---
_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'
...
---
_id: '9704'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence
of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1'
apa: 'Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1'
chicago: 'Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated
Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad,
2016. https://doi.org/10.5061/dryad.cq7t1.'
ieee: 'D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral
genotype as a driver of honeybee loss.” Dryad, 2016.'
ista: 'Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.'
mla: 'Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral
Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.'
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, (2016).
date_created: 2021-07-23T08:30:38Z
date_published: 2016-05-06T00:00:00Z
date_updated: 2025-09-22T08:59:29Z
day: '06'
department:
- _id: SyCr
doi: 10.5061/dryad.cq7t1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cq7t1
month: '05'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1262'
relation: used_in_publication
status: public
status: public
title: 'Data from: Elevated virulence of an emerging viral genotype as a driver of
honeybee loss'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2025-04-15T07:11:02Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9720'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A
sting in the spit: widespread cross-infection of multiple RNA viruses across wild
and managed bees. 2016. doi:10.5061/dryad.4b565'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple
RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees.” Dryad, 2016.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees, Dryad, 10.5061/dryad.4b565.'
mla: 'Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).
date_created: 2021-07-26T09:14:19Z
date_published: 2016-01-22T00:00:00Z
date_updated: 2025-09-23T07:26:23Z
day: '22'
department:
- _id: SyCr
doi: 10.5061/dryad.4b565
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.4b565
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1855'
relation: used_in_publication
status: public
status: public
title: 'Data from: A sting in the spit: widespread cross-infection of multiple RNA
viruses across wild and managed bees'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '478'
abstract:
- lang: eng
text: 'Magic: the Gathering is a game about magical combat for any number of players.
Formally it is a zero-sum, imperfect information stochastic game that consists
of a potentially unbounded number of steps. We consider the problem of deciding
if a move is legal in a given single step of Magic. We show that the problem is
(a) coNP-complete in general; and (b) in P if either of two small sets of cards
are not used. Our lower bound holds even for single-player Magic games. The significant
aspects of our results are as follows: First, in most real-life game problems,
the task of deciding whether a given move is legal in a single step is trivial,
and the computationally hard task is to find the best sequence of legal moves
in the presence of multiple players. In contrast, quite uniquely our hardness
result holds for single step and with only one-player. Second, we establish efficient
algorithms for important special cases of Magic.'
alternative_title:
- Frontiers in Artificial Intelligence and Applications
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single
step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:10.3233/978-1-61499-672-9-1432'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2016). The complexity of deciding
legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented
at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands:
IOS Press. https://doi.org/10.3233/978-1-61499-672-9-1432'
chicago: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016.
https://doi.org/10.3233/978-1-61499-672-9-1432.'
ieee: 'K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of
a single step of magic: The gathering,” presented at the ECAI: European Conference
on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.'
ista: 'Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of
a single step of magic: The gathering. ECAI: European Conference on Artificial
Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285,
1432–1439.'
mla: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering. Vol. 285, IOS Press, 2016,
pp. 1432–39, doi:10.3233/978-1-61499-672-9-1432.'
short: K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.
conference:
end_date: 2016-09-02
location: The Hague, Netherlands
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2016-08-29
corr_author: '1'
date_created: 2018-12-11T11:46:41Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-09-22T14:26:27Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.3233/978-1-61499-672-9-1432
external_id:
isi:
- '000385793700166'
file:
- access_level: open_access
checksum: 848043c812ace05e459579c923f3d3cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:59Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4658'
file_name: IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf
file_size: 2116225
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 285'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1432 - 1439
publication_status: published
publisher: IOS Press
publist_id: '7342'
pubrep_id: '950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The complexity of deciding legality of a single step of magic: The gathering'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 285
year: '2016'
...
