---
_id: '17693'
abstract:
- lang: eng
text: We perform one-dimensional radiation hydrodynamical simulations to solve accretion
flows onto massive black holes (BHs) with a very high rate. Assuming that photon
trapping limits the luminosity emerging from the central region to L≲LEdd, Inayoshi,
Haiman & Ostriker (2016) have shown that an accretion flow settles to a "hyper-Eddington"
solution, with a steady and isothermal (T≃8000 K) Bondi profile reaching ≳5000
times the Eddington accretion rate M˙Edd≡LEdd/c2. Here we address the possibility
that gas accreting with finite angular momentum forms a bright nuclear accretion
disc, with a luminosity exceeding the Eddington limit (1≲L/LEdd≲100). Combining
our simulations with an analytic model, we find that a transition to steady hyper-Eddington
accretion still occurs, as long as the luminosity remains below L/LEdd≲35 (MBH/10^4
M⊙)^3/2(n∞/10^5 cm^−3)(T∞/10^4 K)^−3/2(r⋆/10^14 cm)^−1/2, where n∞ and T∞ are
the density and temperature of the ambient gas, and r⋆ is the radius of the photosphere,
at which radiation emerges. If the luminosity exceeds this value, accretion becomes
episodic. Our results can be accurately recovered in a toy model of an optically
thick spherical shell, driven by radiation force into a collapsing medium. When
the central source is dimmer than the above critical value, the expansion of the
shell is halted and reversed by ram pressure of the collapsing medium, and by
shell's weight. Our results imply that rapid, unimpeded hyper-Eddington accretion
is possible even if the luminosity of the central source far exceeds the Eddington
limit, and can be either steady or strongly episodic.
article_processing_charge: No
article_type: original
author:
- first_name: Yuya
full_name: Sakurai, Yuya
last_name: Sakurai
- first_name: Kohei
full_name: Inayoshi, Kohei
last_name: Inayoshi
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Sakurai Y, Inayoshi K, Haiman Z. Hyper-Eddington mass accretion on to a black
hole with super-Eddington luminosity. Monthly Notices of the Royal Astronomical
Society. 2016;461(4):4496-4504. doi:10.1093/mnras/stw1652
apa: Sakurai, Y., Inayoshi, K., & Haiman, Z. (2016). Hyper-Eddington mass accretion
on to a black hole with super-Eddington luminosity. Monthly Notices of the
Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw1652
chicago: Sakurai, Yuya, Kohei Inayoshi, and Zoltán Haiman. “Hyper-Eddington Mass
Accretion on to a Black Hole with Super-Eddington Luminosity.” Monthly Notices
of the Royal Astronomical Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw1652.
ieee: Y. Sakurai, K. Inayoshi, and Z. Haiman, “Hyper-Eddington mass accretion on
to a black hole with super-Eddington luminosity,” Monthly Notices of the Royal
Astronomical Society, vol. 461, no. 4. Oxford University Press, pp. 4496–4504,
2016.
ista: Sakurai Y, Inayoshi K, Haiman Z. 2016. Hyper-Eddington mass accretion on to
a black hole with super-Eddington luminosity. Monthly Notices of the Royal Astronomical
Society. 461(4), 4496–4504.
mla: Sakurai, Yuya, et al. “Hyper-Eddington Mass Accretion on to a Black Hole with
Super-Eddington Luminosity.” Monthly Notices of the Royal Astronomical Society,
vol. 461, no. 4, Oxford University Press, 2016, pp. 4496–504, doi:10.1093/mnras/stw1652.
short: Y. Sakurai, K. Inayoshi, Z. Haiman, Monthly Notices of the Royal Astronomical
Society 461 (2016) 4496–4504.
date_created: 2024-09-06T08:39:53Z
date_published: 2016-07-08T00:00:00Z
date_updated: 2024-09-25T10:02:57Z
day: '08'
doi: 10.1093/mnras/stw1652
extern: '1'
intvolume: ' 461'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/mnras/stw1652
month: '07'
oa: 1
oa_version: Published Version
page: 4496-4504
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hyper-Eddington mass accretion on to a black hole with super-Eddington luminosity
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 461
year: '2016'
...
