---
_id: '18430'
abstract:
- lang: eng
text: Sparse models in dictionary learning have been successfully applied in a wide
variety of machine learning and computer vision problems, and as a result have
recently attracted increased research interest. Another interesting related problem
based on linear equality constraints, namely the sparse null space (SNS) problem,
first appeared in 1986 and has since inspired results on sparse basis pursuit.
In this paper, we investigate the relation between the SNS problem and the analysis
dictionary learning (ADL) problem, and show that the SNS problem plays a central
role, and may be utilized to solve dictionary learning problems. Moreover, we
propose an efficient algorithm of sparse null space basis pursuit (SNS-BP) and
extend it to a solution of ADL. Experimental results on numerical synthetic data
and real-world data are further presented to validate the performance of our method.
article_processing_charge: No
author:
- first_name: Xiao
full_name: Bian, Xiao
last_name: Bian
- first_name: Hamid
full_name: Krim, Hamid
last_name: Krim
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Liyi
full_name: Dai, Liyi
last_name: Dai
citation:
ama: 'Bian X, Krim H, Bronstein AM, Dai L. Sparsity and nullity: Paradigms for analysis
dictionary learning. SIAM Journal on Imaging Sciences. 2016;9(3):1107-1126.
doi:10.1137/15m1030376'
apa: 'Bian, X., Krim, H., Bronstein, A. M., & Dai, L. (2016). Sparsity and nullity:
Paradigms for analysis dictionary learning. SIAM Journal on Imaging Sciences.
Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1030376'
chicago: 'Bian, Xiao, Hamid Krim, Alex M. Bronstein, and Liyi Dai. “Sparsity and
Nullity: Paradigms for Analysis Dictionary Learning.” SIAM Journal on Imaging
Sciences. Society for Industrial & Applied Mathematics, 2016. https://doi.org/10.1137/15m1030376.'
ieee: 'X. Bian, H. Krim, A. M. Bronstein, and L. Dai, “Sparsity and nullity: Paradigms
for analysis dictionary learning,” SIAM Journal on Imaging Sciences, vol.
9, no. 3. Society for Industrial & Applied Mathematics, pp. 1107–1126, 2016.'
ista: 'Bian X, Krim H, Bronstein AM, Dai L. 2016. Sparsity and nullity: Paradigms
for analysis dictionary learning. SIAM Journal on Imaging Sciences. 9(3), 1107–1126.'
mla: 'Bian, Xiao, et al. “Sparsity and Nullity: Paradigms for Analysis Dictionary
Learning.” SIAM Journal on Imaging Sciences, vol. 9, no. 3, Society for
Industrial & Applied Mathematics, 2016, pp. 1107–26, doi:10.1137/15m1030376.'
short: X. Bian, H. Krim, A.M. Bronstein, L. Dai, SIAM Journal on Imaging Sciences
9 (2016) 1107–1126.
date_created: 2024-10-15T11:20:55Z
date_published: 2016-08-09T00:00:00Z
date_updated: 2024-12-19T13:05:21Z
day: '09'
doi: 10.1137/15m1030376
extern: '1'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 1107-1126
publication: SIAM Journal on Imaging Sciences
publication_identifier:
eissn:
- 1936-4954
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Sparsity and nullity: Paradigms for analysis dictionary learning'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
OA_place: repository
OA_type: green
_id: '18434'
abstract:
- lang: eng
text: "Notions of similarity and correspondence between geometric shapes and images
are central to many tasks in geometry processing, computer vision, and computer
graphics. The goal of this course is to familiarize the audience with a set of
recent techniques that greatly facilitate the computation of mappings or correspondences
between geometric datasets, such as 3D shapes or 2D images by formulating them
as mappings between functions rather than points or triangles.\r\nMethods based
on the functional map framework have recently led to state-of-the-art results
in problems as diverse as non-rigid shape matching, image co-segmentation and
even some aspects of tangent vector field design. One challenge in adopting these
methods in practice, however, is that their exposition often assumes a significant
amount of background in geometry processing, spectral methods and functional analysis,
which can make it difficult to gain an intuition about their performance or about
their applicability to real-life problems. In this course, we try to provide all
the tools necessary to appreciate and use these techniques, while assuming very
little background knowledge. We also give a unifying treatment of these techniques,
which may be difficult to extract from the individual publications and, at the
same time, hint at the generality of this point of view, which can help tackle
many problems in the analysis and creation of visual content.\r\nThis course is
structured as a half day course. We will assume that the participants have knowledge
of basic linear algebra and some knowledge of differential geometry, to the extent
of being familiar with the concepts of a manifold and a tangent vector space.
We will discuss in detail the functional approach to finding correspondences between
non-rigid shapes, the design and analysis of tangent vector fields on surfaces,
consistent map estimation in networks of shapes and applications to shape and
image segmentation, shape variability analysis, and other areas."
article_number: '9'
article_processing_charge: No
author:
- first_name: Maks
full_name: Ovsjanikov, Maks
last_name: Ovsjanikov
- first_name: Etienne
full_name: Corman, Etienne
last_name: Corman
- first_name: Michael
full_name: Bronstein, Michael
last_name: Bronstein
- first_name: Emanuele
full_name: Rodolà, Emanuele
last_name: Rodolà
- first_name: Mirela
full_name: Ben-Chen, Mirela
last_name: Ben-Chen
- first_name: Leonidas
full_name: Guibas, Leonidas
last_name: Guibas
- first_name: Frederic
full_name: Chazal, Frederic
last_name: Chazal
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Ovsjanikov M, Corman E, Bronstein M, et al. Computing and processing correspondences
with functional maps. In: SIGGRAPH ASIA 2016 Courses. ACM; 2016. doi:10.1145/2988458.2988494'
apa: 'Ovsjanikov, M., Corman, E., Bronstein, M., Rodolà, E., Ben-Chen, M., Guibas,
L., … Bronstein, A. M. (2016). Computing and processing correspondences with functional
maps. In SIGGRAPH ASIA 2016 Courses. Macau: ACM. https://doi.org/10.1145/2988458.2988494'
chicago: Ovsjanikov, Maks, Etienne Corman, Michael Bronstein, Emanuele Rodolà, Mirela
Ben-Chen, Leonidas Guibas, Frederic Chazal, and Alex M. Bronstein. “Computing
and Processing Correspondences with Functional Maps.” In SIGGRAPH ASIA 2016
Courses. ACM, 2016. https://doi.org/10.1145/2988458.2988494.
