---
_id: '7742'
abstract:
- lang: eng
text: Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8,
but the reasons for these differences are unknown. Here we find that many independent
loci contribute to population genetic differences in height and body mass index
(BMI) in 9,416 individuals across 14 European countries. Using discovery data
on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling
pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95%
CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively,
reflect population genetic differences. Population genetic divergence differed
significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95
× 10−4), and we find an among-population genetic correlation for tall and slender
individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection
for both phenotypes. Observed differences in height among populations reflected
the predicted genetic means (r = 0.51; P < 0.001), but environmental differences
across Europe masked genetic differentiation for BMI (P < 0.58).
article_processing_charge: No
article_type: original
author:
- 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: Gibran
full_name: Hemani, Gibran
last_name: Hemani
- first_name: Carolina
full_name: Medina-Gomez, Carolina
last_name: Medina-Gomez
- first_name: Massimo
full_name: Mezzavilla, Massimo
last_name: Mezzavilla
- first_name: Tonu
full_name: Esko, Tonu
last_name: Esko
- first_name: Konstantin
full_name: Shakhbazov, Konstantin
last_name: Shakhbazov
- first_name: Joseph E
full_name: Powell, Joseph E
last_name: Powell
- first_name: Anna
full_name: Vinkhuyzen, Anna
last_name: Vinkhuyzen
- first_name: Sonja I
full_name: Berndt, Sonja I
last_name: Berndt
- first_name: Stefan
full_name: Gustafsson, Stefan
last_name: Gustafsson
- first_name: Anne E
full_name: Justice, Anne E
last_name: Justice
- first_name: Bratati
full_name: Kahali, Bratati
last_name: Kahali
- first_name: Adam E
full_name: Locke, Adam E
last_name: Locke
- first_name: Tune H
full_name: Pers, Tune H
last_name: Pers
- first_name: Sailaja
full_name: Vedantam, Sailaja
last_name: Vedantam
- first_name: Andrew R
full_name: Wood, Andrew R
last_name: Wood
- first_name: Wouter
full_name: van Rheenen, Wouter
last_name: van Rheenen
- first_name: Ole A
full_name: Andreassen, Ole A
last_name: Andreassen
- first_name: Paolo
full_name: Gasparini, Paolo
last_name: Gasparini
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Leonard H van den
full_name: Berg, Leonard H van den
last_name: Berg
- first_name: Jan H
full_name: Veldink, Jan H
last_name: Veldink
- first_name: Fernando
full_name: Rivadeneira, Fernando
last_name: Rivadeneira
- first_name: Thomas M
full_name: Werge, Thomas M
last_name: Werge
- first_name: Goncalo R
full_name: Abecasis, Goncalo R
last_name: Abecasis
- first_name: Dorret I
full_name: Boomsma, Dorret I
last_name: Boomsma
- first_name: Daniel I
full_name: Chasman, Daniel I
last_name: Chasman
- first_name: Eco J C
full_name: de Geus, Eco J C
last_name: de Geus
- first_name: Timothy M
full_name: Frayling, Timothy M
last_name: Frayling
- first_name: Joel N
full_name: Hirschhorn, Joel N
last_name: Hirschhorn
- first_name: Jouke Jan
full_name: Hottenga, Jouke Jan
last_name: Hottenga
- first_name: Erik
full_name: Ingelsson, Erik
last_name: Ingelsson
- first_name: Ruth J F
full_name: Loos, Ruth J F
last_name: Loos
- first_name: Patrik K E
full_name: Magnusson, Patrik K E
last_name: Magnusson
- first_name: Nicholas G
full_name: Martin, Nicholas G
last_name: Martin
- first_name: Grant W
full_name: Montgomery, Grant W
last_name: Montgomery
- first_name: Kari E
full_name: North, Kari E
last_name: North
- first_name: Nancy L
full_name: Pedersen, Nancy L
last_name: Pedersen
- first_name: Timothy D
full_name: Spector, Timothy D
last_name: Spector
- first_name: Elizabeth K
full_name: Speliotes, Elizabeth K
last_name: Speliotes
- first_name: Michael E
full_name: Goddard, Michael E
last_name: Goddard
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Peter M
full_name: Visscher, Peter M
last_name: Visscher
citation:
ama: Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362.
