.” Physical Review
Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement
in interacting strongly disordered systems,” Physical Review Letters, vol.
110, no. 26. American Physical Society, 2013.
ista: Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in
interacting strongly disordered systems. Physical Review Letters. 110(26).
mla: Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting
Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26,
American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:49:29Z
date_published: 2013-06-28T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '28'
doi: 10.1103/PhysRevLett.110.260601
extern: 1
intvolume: ' 110'
issue: '26'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.4605
month: '06'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6426'
quality_controlled: 0
status: public
title: Universal slow growth of entanglement in interacting strongly disordered systems
type: journal_article
volume: 110
year: '2013'
...
---
_id: '9751'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence
for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding
to the attack of an obligately lytic phage by committing suicide in order to prevent
parasite transmission to nearby relatives. We found that bacterial suicide provides
large benefits to survivors at marginal costs to committers. The cost of suicide
was low because infected cells are moribund, rapidly dying upon phage infection,
such that no more opportunity for reproduction remains. As a consequence of its
marginal cost, host suicide was selectively favoured even when relatedness between
committers and survivors approached zero. Altogether, our findings demonstrate
that low-cost suicide can evolve with ease, represents an effective host-defence
strategy, and seems to be widespread among microbes. Moreover, low-cost suicide
might also occur in higher organisms as exemplified by infected social insect
workers leaving the colony to die in isolation.
article_processing_charge: No
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness
is low: evidence from bacteria committing suicide upon phage infection. 2013.
doi:10.5061/dryad.b1q2n'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism
can evolve when relatedness is low: evidence from bacteria committing suicide
upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism
Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide
upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection.” Dryad, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection, Dryad, 10.5061/dryad.b1q2n.'
mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness
Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad,
2013, doi:10.5061/dryad.b1q2n.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013).
date_created: 2021-07-30T08:08:09Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2025-09-29T13:41:12Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.b1q2n
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.b1q2n
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2853'
relation: used_in_publication
status: public
status: public
title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria
committing suicide upon phage infection'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- 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: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2025-09-29T11:38:51Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '976'
abstract:
- lang: eng
text: 'Motivated by a search for experimental probes to access the physics of fractionalized
excitations called spinons in spin liquids, we study the interaction of spinons
with lattice vibrations. We consider the case of algebraic spin liquid, when spinons
have fermionic statistics and a Dirac-like dispersion. We establish the general
procedure for deriving spinon-phonon interactions, which is based on symmetry
considerations. The procedure is illustrated for four different algebraic spin
liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on
a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy
description is similar for all these phases, different underlying symmetry groups
lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit
form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound
in an algebraic spin liquid. The prospects of the sound attenuation as a probe
of spinons are discussed.'
acknowledgement: M. S. is grateful to X.-G. Wen, L. Levitov, M. Metlitski, K. Michaeli,
K.-T. Chen, and A. Potter for many useful discussions. We acknowledge support by
Grant No. NSF DMR 1104498. We acknowledge the hospitality of KITP, where final stages
of this project were completed.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Patrick
full_name: Lee, Patrick
last_name: Lee
citation:
ama: Serbyn M, Lee P. Spinon-phonon interaction in algebraic spin liquids. Physical
Review B - Condensed Matter and Materials Physics. 2013;87(17). doi:10.1103/PhysRevB.87.174424
apa: Serbyn, M., & Lee, P. (2013). Spinon-phonon interaction in algebraic spin
liquids. Physical Review B - Condensed Matter and Materials Physics. American
Physical Society. https://doi.org/10.1103/PhysRevB.87.174424
chicago: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic
Spin Liquids.” Physical Review B - Condensed Matter and Materials Physics.
American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.174424.
ieee: M. Serbyn and P. Lee, “Spinon-phonon interaction in algebraic spin liquids,”
Physical Review B - Condensed Matter and Materials Physics, vol. 87, no.
17. American Physical Society, 2013.
ista: Serbyn M, Lee P. 2013. Spinon-phonon interaction in algebraic spin liquids.
Physical Review B - Condensed Matter and Materials Physics. 87(17).
mla: Serbyn, Maksym, and Patrick Lee. “Spinon-Phonon Interaction in Algebraic Spin
Liquids.” Physical Review B - Condensed Matter and Materials Physics, vol.
87, no. 17, American Physical Society, 2013, doi:10.1103/PhysRevB.87.174424.
short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics
87 (2013).
date_created: 2018-12-11T11:49:30Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2021-01-12T08:22:22Z
day: '22'
doi: 10.1103/PhysRevB.87.174424
extern: 1
intvolume: ' 87'
issue: '17'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1303.0772
month: '05'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6427'
quality_controlled: 0
status: public
title: Spinon-phonon interaction in algebraic spin liquids
type: journal_article
volume: 87
year: '2013'
...
---
_id: '476'
abstract:
- lang: eng
text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold
increase in the risk of schizophrenia in the offspring. The critical initiating
factor appears to be the maternal immune activation (MIA) that follows infection.