ieee: M. Ovsjanikov et al., “Computing and processing correspondences with
functional maps,” in SIGGRAPH ASIA 2016 Courses, Macau, 2016.
ista: 'Ovsjanikov M, Corman E, Bronstein M, Rodolà E, Ben-Chen M, Guibas L, Chazal
F, Bronstein AM. 2016. Computing and processing correspondences with functional
maps. SIGGRAPH ASIA 2016 Courses. SA ’16: SIGGRAPH ASIA 2016 Courses, 9.'
mla: Ovsjanikov, Maks, et al. “Computing and Processing Correspondences with Functional
Maps.” SIGGRAPH ASIA 2016 Courses, 9, ACM, 2016, doi:10.1145/2988458.2988494.
short: M. Ovsjanikov, E. Corman, M. Bronstein, E. Rodolà, M. Ben-Chen, L. Guibas,
F. Chazal, A.M. Bronstein, in:, SIGGRAPH ASIA 2016 Courses, ACM, 2016.
conference:
end_date: 2016-12-08
location: Macau
name: 'SA ''16: SIGGRAPH ASIA 2016 Courses'
start_date: 2016-12-05
date_created: 2024-10-15T11:20:55Z
date_published: 2016-11-28T00:00:00Z
date_updated: 2025-02-04T15:03:47Z
day: '28'
doi: 10.1145/2988458.2988494
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://inria.hal.science/hal-01664767/
month: '11'
oa: 1
oa_version: Preprint
publication: SIGGRAPH ASIA 2016 Courses
publication_identifier:
isbn:
- '9781450345385'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing and processing correspondences with functional maps
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '7599'
abstract:
- lang: eng
text: Normal leaf margin development is important for leaf morphogenesis and contributes
to diverse leaf shapes in higher plants. We here show the crucial roles of an
atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin
development. PI4Kγ5 presents a dynamics expression pattern along with leaf development
and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is
resulted from the accelerated cell division and increased auxin concentration
at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates
a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated
that membrane-bound transcription factors regulate gene transcription by undergoing
proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis
by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis
indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced
in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078.
This is consistent with the subcellular localization observation showing that
fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in
pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal,
driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1.
Further analysis showed that ANAC078 suppresses the auxin synthesis by directly
binding and regulating the expression of auxin synthesis-related genes. These
results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin
synthesis and hence influences cell proliferation and leaf development, providing
informative clues for the regulation of in situ auxin synthesis and cell division,
as well as the cleavage and functional mechanism of membrane-bound transcription
factors.
article_number: e1006252
article_processing_charge: No
article_type: original
author:
- first_name: Yong
full_name: Tang, Yong
last_name: Tang
- first_name: Chun-Yan
full_name: Zhao, Chun-Yan
last_name: Zhao
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
citation:
ama: Tang Y, Zhao C-Y, Tan S, Xue H-W. Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078. PLOS Genetics.
2016;12(8). doi:10.1371/journal.pgen.1006252
apa: Tang, Y., Zhao, C.-Y., Tan, S., & Xue, H.-W. (2016). Arabidopsis type II
phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin
development through interacting with membrane-bound transcription factor ANAC078.
PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1006252
chicago: Tang, Yong, Chun-Yan Zhao, Shutang Tan, and Hong-Wei Xue. “Arabidopsis
Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and
Leaf Margin Development through Interacting with Membrane-Bound Transcription
Factor ANAC078.” PLOS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1006252.
ieee: Y. Tang, C.-Y. Zhao, S. Tan, and H.-W. Xue, “Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078,” PLOS Genetics,
vol. 12, no. 8. Public Library of Science, 2016.
ista: Tang Y, Zhao C-Y, Tan S, Xue H-W. 2016. Arabidopsis type II phosphatidylinositol
4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through
interacting with membrane-bound transcription factor ANAC078. PLOS Genetics. 12(8),
e1006252.
mla: Tang, Yong, et al. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5
Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with
Membrane-Bound Transcription Factor ANAC078.” PLOS Genetics, vol. 12, no.
8, e1006252, Public Library of Science, 2016, doi:10.1371/journal.pgen.1006252.
short: Y. Tang, C.-Y. Zhao, S. Tan, H.-W. Xue, PLOS Genetics 12 (2016).
date_created: 2020-03-21T16:08:33Z
date_published: 2016-08-16T00:00:00Z
date_updated: 2021-01-12T08:14:25Z
day: '16'
ddc:
- '580'
doi: 10.1371/journal.pgen.1006252
extern: '1'
file:
- access_level: open_access
checksum: ff0ab9a6bed11cda800a6e59820866a0
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T12:15:31Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7612'
file_name: 2016_PlosGenetics_Tang.PDF
file_size: 3266119
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis
and leaf margin development through interacting with membrane-bound transcription
factor ANAC078
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '7734'
abstract:
- lang: eng
text: "Importance: Considerable partner resemblances have been found for a wide
range of psychiatric disorders, meaning that partners of affected individuals
have an increased risk of being affected compared with partners of unaffected
individuals. If this resemblance is reflected in genetic similarity between partners,
genetic risk is anticipated to accumulate in offspring, but these potential consequences
have not been quantified and have been left implicit.\r\n\r\nObservations: The
anticipated consequences of partner resemblance on prevalence and heritability
of psychiatric traits in the offspring generation were modeled for disorders with
varying heritabilities, population prevalence (lifetime risk), and magnitudes
of partner resemblance. These models facilitate interpretation for a wide range
of psychiatric disorders, such as autism, schizophrenia, and depression. The genetic
consequences of partner resemblance are most pronounced when attributable to phenotypic
assortment (driven by the psychiatric trait). Phenotypic assortment results in
increased genetic variance in the offspring generation, which may result in increased
heritability and population prevalence. These consequences add generation after
generation to a limit, but assortative mating is unlikely to balance the impact
of reduced fecundity of patients with psychiatric disorders in the long term.