---
_id: '17699'
abstract:
- lang: eng
text: 'We quantify the presence of Ly\alpha\ damping wing absorption from a partially-neutral
intergalactic medium (IGM) in the spectrum of the z=7.08 QSO, ULASJ1120+0641.
Using a Bayesian framework, we simultaneously account for uncertainties in: (i)
the intrinsic QSO emission spectrum; and (ii) the distribution of cosmic HI patches
during the epoch of reionisation (EoR). For (i) we use a new intrinsic Ly\alpha\
emission line reconstruction method (Greig et al.), sampling a covariance matrix
of emission line properties built from a large database of moderate-z QSOs. For
(ii), we use the Evolution of 21-cm Structure (EOS; Mesinger et al.) simulations,
which span a range of physically-motivated EoR models. We find strong evidence
for the presence of damping wing absorption redward of Ly\alpha\ (where there
is no contamination from the Ly\alpha\ forest). Our analysis implies that the
EoR is not yet complete by z=7.1, with the volume-weighted IGM neutral fraction
constrained to x¯HI=0.40+0.21−0.19 at 1σ (x¯HI=0.40+0.41−0.32 at 2σ). This result
is insensitive to the EoR morphology. Our detection of significant neutral HI
in the IGM at z=7.1 is consistent with the latest Planck 2016 measurements of
the CMB Thompson scattering optical depth (Planck Collaboration XLVII).'
article_number: stw3351
article_processing_charge: No
article_type: original
author:
- first_name: Bradley
full_name: Greig, Bradley
last_name: Greig
- first_name: Andrei
full_name: Mesinger, Andrei
last_name: Mesinger
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Robert A.
full_name: Simcoe, Robert A.
last_name: Simcoe
citation:
ama: Greig B, Mesinger A, Haiman Z, Simcoe RA. Are we witnessing the epoch of reionization
at z=7.1 from the spectrum of J1120+0641? Monthly Notices of the Royal Astronomical
Society. 2016. doi:10.1093/mnras/stw3351
apa: Greig, B., Mesinger, A., Haiman, Z., & Simcoe, R. A. (2016). Are we witnessing
the epoch of reionization at z=7.1 from the spectrum of J1120+0641? Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw3351
chicago: Greig, Bradley, Andrei Mesinger, Zoltán Haiman, and Robert A. Simcoe. “Are
We Witnessing the Epoch of Reionization at Z=7.1 from the Spectrum of J1120+0641?”
Monthly Notices of the Royal Astronomical Society. Oxford University Press,
2016. https://doi.org/10.1093/mnras/stw3351.
ieee: B. Greig, A. Mesinger, Z. Haiman, and R. A. Simcoe, “Are we witnessing the
epoch of reionization at z=7.1 from the spectrum of J1120+0641?,” Monthly Notices
of the Royal Astronomical Society. Oxford University Press, 2016.
ista: Greig B, Mesinger A, Haiman Z, Simcoe RA. 2016. Are we witnessing the epoch
of reionization at z=7.1 from the spectrum of J1120+0641? Monthly Notices of the
Royal Astronomical Society., stw3351.
mla: Greig, Bradley, et al. “Are We Witnessing the Epoch of Reionization at Z=7.1
from the Spectrum of J1120+0641?” Monthly Notices of the Royal Astronomical
Society, stw3351, Oxford University Press, 2016, doi:10.1093/mnras/stw3351.
short: B. Greig, A. Mesinger, Z. Haiman, R.A. Simcoe, Monthly Notices of the Royal
Astronomical Society (2016).
date_created: 2024-09-06T08:45:10Z
date_published: 2016-12-24T00:00:00Z
date_updated: 2024-09-25T11:19:08Z
day: '24'
doi: 10.1093/mnras/stw3351
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/mnras/stw3351
month: '12'
oa: 1
oa_version: Published Version
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are we witnessing the epoch of reionization at z=7.1 from the spectrum of J1120+0641?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2016'
...