doi:10.1038/ng.3401
apa: Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov,
K., … Visscher, P. M. (2015). Population genetic differentiation of height and
body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401
chicago: Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo
Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population
Genetic Differentiation of Height and Body Mass Index across Europe.” Nature
Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401.
ieee: M. R. Robinson et al., “Population genetic differentiation of height
and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer
Nature, pp. 1357–1362, 2015.
ista: Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K,
Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke
AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu
A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma
DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson
E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector
TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.
mla: Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height
and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer
Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.
short: M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov,
J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali,
A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen,
P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M.
Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling,
J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G.
Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes,
M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.
date_created: 2020-04-30T10:58:23Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '14'
doi: 10.1038/ng.3401
extern: '1'
intvolume: ' 47'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1357-1362
publication: Nature Genetics
publication_identifier:
issn:
- 1061-4036
- 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Population genetic differentiation of height and body mass index across Europe
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '7741'
abstract:
- lang: eng
text: Phenotypes expressed in a social context are not only a function of the individual,
but can also be shaped by the phenotypes of social partners. These social effects
may play a major role in the evolution of cooperative breeding if social partners
differ in the quality of care they provide and if individual carers adjust their
effort in relation to that of other carers. When applying social effects models
to wild study systems, it is also important to explore sources of individual plasticity
that could masquerade as social effects. We studied offspring provisioning rates
of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus
using a quantitative genetic framework to identify these social effects and partition
them into genetic, permanent environment and current environment components. Controlling
for other effects, individuals were consistent in their provisioning effort at
a given nest, but adjusted their effort based on who was in their social group,
indicating the presence of social effects. However, these social effects differed
between years and social contexts, indicating a current environment effect, rather
than indicating a genetic or permanent environment effect. While this study reveals
the importance of examining environmental and genetic sources of social effects,
the framework we present is entirely general, enabling a greater understanding
of potentially important social effects within any ecological population.
article_number: '20150689'
article_processing_charge: No
article_type: original
author:
- first_name: Mark James
full_name: Adams, Mark James
last_name: Adams
- 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: Maria-Elena
full_name: Mannarelli, Maria-Elena
last_name: Mannarelli
- first_name: Ben J.
full_name: Hatchwell, Ben J.
last_name: Hatchwell
citation:
ama: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social
environment effects on parental and helper care in a cooperatively breeding bird.
Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810).
doi:10.1098/rspb.2015.0689'
apa: 'Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015).
Social genetic and social environment effects on parental and helper care in a
cooperatively breeding bird. Proceedings of the Royal Society B: Biological
Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689'
chicago: 'Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and
Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and
Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society
B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.'
ieee: 'M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social
genetic and social environment effects on parental and helper care in a cooperatively
breeding bird,” Proceedings of the Royal Society B: Biological Sciences,
vol. 282, no. 1810. The Royal Society, 2015.'
ista: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic
and social environment effects on parental and helper care in a cooperatively
breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810),
20150689.'
mla: 'Adams, Mark James, et al. “Social Genetic and Social Environment Effects on
Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of
the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The
Royal Society, 2015, doi:10.1098/rspb.2015.0689.'
short: 'M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings
of the Royal Society B: Biological Sciences 282 (2015).'