This modeling suggests that the heritabilities of psychiatric disorders are unlikely
to increase by more than 5% from 1 generation of assortative mating (maximally
13% across multiple generations). The population prevalence will increase most
for less common disorders with high heritability; for example, the prevalence
of autism might increase by 1.5-fold after 1 generation of assortative mating
(≥2.4-fold in the long term) depending on several assumptions.\r\n\r\nConclusions
and Relevance: The considerable partner resemblances found for psychiatric disorders
deserve more detailed interpretation than has been provided thus far. Although
the limitations of modeling are emphasized, the anticipated consequences are at
most modest for the heritability but may be considerable for the population prevalence
of rare disorders with a high heritability."
article_processing_charge: No
article_type: original
author:
- first_name: Wouter J.
full_name: Peyrot, Wouter J.
last_name: Peyrot
- 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: Brenda W. J. H.
full_name: Penninx, Brenda W. J. H.
last_name: Penninx
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
citation:
ama: Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. Exploring boundaries for the
genetic consequences of assortative mating for psychiatric traits. JAMA Psychiatry.
2016;73(11):1189-1195. doi:10.1001/jamapsychiatry.2016.2566
apa: Peyrot, W. J., Robinson, M. R., Penninx, B. W. J. H., & Wray, N. R. (2016).
Exploring boundaries for the genetic consequences of assortative mating for psychiatric
traits. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2016.2566
chicago: Peyrot, Wouter J., Matthew Richard Robinson, Brenda W. J. H. Penninx, and
Naomi R. Wray. “Exploring Boundaries for the Genetic Consequences of Assortative
Mating for Psychiatric Traits.” JAMA Psychiatry. American Medical Association,
2016. https://doi.org/10.1001/jamapsychiatry.2016.2566.
ieee: W. J. Peyrot, M. R. Robinson, B. W. J. H. Penninx, and N. R. Wray, “Exploring
boundaries for the genetic consequences of assortative mating for psychiatric
traits,” JAMA Psychiatry, vol. 73, no. 11. American Medical Association,
pp. 1189–1195, 2016.
ista: Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. 2016. Exploring boundaries
for the genetic consequences of assortative mating for psychiatric traits. JAMA
Psychiatry. 73(11), 1189–1195.
mla: Peyrot, Wouter J., et al. “Exploring Boundaries for the Genetic Consequences
of Assortative Mating for Psychiatric Traits.” JAMA Psychiatry, vol. 73,
no. 11, American Medical Association, 2016, pp. 1189–95, doi:10.1001/jamapsychiatry.2016.2566.
short: W.J. Peyrot, M.R. Robinson, B.W.J.H. Penninx, N.R. Wray, JAMA Psychiatry
73 (2016) 1189–1195.
date_created: 2020-04-30T10:48:41Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T08:15:11Z
day: '01'
doi: 10.1001/jamapsychiatry.2016.2566
extern: '1'
intvolume: ' 73'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1189-1195
publication: JAMA Psychiatry
publication_identifier:
issn:
- 2168-622X
publication_status: published
publisher: American Medical Association
quality_controlled: '1'
status: public
title: Exploring boundaries for the genetic consequences of assortative mating for
psychiatric traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2016'
...
---
_id: '7736'
abstract:
- lang: eng
text: We develop a novel approach to identify regions of the genome underlying population
genetic differentiation in any genetic data where the underlying population structure
is unknown, or where the interest is assessing divergence along a gradient. By
combining the statistical framework for genome-wide association studies (GWASs)
with eigenvector decomposition (EigenGWAS), which is commonly used in population
genetics to characterize the structure of genetic data, loci under selection can
be identified without a requirement for discrete populations. We show through
theory and simulation that our approach can identify regions under selection along
gradients of ancestry, and in real data we confirm this by demonstrating LCT to
be under selection between HapMap CEU–TSI cohorts, and we then validate this selection
signal across European countries in the POPRES samples. HERC2 was also found to
be differentiated between both the CEU–TSI cohort and within the POPRES sample,
reflecting the likely anthropological differences in skin and hair colour between
northern and southern European populations. Controlling for population stratification
is of great importance in any quantitative genetic study and our approach also
provides a simple, fast and accurate way of predicting principal components in
independent samples. With ever increasing sample sizes across many fields, this
approach is likely to be greatly utilized to gain individual-level eigenvectors
avoiding the computational challenges associated with conducting singular value
decomposition in large data sets. We have developed freely available software,
Genetic Analysis Repository (GEAR), to facilitate the application of the methods.
article_processing_charge: No
article_type: original
author:
- first_name: G-B
full_name: Chen, G-B
last_name: Chen
- first_name: S H
full_name: Lee, S H
last_name: Lee
- first_name: Z-X
full_name: Zhu, Z-X
last_name: Zhu
- first_name: B
full_name: Benyamin, B
last_name: Benyamin
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: 'Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. EigenGWAS: Finding loci
under selection through genome-wide association studies of eigenvectors in structured
populations. Heredity. 2016;117:51-61. doi:10.1038/hdy.2016.25'
apa: 'Chen, G.-B., Lee, S. H., Zhu, Z.-X., Benyamin, B., & Robinson, M. R. (2016).
EigenGWAS: Finding loci under selection through genome-wide association studies
of eigenvectors in structured populations. Heredity. Springer Nature. https://doi.org/10.1038/hdy.2016.25'
chicago: 'Chen, G-B, S H Lee, Z-X Zhu, B Benyamin, and Matthew Richard Robinson.