---
_id: '17700'
abstract:
- lang: eng
text: We report the formation of intermediate-mass black holes (IMBHs) in suites
of numerical N-body simulations of Population III remnant black holes (BHs) embedded
in gas-rich protogalaxies at redshifts z≳10. We model the effects of gas drag
on the BHs' orbits, and allow BHs to grow via gas accretion, including a mode
of hyper-Eddington accretion in which photon trapping and rapid gas inflow suppress
any negative radiative feedback. Most initial BH configurations lead to the formation
of one (but never more than one) IMBH in the center of the protogalaxy, reaching
a mass of 10^3−5M⊙ through hyper-Eddington growth. Our results suggest a viable
pathway to forming the earliest massive BHs in the centers of early galaxies.
We also find that the nuclear IMBH typically captures a stellar-mass BH companion,
making these systems observable in gravitational waves as extreme mass-ratio inspirals
(EMRIs) with eLISA.
article_processing_charge: No
article_type: original
author:
- first_name: Taeho
full_name: Ryu, Taeho
last_name: Ryu
- first_name: Takamitsu L.
full_name: Tanaka, Takamitsu L.
last_name: Tanaka
- first_name: Rosalba
full_name: Perna, Rosalba
last_name: Perna
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
citation:
ama: Ryu T, Tanaka TL, Perna R, Haiman Z. Intermediate-mass black holes from Population
III remnants in the first galactic nuclei. Monthly Notices of the Royal Astronomical
Society. 2016;460(4):4122-4134. doi:10.1093/mnras/stw1241
apa: Ryu, T., Tanaka, T. L., Perna, R., & Haiman, Z. (2016). Intermediate-mass
black holes from Population III remnants in the first galactic nuclei. Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw1241
chicago: Ryu, Taeho, Takamitsu L. Tanaka, Rosalba Perna, and Zoltán Haiman. “Intermediate-Mass
Black Holes from Population III Remnants in the First Galactic Nuclei.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2016.
https://doi.org/10.1093/mnras/stw1241.
ieee: T. Ryu, T. L. Tanaka, R. Perna, and Z. Haiman, “Intermediate-mass black holes
from Population III remnants in the first galactic nuclei,” Monthly Notices
of the Royal Astronomical Society, vol. 460, no. 4. Oxford University Press,
pp. 4122–4134, 2016.
ista: Ryu T, Tanaka TL, Perna R, Haiman Z. 2016. Intermediate-mass black holes from
Population III remnants in the first galactic nuclei. Monthly Notices of the Royal
Astronomical Society. 460(4), 4122–4134.
mla: Ryu, Taeho, et al. “Intermediate-Mass Black Holes from Population III Remnants
in the First Galactic Nuclei.” Monthly Notices of the Royal Astronomical Society,
vol. 460, no. 4, Oxford University Press, 2016, pp. 4122–34, doi:10.1093/mnras/stw1241.
short: T. Ryu, T.L. Tanaka, R. Perna, Z. Haiman, Monthly Notices of the Royal Astronomical
Society 460 (2016) 4122–4134.
date_created: 2024-09-06T08:46:28Z
date_published: 2016-05-24T00:00:00Z
date_updated: 2024-09-25T11:22:16Z
day: '24'
doi: 10.1093/mnras/stw1241
extern: '1'
intvolume: ' 460'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/mnras/stw1241
month: '05'
oa: 1
oa_version: Published Version
page: 4122-4134
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intermediate-mass black holes from Population III remnants in the first galactic
nuclei
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 460
year: '2016'
...