date_created: 2020-04-30T10:58:07Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '07'
doi: 10.1098/rspb.2015.0689
extern: '1'
external_id:
pmid:
- '26063846'
intvolume: ' 282'
issue: '1810'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rspb.2015.0689
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
issn:
- 0962-8452
- 1471-2954
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
status: public
title: Social genetic and social environment effects on parental and helper care in
a cooperatively breeding bird
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '7739'
abstract:
- lang: eng
text: Currently, there is much debate on the genetic architecture of quantitative
traits in wild populations. Is trait variation influenced by many genes of small
effect or by a few genes of major effect? Where is additive genetic variation
located in the genome? Do the same loci cause similar phenotypic variation in
different populations? Great tits (Parus major) have been studied extensively
in long‐term studies across Europe and consequently are considered an ecological
‘model organism’. Recently, genomic resources have been developed for the great
tit, including a custom SNP chip and genetic linkage map. In this study, we used
a suite of approaches to investigate the genetic architecture of eight quantitative
traits in two long‐term study populations of great tits—one in the Netherlands
and the other in the United Kingdom. Overall, we found little evidence for the
presence of genes of large effects in either population. Instead, traits appeared
to be influenced by many genes of small effect, with conservative estimates of
the number of contributing loci ranging from 31 to 310. Despite concordance between
population‐specific heritabilities, we found no evidence for the presence of loci
having similar effects in both populations. While population‐specific genetic
architectures are possible, an undetected shared architecture cannot be rejected
because of limited power to map loci of small and moderate effects. This study
is one of few examples of genetic architecture analysis in replicated wild populations
and highlights some of the challenges and limitations researchers will face when
attempting similar molecular quantitative genetic studies in free‐living populations.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Kees
full_name: van Oers, Kees
last_name: van Oers
- 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: John L.
full_name: Quinn, John L.
last_name: Quinn
- first_name: Martien A. M.
full_name: Groenen, Martien A. M.
last_name: Groenen
- first_name: Marcel E.
full_name: Visser, Marcel E.
last_name: Visser
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452
apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R.,
Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations. Molecular Ecology.
Wiley. https://doi.org/10.1111/mec.13452
chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers,
Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser,
Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture
of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology.
Wiley, 2015. https://doi.org/10.1111/mec.13452.
ieee: A. W. Santure et al., “Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations,” Molecular Ecology,
vol. 24. Wiley, pp. 6148–6162, 2015.
ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen
MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 24, 6148–6162.
mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of
Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology,
vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.
short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L.
Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology
24 (2015) 6148–6162.
date_created: 2020-04-30T10:51:01Z
date_published: 2015-12-10T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '10'
doi: 10.1111/mec.13452
extern: '1'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.13452
month: '12'
oa: 1
oa_version: Published Version
page: 6148-6162
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Replicated analysis of the genetic architecture of quantitative traits in two
wild great tit populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '776'
abstract:
- lang: eng
text: High-performance concurrent priority queues are essential for applications
such as task scheduling and discrete event simulation. Unfortunately, even the
best performing implementations do not scale past a number of threads in the single
digits. This is because of the sequential bottleneck in accessing the elements
at the head of the queue in order to perform a DeleteMin operation. In this paper,
we present the SprayList, a scalable priority queue with relaxed ordering semantics.
Starting from a non-blocking SkipList, the main innovation behind our design is
that the DeleteMin operations avoid a sequential bottleneck by "spraying"
themselves onto the head of the SkipList list in a coordinated fashion. The spraying
is implemented using a carefully designed random walk, so that DeleteMin returns
an element among the first O(plog3p) in the list, with high probability, where
p is the number of threads. We prove that the running time of a DeleteMin operation
is O(log3p), with high probability, independent of the size of the list. Our experiments
show that the relaxed semantics allow the data structure to scale for high thread
counts, comparable to a classic unordered SkipList. Furthermore, we observe that,
for reasonably parallel workloads, the scalability benefits of relaxation considerably
outweigh the additional work due to out-of-order execution.