“EigenGWAS: Finding Loci under Selection through Genome-Wide Association Studies
of Eigenvectors in Structured Populations.” Heredity. Springer Nature,
2016. https://doi.org/10.1038/hdy.2016.25.'
ieee: 'G.-B. Chen, S. H. Lee, Z.-X. Zhu, B. Benyamin, and M. R. Robinson, “EigenGWAS:
Finding loci under selection through genome-wide association studies of eigenvectors
in structured populations,” Heredity, vol. 117. Springer Nature, pp. 51–61,
2016.'
ista: 'Chen G-B, Lee SH, Zhu Z-X, Benyamin B, Robinson MR. 2016. EigenGWAS: Finding
loci under selection through genome-wide association studies of eigenvectors in
structured populations. Heredity. 117, 51–61.'
mla: 'Chen, G. B., et al. “EigenGWAS: Finding Loci under Selection through Genome-Wide
Association Studies of Eigenvectors in Structured Populations.” Heredity,
vol. 117, Springer Nature, 2016, pp. 51–61, doi:10.1038/hdy.2016.25.'
short: G.-B. Chen, S.H. Lee, Z.-X. Zhu, B. Benyamin, M.R. Robinson, Heredity 117
(2016) 51–61.
date_created: 2020-04-30T10:50:03Z
date_published: 2016-05-04T00:00:00Z
date_updated: 2021-01-12T08:15:11Z
day: '04'
doi: 10.1038/hdy.2016.25
extern: '1'
intvolume: ' 117'
language:
- iso: eng
month: '05'
oa_version: None
page: 51-61
publication: Heredity
publication_identifier:
issn:
- 0018-067X
- 1365-2540
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'EigenGWAS: Finding loci under selection through genome-wide association studies
of eigenvectors in structured populations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
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: '7760'
abstract:
- lang: eng
text: We propose a Widom-like scaling ansatz for the critical jamming transition.
Our ansatz for the elastic energy shows that the scaling of the energy, compressive
strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear
modulus are all related to each other via scaling relations, with only three independent
scaling exponents. We extract the values of these exponents from already known
numerical or theoretical results, and we numerically verify the resulting predictions
of the scaling theory for the energy and residual shear stress. We also derive
a scaling relation between pressure and residual shear stress that yields insight
into why the shear and bulk moduli scale differently. Our theory shows that the
jamming transition exhibits an emergent scale invariance, setting the stage for
the potential development of a renormalization group theory for jamming.
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
ama: Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition.
Proceedings of the National Academy of Sciences. 2016;113(35):9745-9750.
doi:10.1073/pnas.1601858113
apa: Goodrich, C. P., Liu, A. J., & Sethna, J. P. (2016). Scaling ansatz for
the jamming transition. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1601858113
chicago: Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz
for the Jamming Transition.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1601858113.
ieee: C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming
transition,” Proceedings of the National Academy of Sciences, vol. 113,
no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.
ista: Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition.
Proceedings of the National Academy of Sciences. 113(35), 9745–9750.
mla: Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” Proceedings
of the National Academy of Sciences, vol. 113, no. 35, Proceedings of the
National Academy of Sciences, 2016, pp. 9745–50, doi:10.1073/pnas.1601858113.
short: C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy
of Sciences 113 (2016) 9745–9750.
date_created: 2020-04-30T11:39:53Z
date_published: 2016-08-30T00:00:00Z
date_updated: 2021-01-12T08:15:21Z
day: '30'
doi: 10.1073/pnas.1601858113
extern: '1'
intvolume: ' 113'
issue: '35'
language:
- iso: eng
month: '08'
oa_version: None
page: 9745-9750
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Scaling ansatz for the jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '7761'
abstract:
- lang: eng
text: We study the effect of dilute pinning on the jamming transition. Pinning reduces
the average contact number needed to jam unpinned particles and shifts the jamming
threshold to lower densities, leading to a pinning susceptibility, χp. Our main
results are that this susceptibility obeys scaling form and diverges in the thermodynamic
limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins.
Finite-size scaling arguments yield these values with associated statistical (systematic)
errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic
corrections raise the exponent in d=2 to close to the d=3 value, although the
systematic errors are very large.
article_number: '235501'
article_processing_charge: No
article_type: original
author:
- first_name: Amy L.
full_name: Graves, Amy L.
last_name: Graves
- first_name: Samer
full_name: Nashed, Samer
last_name: Nashed
- first_name: Elliot
full_name: Padgett, Elliot
last_name: Padgett
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
ama: 'Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. Pinning susceptibility:
The effect of dilute, quenched disorder on jamming. Physical Review Letters.
2016;116(23). doi:10.1103/physrevlett.116.235501'
apa: 'Graves, A. L., Nashed, S., Padgett, E., Goodrich, C. P., Liu, A. J., &
Sethna, J. P. (2016). Pinning susceptibility: The effect of dilute, quenched disorder
on jamming. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.116.235501'
chicago: 'Graves, Amy L., Samer Nashed, Elliot Padgett, Carl Peter Goodrich, Andrea
J. Liu, and James P. Sethna. “Pinning Susceptibility: The Effect of Dilute, Quenched
Disorder on Jamming.” Physical Review Letters. American Physical Society,
2016. https://doi.org/10.1103/physrevlett.116.235501.'
ieee: 'A. L. Graves, S. Nashed, E. Padgett, C. P. Goodrich, A. J. Liu, and J. P.
Sethna, “Pinning susceptibility: The effect of dilute, quenched disorder on jamming,”
Physical Review Letters, vol. 116, no. 23. American Physical Society, 2016.'
ista: 'Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. 2016. Pinning
susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review
Letters. 116(23), 235501.'
mla: 'Graves, Amy L., et al. “Pinning Susceptibility: The Effect of Dilute, Quenched
Disorder on Jamming.” Physical Review Letters, vol. 116, no. 23, 235501,
American Physical Society, 2016, doi:10.1103/physrevlett.116.235501.'
short: A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna,
Physical Review Letters 116 (2016).
date_created: 2020-04-30T11:40:10Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-01-12T08:15:21Z
day: '10'
doi: 10.1103/physrevlett.116.235501
extern: '1'
intvolume: ' 116'
issue: '23'
language:
- iso: eng
month: '06'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Pinning susceptibility: The effect of dilute, quenched disorder on jamming'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2016'
...
---
_id: '7762'
abstract:
- lang: eng
text: Characterizing structural inhomogeneity is an essential step in understanding
the mechanical response of amorphous materials. We introduce a threshold-free
measure based on the field of vectors pointing from the center of each particle
to the centroid of the Voronoi cell in which the particle resides. These vectors
tend to point in toward regions of high free volume and away from regions of low
free volume, reminiscent of sinks and sources in a vector field. We compute the
local divergence of these vectors, where positive values correspond to overpacked
regions and negative values identify underpacked regions within the material.