---
_id: '17709'
abstract:
- lang: eng
text: 'We study very-high rate spherically symmetric accretion flows onto a massive
black hole (BH; 10^2 < M_BH < 10^6 Msun) embedded in a dense gas cloud with a
low abundance of metals, performing one-dimensional hydrodynamical simulations
which include multi-frequency radiation transfer and non-equilibrium primordial
chemistry. We find that rapid gas supply from the Bondi radius at a hyper-Eddington
rate can occur without being impeded by radiation feedback when (n/10^5 cm^-3)
> (M_BH/10^4Msun)^{-1}(T/10^4 K)^{3/2}, where n and T are the density and temperature
of ambient gas outside of the Bondi radius. The resulting accretion rate in this
regime is steady, and larger than 3000 times the Eddington rate. At lower Bondi
rates, the accretion is episodic due to radiative feedback and the average rate
is limited below the Eddington rate. For the hyper-Eddington case, the steady
solution consists of two parts: a radiation-dominated central core, where photon
trapping due to electron scattering is important, and an accreting envelope which
follows a Bondi profile with T~8000 K. When the emergent luminosity is limited
below the Eddington luminosity because of photon trapping, radiation from the
central region does not affect the gas dynamics at larger scales. We apply our
result to the rapid formation of massive BHs in protogalaxies with a virial temperature
of T_vir> 10^4 K. Once a seed BH forms at the center of the galaxy, it can grow
up to a maximum ~10^5 (T_vir/10^4 K) Msun via gas accretion independent of the
initial BH mass. Finally, we discuss possible observational signatures of rapidly
accreting BHs with/without allowance for dust. We suggest that these systems could
explain Lya emitters without X-rays and luminous infrared sources with hot dust
emission, respectively.'
article_processing_charge: No
article_type: original
author:
- first_name: Kohei
full_name: Inayoshi, Kohei
last_name: Inayoshi
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Jeremiah P.
full_name: Ostriker, Jeremiah P.
last_name: Ostriker
citation:
ama: Inayoshi K, Haiman Z, Ostriker JP. Hyper-Eddington accretion flows on to massive
black holes. Monthly Notices of the Royal Astronomical Society. 2016;459(4):3738-3755.
doi:10.1093/mnras/stw836
apa: Inayoshi, K., Haiman, Z., & Ostriker, J. P. (2016). Hyper-Eddington accretion
flows on to massive black holes. Monthly Notices of the Royal Astronomical
Society. Oxford University Press. https://doi.org/10.1093/mnras/stw836
chicago: Inayoshi, Kohei, Zoltán Haiman, and Jeremiah P. Ostriker. “Hyper-Eddington
Accretion Flows on to Massive Black Holes.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2016. https://doi.org/10.1093/mnras/stw836.
ieee: K. Inayoshi, Z. Haiman, and J. P. Ostriker, “Hyper-Eddington accretion flows
on to massive black holes,” Monthly Notices of the Royal Astronomical Society,
vol. 459, no. 4. Oxford University Press, pp. 3738–3755, 2016.
ista: Inayoshi K, Haiman Z, Ostriker JP. 2016. Hyper-Eddington accretion flows on
to massive black holes. Monthly Notices of the Royal Astronomical Society. 459(4),
3738–3755.
mla: Inayoshi, Kohei, et al. “Hyper-Eddington Accretion Flows on to Massive Black
Holes.” Monthly Notices of the Royal Astronomical Society, vol. 459, no.
4, Oxford University Press, 2016, pp. 3738–55, doi:10.1093/mnras/stw836.
short: K. Inayoshi, Z. Haiman, J.P. Ostriker, Monthly Notices of the Royal Astronomical
Society 459 (2016) 3738–3755.
date_created: 2024-09-06T08:54:12Z
date_published: 2016-04-12T00:00:00Z
date_updated: 2024-09-25T12:00:22Z
day: '12'
doi: 10.1093/mnras/stw836
extern: '1'
intvolume: ' 459'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/mnras/stw836
month: '04'
oa: 1
oa_version: Published Version
page: 3738-3755
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hyper-Eddington accretion flows on to massive black holes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 459
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'
...
---
_id: '8094'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. The idea is that the controller controls the world---the body plus
its environment---as reliably as possible. This paper focuses on new lines of
self-organization for developmental robotics. We apply the recently developed
differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder
system from the Myorobotics toolkit. In the experiments, we observe a vast variety
of self-organized behavior patterns: when left alone, the arm realizes pseudo-random
sequences of different poses. By applying physical forces, the system can be entrained
into definite motion patterns like wiping a table. Most interestingly, after attaching
an object, the controller gets in a functional resonance with the object''s internal
dynamics, starting to shake spontaneously bottles half-filled with water or sensitively
driving an attached pendulum into a circular mode. When attached to the crank
of a wheel the neural system independently discovers how to rotate it. In this
way, the robot discovers affordances of objects its body is interacting with.'