---
_id: '480'
abstract:
- lang: eng
text: Graph games provide the foundation for modeling and synthesizing reactive
processes. In the synthesis of stochastic reactive processes, the traditional
model is perfect-information stochastic games, where some transitions of the game
graph are controlled by two adversarial players, and the other transitions are
executed probabilistically. We consider such games where the objective is the
conjunction of several quantitative objectives (specified as mean-payoff conditions),
which we refer to as generalized mean-payoff objectives. The basic decision problem
asks for the existence of a finite-memory strategy for a player that ensures the
generalized mean-payoff objective be satisfied with a desired probability against
all strategies of the opponent. A special case of the decision problem is the
almost-sure problem where the desired probability is 1. Previous results presented
a semi-decision procedure for -approximations of the almost-sure problem. In this
work, we show that both the almost-sure problem as well as the general basic decision
problem are coNP-complete, significantly improving the previous results. Moreover,
we show that in the case of 1-player stochastic games, randomized memoryless strategies
are sufficient and the problem can be solved in polynomial time. In contrast,
in two-player stochastic games, we show that even with randomized strategies exponential
memory is required in general, and present a matching exponential upper bound.
We also study the basic decision problem with infinite-memory strategies and present
computational complexity results for the problem. Our results are relevant in
the synthesis of stochastic reactive systems with multiple quantitative requirements.
alternative_title:
- Proceedings Symposium on Logic in Computer Science
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Perfect-information stochastic games with generalized
mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:10.1145/2933575.2934513'
apa: 'Chatterjee, K., & Doyen, L. (2016). Perfect-information stochastic games
with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented
at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934513'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE,
2016. https://doi.org/10.1145/2933575.2934513.
ieee: 'K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized
mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New
York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.'
ista: 'Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized
mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium
on Logic in Computer Science, vol. 05-08-July-2016, 247–256.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives. Vol. 05-08-July-2016, IEEE,
2016, pp. 247–56, doi:10.1145/2933575.2934513.
short: K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:46:42Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2025-09-22T14:22:08Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2934513
ec_funded: 1
external_id:
arxiv:
- '1604.06376'
isi:
- '000387609200025'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06376
month: '07'
oa: 1
oa_version: Preprint
page: 247 - 256
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: IEEE
publist_id: '7340'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Perfect-information stochastic games with generalized mean-payoff objectives
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 05-08-July-2016
year: '2016'
...
---
_id: '510'
abstract:
- lang: eng
text: 'The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted
signaling peptides that are primarily involved in the regulation of stem cell
homeostasis in different plant meristems. Particularly, the characterization of
the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on
the potential roles of CLE peptides in vascular development and wood formation.
Nevertheless, our knowledge on this gene family in a tree species is limited.
In a recent study, we reported on a systematically investigation of the CLE gene
family in Populus trichocarpa . The potential roles of PtCLE genes were studied
by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members,
many PtCLE proteins share identical CLE motifs or contain the same CLE motif as
that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression
patterns comparing to their Arabidopsis counterparts. These fi ndings indicate
the existence of both functional conservation and functional divergence between
PtCLEs and their AtCLE orthologues. Our results provide valuable resources for
future functional investigations of these critical signaling molecules in woody
plants. '
acknowledgement: 'We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement
des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading
of the article. Work in our group is supported by the National Natural Science Foundation
of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ
ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of
Higher Education from the Ministry of Education of China (20120202120009), the Scientific
Research Foundation for the Returned Overseas Chinese Scholars, State Education
Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China
(2014JM3064). '
article_number: e1191734
article_processing_charge: No
author:
- first_name: Zhijun
full_name: Liu, Zhijun
last_name: Liu
- first_name: 'Nan'
full_name: Yang, Nan
last_name: Yang
- first_name: Yanting
full_name: Lv, Yanting
last_name: Lv
- first_name: Lixia
full_name: Pan, Lixia
last_name: Pan
- first_name: Shuo
full_name: Lv, Shuo
last_name: Lv
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Guodong
full_name: Wang, Guodong
last_name: Wang
citation:
ama: Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant
Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734
apa: Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016).
The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior.
Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734
chicago: Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and
Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling
& Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.
ieee: Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant
Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.
ista: Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family
in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.
mla: Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant
Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis,
2016, doi:10.1080/15592324.2016.1191734.
short: Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &
Behavior 11 (2016).
date_created: 2018-12-11T11:46:53Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2025-09-22T14:21:19Z
day: '02'
department:
- _id: JiFr
doi: 10.1080/15592324.2016.1191734
external_id:
isi:
- '000378740600025'
intvolume: ' 11'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/
month: '06'
oa: 1
oa_version: Submitted Version
publication: Plant Signaling & Behavior
publication_status: published
publisher: Taylor & Francis
publist_id: '7308'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The CLE gene family in Populus trichocarpa
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2016'
...
---
_id: '5445'
abstract:
- lang: eng
text: 'We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis.
IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1
apa: Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative
interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. Quantitative
Interprocedural Analysis. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-523-v1-1.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural
analysis. IST Austria, 2016.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural
analysis, IST Austria, 33p.
mla: Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis.
IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis,
IST Austria, 2016.
date_created: 2018-12-12T11:39:22Z
date_published: 2016-03-31T00:00:00Z
date_updated: 2025-04-15T08:11:41Z
day: '31'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-523-v1-1
file:
- access_level: open_access
checksum: cef516fa091925b5868813e355268fb4
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:52Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5513'
file_name: IST-2016-523-v1+1_main.pdf
file_size: 1012204
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '523'
related_material:
record:
- id: '1604'
relation: later_version
status: public
status: public
title: Quantitative interprocedural analysis
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5446'
abstract:
- lang: eng
text: "We study the problem of developing efficient approaches for proving termination
of recursive programs with one-dimensional arrays. Ranking functions serve as
a sound and complete approach for proving termination of non-recursive programs
without array operations. First, we generalize ranking functions to the notion
of measure functions, and prove that measure functions (i) provide a sound method
to prove termination of recursive programs (with one-dimensional arrays), and
(ii) is both sound and complete over recursive programs without array operations.
Our second contribution is the synthesis of measure functions of specific forms
in polynomial time. More precisely, we prove that (i) polynomial measure functions
over recursive programs can be synthesized in polynomial time through Farkas’
Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm
and exponentiation can be synthesized in polynomial time through abstraction of
logarithmic or exponential terms and Handelman’s Theorem. A key application of
our method is the worst-case analysis of recursive programs. While previous methods
obtain worst-case polynomial bounds of the form O(n^k), where k is an integer,
our polynomial time methods can synthesize bounds of the form O(n log n), as well
as O(n^x), where x is not an integer. We show the applicability of our automated
technique to obtain worst-case complexity of classical recursive algorithms such
as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem,
where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for
polynomial multiplication and Strassen’s algorithm for matrix multiplication,
where we obtain O(n^x) bound, where x is not an integer and close to the best-known
bounds for the respective algorithms. Finally, we present experimental results
to demonstrate the\r\neffectiveness of our approach."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3. Termination and Worst-Case Analysis
of Recursive Programs. IST Austria; 2016.
apa: Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Termination and
worst-case analysis of recursive programs. IST Austria.
chicago: Anonymous, 1, 2 Anonymous, and 3 Anonymous. Termination and Worst-Case
Analysis of Recursive Programs. IST Austria, 2016.
ieee: 1 Anonymous, 2 Anonymous, and 3 Anonymous, Termination and worst-case analysis
of recursive programs. IST Austria, 2016.
ista: Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis
of recursive programs, IST Austria, 26p.
mla: Anonymous, 1, et al. Termination and Worst-Case Analysis of Recursive Programs.
IST Austria, 2016.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis
of Recursive Programs, IST Austria, 2016.