Distributions of this divergence are nearly Gaussian with zero mean, allowing
for structural characterization using only the moments of the distribution. We
explore how the standard deviation and skewness vary with the packing fraction
for simulations of bidisperse systems and find a kink in these moments that coincides
with the jamming transition.
article_number: '088001 '
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Rieser, Jennifer M.
last_name: Rieser
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Douglas J.
full_name: Durian, Douglas J.
last_name: Durian
citation:
ama: 'Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy
vector: A threshold-free characterization of local structure in amorphous materials.
Physical Review Letters. 2016;116(8). doi:10.1103/physrevlett.116.088001'
apa: 'Rieser, J. M., Goodrich, C. P., Liu, A. J., & Durian, D. J. (2016). Divergence
of Voronoi cell anisotropy vector: A threshold-free characterization of local
structure in amorphous materials. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.116.088001'
chicago: 'Rieser, Jennifer M., Carl Peter Goodrich, Andrea J. Liu, and Douglas J.
Durian. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization
of Local Structure in Amorphous Materials.” Physical Review Letters. American
Physical Society, 2016. https://doi.org/10.1103/physrevlett.116.088001.'
ieee: 'J. M. Rieser, C. P. Goodrich, A. J. Liu, and D. J. Durian, “Divergence of
Voronoi cell anisotropy vector: A threshold-free characterization of local structure
in amorphous materials,” Physical Review Letters, vol. 116, no. 8. American
Physical Society, 2016.'
ista: 'Rieser JM, Goodrich CP, Liu AJ, Durian DJ. 2016. Divergence of Voronoi cell
anisotropy vector: A threshold-free characterization of local structure in amorphous
materials. Physical Review Letters. 116(8), 088001.'
mla: 'Rieser, Jennifer M., et al. “Divergence of Voronoi Cell Anisotropy Vector:
A Threshold-Free Characterization of Local Structure in Amorphous Materials.”
Physical Review Letters, vol. 116, no. 8, 088001, American Physical Society,
2016, doi:10.1103/physrevlett.116.088001.'
short: J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters
116 (2016).
date_created: 2020-04-30T11:40:25Z
date_published: 2016-02-23T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '23'
doi: 10.1103/physrevlett.116.088001
extern: '1'
intvolume: ' 116'
issue: '8'
language:
- iso: eng
month: '02'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Divergence of Voronoi cell anisotropy vector: A threshold-free characterization
of local structure in amorphous materials'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2016'
...
---
_id: '7763'
abstract:
- lang: eng
text: An orthogonal wavelet basis is characterized by its approximation order, which
relates to the ability of the basis to represent general smooth functions on a
given scale. It is known, though perhaps not widely known, that there are ways
of exceeding the approximation order, i.e., achieving higher-order error in the
discretized wavelet transform and its inverse. The focus here is on the development
of a practical formulation to accomplish this first for 1D smooth functions, then
for 1D functions with discontinuities and then for multidimensional (here 2D)
functions with discontinuities. It is shown how to transcend both the wavelet
approximation order and the 2D Gibbs phenomenon in representing electromagnetic
fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis
grid.
article_processing_charge: No
article_type: original
author:
- first_name: Richard
full_name: Lombardini, Richard
last_name: Lombardini
- first_name: Ramiro
full_name: Acevedo, Ramiro
last_name: Acevedo
- first_name: Alexander
full_name: Kuczala, Alexander
last_name: Kuczala
- first_name: Kerry P.
full_name: Keys, Kerry P.
last_name: Keys
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Bruce R.
full_name: Johnson, Bruce R.
last_name: Johnson
citation:
ama: Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order
wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal
of Computational Physics. 2016;305:244-262. doi:10.1016/j.jcp.2015.10.035
apa: Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., &
Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters
and Gibbs phenomena. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2015.10.035
chicago: Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys,
Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation
Filters and Gibbs Phenomena.” Journal of Computational Physics. Elsevier,
2016. https://doi.org/10.1016/j.jcp.2015.10.035.
ieee: R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B.
R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs
phenomena,” Journal of Computational Physics, vol. 305. Elsevier, pp. 244–262,
2016.
ista: Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016.
Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena.
Journal of Computational Physics. 305, 244–262.
mla: Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation
Filters and Gibbs Phenomena.” Journal of Computational Physics, vol. 305,
Elsevier, 2016, pp. 244–62, doi:10.1016/j.jcp.2015.10.035.
short: R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson,
Journal of Computational Physics 305 (2016) 244–262.
date_created: 2020-04-30T11:40:41Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '15'
doi: 10.1016/j.jcp.2015.10.035
extern: '1'
intvolume: ' 305'
language:
- iso: eng
month: '01'
oa_version: None
page: 244-262
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 305
year: '2016'
...
---
_id: '7764'
abstract:
- lang: eng
text: States of self stress, organizations of internal forces in many-body systems
that are in equilibrium with an absence of external forces, can be thought of
as the constitutive building blocks of the elastic response of a material. In
overconstrained disordered packings they have a natural mathematical correspondence
with the zero-energy vibrational modes in underconstrained systems. While substantial
attention in the literature has been paid to diverging length scales associated
with zero- and finite-energy vibrational modes in jammed systems, less is known
about the spatial structure of the states of self stress. In this work we define
a natural way in which a unique state of self stress can be associated with each
bond in a disordered spring network derived from a jammed packing, and then investigate
the spatial structure of these bond-localized states of self stress. This allows
for an understanding of how the elastic properties of a system would change upon
changing the strength or even existence of any bond in the system.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress
in jammed systems. Soft Matter. 2016;12(17):3982-3990. doi:10.1039/c6sm00094k
apa: Sussman, D. M., Goodrich, C. P., & Liu, A. J. (2016). Spatial structure
of states of self stress in jammed systems. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c6sm00094k
chicago: Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure
of States of Self Stress in Jammed Systems.” Soft Matter. Royal Society
of Chemistry, 2016. https://doi.org/10.1039/c6sm00094k.