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Rafael
full_name: Hostettler, Rafael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon
driven arm by differential extrinsic plasticity. In: 15th International Conference
on the Synthesis and Simulation of Living Systems. Vol 28. MIT Press; 2016:142-143.
doi:10.7551/978-0-262-33936-0-ch029'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized
control of an tendon driven arm by differential extrinsic plasticity. In 15th
International Conference on the Synthesis and Simulation of Living Systems
(Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029'
chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized
Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In 15th
International Conference on the Synthesis and Simulation of Living Systems,
28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control
of an tendon driven arm by differential extrinsic plasticity,” in 15th International
Conference on the Synthesis and Simulation of Living Systems, Cancun, Mexico,
2016, vol. 28, pp. 142–143.
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of
an tendon driven arm by differential extrinsic plasticity. 15th International
Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference
on the Synthesis and Simulation of Living Systems vol. 28, 142–143.'
mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by
Differential Extrinsic Plasticity.” 15th International Conference on the Synthesis
and Simulation of Living Systems, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference
on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.
conference:
end_date: 2016-07-08
location: Cancun, Mexico
name: 'ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems'
start_date: 2016-07-04
corr_author: '1'
date_created: 2020-07-05T22:00:47Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2025-07-10T11:55:05Z
day: '01'
ddc:
- '610'
department:
- _id: ChLa
- _id: GaTk
doi: 10.7551/978-0-262-33936-0-ch029
ec_funded: 1
file:
- access_level: open_access
checksum: cff63e7a4b8ac466ba51a9c84153a940
content_type: application/pdf
creator: cziletti
date_created: 2020-07-06T12:59:09Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8096'
file_name: 2016_ProcALIFE_Martius.pdf
file_size: 678670
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 28'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 142-143
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 15th International Conference on the Synthesis and Simulation of Living
Systems
publication_identifier:
isbn:
- '9780262339360'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized control of an tendon driven arm by differential extrinsic plasticity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2016'
...
---
_id: '8128'
abstract:
- lang: eng
text: The stimulus selectivity of synaptic currents in cortical neurons often shows
a co-tuning of excitation and inhibition, but the mechanisms that underlie the
emergence and plasticity of this co-tuning are not fully understood. Using a computational
model, we show that an interaction of excitatory and inhibitory synaptic plasticity
reproduces both the developmental and – when combined with a disinhibitory gate
– the adult plasticity of excitatory and inhibitory receptive fields in auditory
cortex. The co-tuning arises from inhibitory plasticity that balances excitation
and inhibition, while excitatory stimulus selectivity can result from two different
mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding
threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus
selectivity at the cost of a broader inhibitory receptive field. Alternatively,
input asymmetries can be amplified by synaptic competition. The latter leaves
any receptive field plasticity transient, a prediction we verify in recordings
in auditory cortex.
article_processing_charge: No
author:
- first_name: Claudia
full_name: Clopath, Claudia
last_name: Clopath
- 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: Robert C.
full_name: Froemke, Robert C.
last_name: Froemke
- first_name: Henning
full_name: Sprekeler, Henning
last_name: Sprekeler
citation:
ama: Clopath C, Vogels TP, Froemke RC, Sprekeler H. Receptive field formation by
interacting excitatory and inhibitory synaptic plasticity. bioRxiv. 2016.
apa: Clopath, C., Vogels, T. P., Froemke, R. C., & Sprekeler, H. (2016). Receptive
field formation by interacting excitatory and inhibitory synaptic plasticity.
bioRxiv. Cold Spring Harbor Laboratory.
chicago: Clopath, Claudia, Tim P Vogels, Robert C. Froemke, and Henning Sprekeler.
“Receptive Field Formation by Interacting Excitatory and Inhibitory Synaptic Plasticity.”