This process can be induced in rodents by exposure of pregnant dams to the viral
mimic Poly I:C, which triggers an immune response that results in structural,
functional, behavioral, and electrophysiological phenotypes in the adult offspring
that model those seen in schizophrenia. We used this model to explore the role
of synchronization in brain neural networks, a process thought to be dysfunctional
in schizophrenia and previously associated with positive, negative, and cognitive
symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced
an impairment in long-range neural synchrony in adult offspring between two regions
implicated in schizophrenia pathology; the hippocampus and the medial prefrontal
cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the
antipsychotic clozapine. MIA animals have previously been shown to have impaired
pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits
in animal models. Our data showed that deficits in synchrony were positively correlated
with the impairments in PPI. Subsequent analysis of LFP activity during the PPI
response also showed that reduced coupling between the mPFC and the hippocampus
following processing of the pre-pulse was associated with reduced PPI. The ability
of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology
provides a useful platform from which to investigate the ontogeny of aberrant
synchronous processes. Further, the way in which the model expresses translatable
deficits such as aberrant synchrony and reduced PPI will allow researchers to
explore novel intervention strategies targeted to these changes. '
article_processing_charge: No
author:
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: David
full_name: Bilkey, David
last_name: Bilkey
citation:
ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation
model: Using translatable measures to explore targeted interventions. Frontiers
in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217'
apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal
immune activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217'
chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the
Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted
Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.'
ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions,”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research
Foundation, 2013.'
ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. 7(DEC).'
mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal
Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research
Foundation, 2013, doi:10.3389/fnbeh.2013.00217.'
short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).
date_created: 2018-12-11T11:46:41Z
date_published: 2013-12-27T00:00:00Z
date_updated: 2025-09-30T07:30:04Z
day: '27'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.3389/fnbeh.2013.00217
external_id:
isi:
- '000329175600001'
file:
- access_level: open_access
checksum: cd7183121e56251176100ccac165c95c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:10Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5128'
file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf
file_size: 530134
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: DEC
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Frontiers in Behavioral Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7346'
pubrep_id: '953'
quality_controlled: '1'
status: public
title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable
measures to explore targeted interventions'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
article_processing_charge: No
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- 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: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2025-09-30T07:29:30Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
external_id:
isi:
- '000312985800059'
intvolume: ' 339'
isi: 1
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 339
year: '2013'
...
---
_id: '500'
abstract:
- lang: eng
text: 'Background: Reassortment between the RNA segments encoding haemagglutinin
(HA) and neuraminidase (NA), the major antigenic influenza proteins, produces
viruses with novel HA and NA subtype combinations and has preceded the emergence
of pandemic strains. It has been suggested that productive viral infection requires
a balance in the level of functional activity of HA and NA, arising from their
closely interacting roles in the viral life cycle, and that this functional balance
could be mediated by genetic changes in the HA and NA. Here, we investigate how
the selective pressure varies for H7 avian influenza HA on different NA subtype
backgrounds. Results: By extending Bayesian stochastic mutational mapping methods
to calculate the ratio of the rate of non-synonymous change to the rate of synonymous
change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1
region to be significantly greater on an N2 NA subtype background than on an N1,
N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different
NA subtype backgrounds could not be attributed to underlying differences between
avian host species or virus pathogenicity. Examination of d N/d S values for each
subtype on a site-by-site basis indicated that the elevated d N/d S on the N2
NA background was a result of increased selection, rather than a relaxation of
selective constraint. Conclusions: Our results are consistent with the hypothesis
that reassortment exposes influenza HA to significant changes in selective pressure
through genetic interactions with NA. Such epistatic effects might be explicitly
accounted for in future models of influenza evolution.'
acknowledgement: "This work was supported by the Biotechnology and Biological Sciences
Research Council, the Government of the Republic of Panama, the Interdisciplinary
Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the
Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC
BY 2.0\r\n"
article_number: '222'
article_processing_charge: No
author:
- first_name: Melissa
full_name: Ward, Melissa
last_name: Ward
- first_name: Samantha
full_name: Lycett, Samantha
last_name: Lycett
- first_name: Dorita
full_name: Avila, Dorita
last_name: Avila
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Leigh Brown, Andrew
last_name: Leigh Brown
citation:
ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions
between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013).
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and
Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase
in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.
ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza,” BMC
Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza. BMC
Evolutionary Biology. 13(1), 222.
mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and
Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no.
1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:46:49Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2025-09-30T07:28:51Z
day: '09'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-222
external_id:
isi:
- '000326620200001'
file:
- access_level: open_access
checksum: 52cf48a7c1794676ae8b0029573a84a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4722'
file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf
file_size: 1150052
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '7320'
pubrep_id: '941'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interactions between haemagglutinin and neuraminidase in avian
influenza
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
article_processing_charge: No
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2025-09-30T07:28:20Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
external_id:
isi:
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publication: Journal of Mammalogy
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title: A new species of tapir from the Amazon
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