ieee: D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states
of self stress in jammed systems,” Soft Matter, vol. 12, no. 17. Royal
Society of Chemistry, pp. 3982–3990, 2016.
ista: Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self
stress in jammed systems. Soft Matter. 12(17), 3982–3990.
mla: Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed
Systems.” Soft Matter, vol. 12, no. 17, Royal Society of Chemistry, 2016,
pp. 3982–90, doi:10.1039/c6sm00094k.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990.
date_created: 2020-04-30T11:40:56Z
date_published: 2016-03-14T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '14'
doi: 10.1039/c6sm00094k
extern: '1'
intvolume: ' 12'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 3982-3990
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://doi.org/10.1039/c6sm02496c
status: public
title: Spatial structure of states of self stress in jammed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '785'
abstract:
- lang: eng
text: High memory contention is generally agreed to be a worst-case scenario for
concurrent data structures. There has been a significant amount of research effort
spent investigating designs which minimize contention, and several programming
techniques have been proposed to mitigate its effects. However, there are currently
few architectural mechanisms to allow scaling contended data structures at high
thread counts. In this paper, we investigate hardware support for scalable contended
data structures. We propose Lease/Release, a simple addition to standard directory-based
MSI cache coherence protocols, allowing participants to lease memory, at the granularity
of cache lines, by delaying coherence messages for a short, bounded period of
time. Our analysis shows that Lease/Release can significantly reduce the overheads
of contention for both non-blocking (lock-free) and lock-based data structure
implementations, while ensuring that no deadlocks are introduced. We validate
Lease/Release empirically on the Graphite multiprocessor simulator, on a range
of data structures, including queue, stack, and priority queue implementations,
as well as on transactional applications. Results show that Lease/Release consistently
improves both throughput and energy usage, by up to 5x, both for lock-free and
lock-based data structure designs.
acknowledgement: We would like to thank Richard Black, Miguel Castro, Dave Dice, Aleksandar
Dragojevic, Maurice Herlihy, Ant Rowstron, Nir Shavit, and Vasileios Trigonakis,
as well as the anonymous reviewers, for helpful suggestions during the development
of this paper.
article_processing_charge: No
author:
- first_name: Syed
full_name: Haider, Syed
last_name: Haider
- first_name: William
full_name: Hasenplaugh, William
last_name: Hasenplaugh
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Haider S, Hasenplaugh W, Alistarh D-A. Lease/Release: Architectural support
for scaling contended data structures. In: Vol 12-16-March-2016. ACM; 2016. doi:10.1145/2851141.2851155'
apa: 'Haider, S., Hasenplaugh, W., & Alistarh, D.-A. (2016). Lease/Release:
Architectural support for scaling contended data structures (Vol. 12-16-March-2016).
Presented at the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2851141.2851155'
chicago: 'Haider, Syed, William Hasenplaugh, and Dan-Adrian Alistarh. “Lease/Release:
Architectural Support for Scaling Contended Data Structures,” Vol. 12-16-March-2016.
ACM, 2016. https://doi.org/10.1145/2851141.2851155.'
ieee: 'S. Haider, W. Hasenplaugh, and D.-A. Alistarh, “Lease/Release: Architectural
support for scaling contended data structures,” presented at the PPoPP: Principles
and Practice of Parallel Pogramming, 2016, vol. 12-16-March-2016.'
ista: 'Haider S, Hasenplaugh W, Alistarh D-A. 2016. Lease/Release: Architectural
support for scaling contended data structures. PPoPP: Principles and Practice
of Parallel Pogramming vol. 12-16-March-2016.'
mla: 'Haider, Syed, et al. Lease/Release: Architectural Support for Scaling Contended
Data Structures. Vol. 12-16-March-2016, ACM, 2016, doi:10.1145/2851141.2851155.'
short: S. Haider, W. Hasenplaugh, D.-A. Alistarh, in:, ACM, 2016.
conference:
name: 'PPoPP: Principles and Practice of Parallel Pogramming'
date_created: 2018-12-11T11:48:29Z
date_published: 2016-02-27T00:00:00Z
date_updated: 2022-03-18T12:56:29Z
day: '27'
doi: 10.1145/2851141.2851155
extern: '1'
language:
- iso: eng
month: '02'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '6871'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lease/Release: Architectural support for scaling contended data structures'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12-16-March-2016
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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '813'
abstract:
- lang: eng
text: The Gag polyprotein of retroviruses drives immature virus assembly by forming
hexameric protein lattices. The assembly is primarily mediated by protein-protein
interactions between capsid (CA) domains and by interactions between nucleocapsid
(NC) domains and RNA. Specific interactions between NC and the viral RNA are required
for genome packaging. Previously reported cryoelectron microscopy analysis of
immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region
(residues RKK) in CA may serve as an additional binding site for nucleic acids.
Here, we have introduced mutations into the RKK region in both bacterial and proviral
M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA
binding, budding/release, nuclear trafficking, and infectivity using in vitro
and in vivo systems. Our data indicate that the RKK region binds and structures
nucleic acid that serves to promote virus particle assembly in the cytoplasm.
Moreover, the RKK region appears to be important for recruitment of viral genomic
RNA into Gag particles, and this function could be linked to changes in nuclear
trafficking. Together these observations suggest that in M-PMV, direct interactions
between CA and nucleic acid play important functions in the late stages of the
viral life cycle.
acknowledgement: "Work in the laboratory of John A. G. Briggs was funded by Deutsche\r\nForschungsgemeinschaft
(DFG) (BR 3635/2-1). This work, including the\r\nefforts of Tomas Ruml, was funded
by the Grant Agency of the Czech\r\nRepublic (14-15326S) and the Czech Ministry
of Education (NPU I sus-\r\ntainability projects LO1302 and LO1304)."
article_processing_charge: No
article_type: original
author:
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Růžena
full_name: Píchalová, Růžena
last_name: Píchalová
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Karolína
full_name: Strohalmová, Karolína
last_name: Strohalmová
- first_name: Ivana
full_name: Křížová, Ivana
last_name: Křížová
- first_name: Romana
full_name: Hadravová, Romana
last_name: Hadravová
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: John
full_name: Briggs, John
last_name: Briggs
- first_name: Pavel
full_name: Ulbrich, Pavel
last_name: Ulbrich
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
citation:
ama: Füzik T, Píchalová R, Schur FK, et al. Nucleic acid binding by Mason-Pfizer
monkey virus CA promotes virus assembly and genome packaging. Journal of Virology.