BioRxiv. Cold Spring Harbor Laboratory, 2016.
ieee: C. Clopath, T. P. Vogels, R. C. Froemke, and H. Sprekeler, “Receptive field
formation by interacting excitatory and inhibitory synaptic plasticity,” bioRxiv.
Cold Spring Harbor Laboratory, 2016.
ista: Clopath C, Vogels TP, Froemke RC, Sprekeler H. 2016. Receptive field formation
by interacting excitatory and inhibitory synaptic plasticity. bioRxiv, .
mla: Clopath, Claudia, et al. “Receptive Field Formation by Interacting Excitatory
and Inhibitory Synaptic Plasticity.” BioRxiv, Cold Spring Harbor Laboratory,
2016.
short: C. Clopath, T.P. Vogels, R.C. Froemke, H. Sprekeler, BioRxiv (2016).
date_created: 2020-07-16T12:26:55Z
date_published: 2016-07-29T00:00:00Z
date_updated: 2021-01-12T08:17:02Z
day: '29'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/066589 '
month: '07'
oa: 1
oa_version: Preprint
page: '43'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Receptive field formation by interacting excitatory and inhibitory synaptic
plasticity
type: preprint
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
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
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: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- 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
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
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: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
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: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '948'
abstract:
- lang: eng
text: Experience constantly shapes neural circuits through a variety of plasticity
mechanisms. While the functional roles of some plasticity mechanisms are well-understood,
it remains unclear how changes in neural excitability contribute to learning.
Here, we develop a normative interpretation of intrinsic plasticity (IP) as a
key component of unsupervised learning. We introduce a novel generative mixture
model that accounts for the class-specific statistics of stimulus intensities,
and we derive a neural circuit that learns the input classes and their intensities.
We will analytically show that inference and learning for our generative model
can be achieved by a neural circuit with intensity-sensitive neurons equipped
with a specific form of IP. Numerical experiments verify our analytical derivations
and show robust behavior for artificial and natural stimuli. Our results link
IP to non-trivial input statistics, in particular the statistics of stimulus intensities
for classes to which a neuron is sensitive. More generally, our work paves the
way toward new classification algorithms that are robust to intensity variations.
acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1
(JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement
no. 291734 (CS)
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Travis
full_name: Monk, Travis
last_name: Monk
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jörg
full_name: Lücke, Jörg
last_name: Lücke
citation:
ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn
stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems
Foundation; 2016:4285-4293.'
apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic
plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented
at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural
Information Processing Systems Foundation.'
chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic
Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information
Processing Systems Foundation, 2016.
ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics,” presented at the NIPS: Neural Information
Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.'
ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 4285–4293.'
mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus
Intensity Statistics. Vol. 29, Neural Information Processing Systems Foundation,
2016, pp. 4285–93.
short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation,
2016, pp. 4285–4293.
conference:
end_date: 2016-12-10
location: Barcelona, Spaine
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:49:21Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-06-03T11:18:32Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics
month: '01'
oa: 1
oa_version: None
page: 4285 - 4293
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6469'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '9591'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Combinatorics, Probability and Computing. 2016;25(6):909-927.
doi:10.1017/s0963548316000079
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2016). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability
and Computing. Cambridge University Press. https://doi.org/10.1017/s0963548316000079
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Combinatorics, Probability
and Computing. Cambridge University Press, 2016. https://doi.org/10.1017/s0963548316000079.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Combinatorics, Probability and Computing,
vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.
ista: Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing.
25(6), 909–927.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Combinatorics, Probability and Computing, vol. 25, no.
6, Cambridge University Press, 2016, pp. 909–27, doi:10.1017/s0963548316000079.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing
25 (2016) 909–927.
date_created: 2021-06-22T12:35:13Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T14:02:07Z
day: '01'
doi: 10.1017/s0963548316000079
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 25'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 909-927
publication: Combinatorics, Probability and Computing
publication_identifier:
eissn:
- 1469-2163
issn:
- 0963-5483
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 25
year: '2016'
...