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2020-07-14T23:05:05Z
day: '15'
ddc:
- '000'
file:
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content_type: application/pdf
creator: dernst
date_created: 2019-05-10T13:27:24Z
date_updated: 2020-07-14T12:46:58Z
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checksum: fc08022bfbaac07bac047a9407c0bbb3
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creator: dernst
date_created: 2019-05-10T13:27:31Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6404'
file_name: author_names.txt
file_size: 258
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '618'
status: public
title: Termination and worst-case analysis of recursive programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5447'
abstract:
- lang: eng
text: "We consider the problem of developing automated techniques to aid the average-case
complexity analysis of programs. Several classical textbook algorithms have quite
efficient average-case complexity, whereas the corresponding worst-case bounds
are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR).
Since the main focus of average-case analysis is to obtain efficient bounds, we
consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log
n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input).
Our main contribution is a sound approach for deriving such average-case bounds
for randomized recursive programs. Our approach is efficient (a simple linear-time
algorithm), and it is based on (a) the analysis of recurrence relations induced
by randomized algorithms, and (b) a guess-and-check technique. Our approach can
infer the asymptotically optimal average-case bounds for classical randomized
algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR,
where the worstcase\r\nbounds are either inefficient (such as linear as compared
to logarithmic of average-case, or quadratic as compared to linear or almost-linear
of average-case), or ineffective. We have implemented our approach, and the experimental
results show that we obtain the bounds efficiently for various classical algorithms."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
citation:
ama: 'Anonymous 1, Anonymous 2, Anonymous 3. Average-Case Analysis of Programs:
Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria; 2016.'
apa: 'Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Average-case analysis
of programs: Automated recurrence analysis for almost-linear bounds. IST Austria.'
chicago: 'Anonymous, 1, 2 Anonymous, and 3 Anonymous. Average-Case Analysis of
Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria,
2016.'
ieee: '1 Anonymous, 2 Anonymous, and 3 Anonymous, Average-case analysis of programs:
Automated recurrence analysis for almost-linear bounds. IST Austria, 2016.'
ista: 'Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs:
Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.'
mla: 'Anonymous, 1, et al. Average-Case Analysis of Programs: Automated Recurrence
Analysis for Almost-Linear Bounds. IST Austria, 2016.'
short: '1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs:
Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016.'
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2020-07-14T23:05:06Z
day: '15'
ddc:
- '000'
file:
- access_level: closed
checksum: cf53cdb6d092e68db0b4a0a1506ef8fb
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:32:16Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6406'
file_name: listofauthors.txt
file_size: 281
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content_type: application/pdf
creator: dernst
date_created: 2019-05-10T13:32:16Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6407'
file_name: popl2017b.pdf
file_size: 563642
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '619'
status: public
title: 'Average-case analysis of programs: Automated recurrence analysis for almost-linear
bounds'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5448'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1.
For acyclic architectures, our algorithm is guaranteed to explore exactly one
representative trace from each observation class, while spending polynomial time
per class. Hence, our algorithm is optimal wrt the observation equivalence, and
in several cases explores exponentially fewer traces than any enumerative method
based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider
an equivalence between traces which is finer than the observation equivalence;
but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially
coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
\r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based
DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show
a significant reduction in both running time and the number of explored equivalence
classes."
alternative_title:
- IST Austria Technical Report
arxiv: 1
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Data-Centric Dynamic
Partial Order Reduction. IST Austria; 2016.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2016). Data-centric
dynamic partial order reduction. IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Data-Centric
Dynamic Partial Order Reduction. IST Austria, 2016.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Data-centric dynamic
partial order reduction. IST Austria, 2016.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic
partial order reduction, IST Austria, 20p.
mla: Anonymous, 1, et al. Data-Centric Dynamic Partial Order Reduction. IST
Austria, 2016.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic
Partial Order Reduction, IST Austria, 2016.
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2025-05-20T09:45:08Z
day: '15'
ddc:
- '000'
external_id:
arxiv:
- '1610.01188'
file:
- access_level: open_access
checksum: 1d69252d66bcdf782615ddfb911d2957
content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:58Z
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file_size: 538881
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content_type: text/plain
creator: dernst
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date_updated: 2020-07-14T12:46:58Z
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file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '620'
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title: Data-centric dynamic partial order reduction
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...