2016;90(9):4593-4603. doi:10.1128/JVI.03197-15
apa: Füzik, T., Píchalová, R., Schur, F. K., Strohalmová, K., Křížová, I., Hadravová,
R., … Ruml, T. (2016). Nucleic acid binding by Mason-Pfizer monkey virus CA promotes
virus assembly and genome packaging. Journal of Virology. American Society
for Microbiology. https://doi.org/10.1128/JVI.03197-15
chicago: Füzik, Tibor, Růžena Píchalová, Florian KM Schur, Karolína Strohalmová,
Ivana Křížová, Romana Hadravová, Michaela Rumlová, John Briggs, Pavel Ulbrich,
and Tomáš Ruml. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes
Virus Assembly and Genome Packaging.” Journal of Virology. American Society
for Microbiology, 2016. https://doi.org/10.1128/JVI.03197-15.
ieee: T. Füzik et al., “Nucleic acid binding by Mason-Pfizer monkey virus
CA promotes virus assembly and genome packaging,” Journal of Virology,
vol. 90, no. 9. American Society for Microbiology, pp. 4593–4603, 2016.
ista: Füzik T, Píchalová R, Schur FK, Strohalmová K, Křížová I, Hadravová R, Rumlová
M, Briggs J, Ulbrich P, Ruml T. 2016. Nucleic acid binding by Mason-Pfizer monkey
virus CA promotes virus assembly and genome packaging. Journal of Virology. 90(9),
4593–4603.
mla: Füzik, Tibor, et al. “Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA
Promotes Virus Assembly and Genome Packaging.” Journal of Virology, vol.
90, no. 9, American Society for Microbiology, 2016, pp. 4593–603, doi:10.1128/JVI.03197-15.
short: T. Füzik, R. Píchalová, F.K. Schur, K. Strohalmová, I. Křížová, R. Hadravová,
M. Rumlová, J. Briggs, P. Ulbrich, T. Ruml, Journal of Virology 90 (2016) 4593–4603.
date_created: 2018-12-11T11:48:38Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2026-05-20T07:34:00Z
day: '01'
doi: 10.1128/JVI.03197-15
extern: '1'
external_id:
pmid:
- '26912613'
intvolume: ' 90'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1128/jvi.03197-15
month: '05'
oa: 1
oa_version: Published Version
page: 4593 - 4603
pmid: 1
publication: Journal of Virology
publication_identifier:
eissn:
- 1098-5514
issn:
- 0022-538X
publication_status: published
publisher: American Society for Microbiology
publist_id: '6835'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleic acid binding by Mason-Pfizer monkey virus CA promotes virus assembly
and genome packaging
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 90
year: '2016'
...
---
_id: '816'
abstract:
- lang: eng
text: Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic
cleavage of the viral Gag polyprotein induces structural maturation. Maturation
can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity.
The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator
of assembly and maturation and is the target of MIs.We applied optimized cryo-electron
tomography and subtomogram averaging to resolve this region within assembled immature
HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure
reveals a network of intra- And intermolecular interactions mediating immature
HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible
to protease.We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure,
and MI resistance develops by destabilizing CA-SP1.
acknowledgement: The authors thank B. Glass for preparation of the immature HIV-1
(D25A) sample; J. Plitzko and D. Tegunov for providing the K2Align software; and
S. Mattei, N. Hoffman, F. Thommen, A. Sonnen, and S. Dodonova for technical assistance
and/or discussion. This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.). The Briggs laboratory acknowledges
financial support from the European Molecular Biology Laboratory (EMBL) and from
the Chica und Heinz Schaller Stiftung. W.W. was supported by a European Molecular
Biology Organization Long-Term Fellowship (ALTF 748-2014). A.J.J. acknowledges support
by the EMBL Interdisciplinary Postdoc Program under the Marie Curie Action COFUND
(PCOFUND-GA-2008-229597) and by the Joachim Herz Stiftung. This study was technically
supported by the EMBL information technology services unit and the EMBL Proteomics
Core Facility. F.K.M.S., M.O., H.-G.K., and J.A.G.B. designed the experiments, with
J.M.K. assisting in the design of those involving mass spectrometry. F.K.M.S. and
M.O. prepared samples. W.J.H.H. implemented tomography acquisition schemes. F.K.M.S.
and W.J.H.H. acquired the data. F.K.M.S. and W.W. processed images. F.K.M.S., A.J.J.,
and C.S. refined the model. F.K.M.S., M.O., and J.A.G.B. analyzed the data. F.K.M.S.
and J.A.G.B. wrote the manuscript with support from all authors. Representative
tomograms and the final electron microscopy structures have been deposited in the
Electron Microscopy Data Bank with accession numbers EMD-4015, EMD-4016, EMD-4017,
EMD-4018, EMD-4019, and EMD-4020. The refined HIV-1 CA-SP1 model has been deposited
in the Protein Data Bank with accession number 5L93.
article_processing_charge: No
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: Arjen
full_name: Jakobi, Arjen
last_name: Jakobi
- first_name: Joanna
full_name: Kirkpatrick, Joanna
last_name: Kirkpatrick
- first_name: Carsten
full_name: Sachse, Carsten
last_name: Sachse
- first_name: Hans
full_name: Kraüsslich, Hans
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Schur FK, Obr M, Hagen W, et al. An Atomic Model of HIV-1 Capsid-SP1 Reveals
Structures Regulating Assembly and Maturation. Vol 353. American Association
for the Advancement of Science; 2016:506-508. doi:10.1126/science.aaf9620
apa: Schur, F. K., Obr, M., Hagen, W., Wan, W., Jakobi, A., Kirkpatrick, J., … Briggs,
J. (2016). An atomic model of HIV-1 capsid-SP1 reveals structures regulating
assembly and maturation (Vol. 353, pp. 506–508). American Association for
the Advancement of Science. https://doi.org/10.1126/science.aaf9620
chicago: Schur, Florian KM, Martin Obr, Wim Hagen, William Wan, Arjen Jakobi, Joanna
Kirkpatrick, Carsten Sachse, Hans Kraüsslich, and John Briggs. An Atomic Model
of HIV-1 Capsid-SP1 Reveals Structures Regulating Assembly and Maturation.
Vol. 353. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf9620.
ieee: F. K. Schur et al., An atomic model of HIV-1 capsid-SP1 reveals
structures regulating assembly and maturation, vol. 353. American Association
for the Advancement of Science, 2016, pp. 506–508.
ista: Schur FK, Obr M, Hagen W, Wan W, Jakobi A, Kirkpatrick J, Sachse C, Kraüsslich
H, Briggs J. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating
assembly and maturation, American Association for the Advancement of Science,p.
mla: Schur, Florian KM, et al. An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures
Regulating Assembly and Maturation. Vol. 353, American Association for the
Advancement of Science, 2016, pp. 506–08, doi:10.1126/science.aaf9620.
short: F.K. Schur, M. Obr, W. Hagen, W. Wan, A. Jakobi, J. Kirkpatrick, C. Sachse,
H. Kraüsslich, J. Briggs, An Atomic Model of HIV-1 Capsid-SP1 Reveals Structures
Regulating Assembly and Maturation, American Association for the Advancement of
Science, 2016.
date_created: 2018-12-11T11:48:39Z
date_published: 2016-07-29T00:00:00Z
date_updated: 2026-05-20T07:41:16Z
day: '29'
doi: 10.1126/science.aaf9620
extern: '1'
external_id:
pmid:
- '27417497'
intvolume: ' 353'
language:
- iso: eng
month: '07'
oa_version: None
page: 506 - 508
pmid: 1
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6834'
scopus_import: '1'
status: public
title: An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly
and maturation
type: report
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 353
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: '8300'
abstract:
- lang: eng
text: The integration of social networking concepts into Internet of Things systems
is a burgeoning topic of research that promises to support novel and more powerful
applications. In this paper we focus on the design and implementation of a highly
scalable Trust and Reputation Model for the Internet of Things based on the social
approach that the COSMOS project introduces, as part of its final results. We
create our model by combining popular solutions proposed for Peer-to-Peer and
mobile ad-hoc networks and adapting them on the Internet of Things concept. Each
Thing can compute the Trust index of another Thing based on its own experiences,
while it has the capability of determining its Reputation Index either by consulting
its other “friends” (Followees) or referring to the Platform, a management system
used in COSMOS. The model is tested through simulations of the proposed social
system, demonstrating the ability of TRM-SIoT to achieve the Social Exclusion
of malicious nodes and collectives from the network, with low computational overhead
and high scalability. Furthermore, due to the adaptive nature of the system, Social
Reintegration of these nodes is also possible.
article_number: '7733612'
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Orfefs
full_name: Voutyras, Orfefs
last_name: Voutyras
- first_name: Theodora
full_name: Varvarigou, Theodora
last_name: Varvarigou
citation:
ama: 'Kokoris Kogias E, Voutyras O, Varvarigou T. TRM-SIoT: A scalable hybrid trust
& reputation model for the social Internet of Things. In: 2016 IEEE 21st
International Conference on Emerging Technologies and Factory Automation.
IEEE; 2016. doi:10.1109/etfa.2016.7733612'
apa: 'Kokoris Kogias, E., Voutyras, O., & Varvarigou, T. (2016). TRM-SIoT: A
scalable hybrid trust & reputation model for the social Internet of Things.
In 2016 IEEE 21st International Conference on Emerging Technologies and Factory
Automation. Berlin, Germany: IEEE. https://doi.org/10.1109/etfa.2016.7733612'
chicago: 'Kokoris Kogias, Eleftherios, Orfefs Voutyras, and Theodora Varvarigou.
“TRM-SIoT: A Scalable Hybrid Trust & Reputation Model for the Social Internet
of Things.” In 2016 IEEE 21st International Conference on Emerging Technologies
and Factory Automation. IEEE, 2016. https://doi.org/10.1109/etfa.2016.7733612.'
ieee: 'E. Kokoris Kogias, O. Voutyras, and T. Varvarigou, “TRM-SIoT: A scalable
hybrid trust & reputation model for the social Internet of Things,” in 2016
IEEE 21st International Conference on Emerging Technologies and Factory Automation,
Berlin, Germany, 2016.'
ista: 'Kokoris Kogias E, Voutyras O, Varvarigou T. 2016. TRM-SIoT: A scalable hybrid
trust & reputation model for the social Internet of Things. 2016 IEEE 21st
International Conference on Emerging Technologies and Factory Automation. ETFA:
Conference on Emerging Technologies and Factory Automation, 7733612.'
mla: 'Kokoris Kogias, Eleftherios, et al. “TRM-SIoT: A Scalable Hybrid Trust &
Reputation Model for the Social Internet of Things.” 2016 IEEE 21st International
Conference on Emerging Technologies and Factory Automation, 7733612, IEEE,
2016, doi:10.1109/etfa.2016.7733612.'
short: E. Kokoris Kogias, O. Voutyras, T. Varvarigou, in:, 2016 IEEE 21st International
Conference on Emerging Technologies and Factory Automation, IEEE, 2016.
conference:
end_date: 2016-09-09
location: Berlin, Germany
name: 'ETFA: Conference on Emerging Technologies and Factory Automation'
start_date: 2016-09-06
date_created: 2020-08-26T11:48:54Z
date_published: 2016-09-09T00:00:00Z
date_updated: 2021-01-12T08:17:59Z
day: '09'
doi: 10.1109/etfa.2016.7733612
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
publication: 2016 IEEE 21st International Conference on Emerging Technologies and
Factory Automation
publication_identifier:
isbn:
- '9781509013142'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'TRM-SIoT: A scalable hybrid trust & reputation model for the social Internet
of Things'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...