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations."
article_processing_charge: No
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed
priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523'
apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList:
A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at
the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523'
chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The
SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015.
https://doi.org/10.1145/2688500.2688523.'
ieee: 'D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable
relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel
Pogramming, 2015, vol. 2015–January, pp. 11–20.'
ista: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable
relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming
vol. 2015–January, 11–20.'
mla: 'Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority
Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.'
short: D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.
conference:
name: 'PPoPP: Principles and Practice of Parallel Pogramming'
date_created: 2018-12-11T11:48:26Z
date_published: 2015-01-24T00:00:00Z
date_updated: 2023-02-23T13:16:43Z
day: '24'
doi: 10.1145/2688500.2688523
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 20
publication_status: published
publisher: ACM
publist_id: '6878'
status: public
title: 'The SprayList: A scalable relaxed priority queue'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '7765'
abstract:
- lang: eng
text: 'We introduce a principle unique to disordered solids wherein the contribution
of any bond to one global perturbation is uncorrelated with its contribution to
another. Coupled with sufficient variability in the contributions of different
bonds, this “independent bond-level response” paves the way for the design of
real materials with unusual and exquisitely tuned properties. To illustrate this,
we choose two global perturbations: compression and shear. By applying a bond
removal procedure that is both simple and experimentally relevant to remove a
very small fraction of bonds, we can drive disordered spring networks to both
the incompressible and completely auxetic limits of mechanical behavior.'
article_number: '225501'
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: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response:
Tuning by pruning to exploit disorder for global behavior. Physical Review
Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501'
apa: 'Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501'
chicago: 'Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle
of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for
Global Behavior.” Physical Review Letters. American Physical Society, 2015.
https://doi.org/10.1103/physrevlett.114.225501.'
ieee: 'C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior,”
Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.'
ista: 'Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level
response: Tuning by pruning to exploit disorder for global behavior. Physical
Review Letters. 114(22), 225501.'
mla: 'Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response:
Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review
Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.'
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).
date_created: 2020-04-30T11:41:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '04'
doi: 10.1103/physrevlett.114.225501
extern: '1'
intvolume: ' 114'
issue: '22'
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: 'The principle of independent bond-level response: Tuning by pruning to exploit
disorder for global behavior'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '7767'
abstract:
- lang: eng
text: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as Vicsek-type
nearest-neighbor alignment, short-range repulsion, and a local boundary term.
Changing the relative strength of these interactions leads to migrating swarms,
rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble
motion, alternating between migration and either rotating or jammed states. Interestingly,
although a migrating swarm moves slower than an individual particle, the diffusion
constant can be up to three orders of magnitude larger, suggesting that collective
motion can be highly advantageous, for example, when searching for food.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- 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: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active
particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706
apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective
dynamics of soft active particles. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.91.032706
chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema.
“Collective Dynamics of Soft Active Particles.” Physical Review E. American
Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.
ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics
of soft active particles,” Physical Review E, vol. 91, no. 3. American
Physical Society, 2015.
ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of
soft active particles. Physical Review E. 91(3), 032706.
mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.”
Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015,
doi:10.1103/physreve.91.032706.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '7766'
abstract:
- lang: eng
text: We study the vibrational properties near a free surface of disordered spring
networks derived from jammed sphere packings. In bulk systems, without surfaces,
it is well understood that such systems have a plateau in the density of vibrational
modes extending down to a frequency scale ω*. This frequency is controlled by
ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres
and twice the spatial dimension, d, of the system, which vanishes at the jamming
transition. In the presence of a free surface we find that there is a density
of disordered vibrational modes associated with the surface that extends far below
ω*. The total number of these low-frequency surface modes is controlled by ΔZ,
and the profile of their decay into the bulk has two characteristic length scales,
which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.
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
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in
jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d
apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered
surface vibrations in jammed sphere packings. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c4sm02905d
chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel.
“Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.
ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface
vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal
Society of Chemistry, pp. 2745–2751, 2015.
ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations
in jammed sphere packings. Soft Matter. 11(14), 2745–2751.
mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere
Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015,
pp. 2745–51, doi:10.1039/c4sm02905d.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015)
2745–2751.
date_created: 2020-04-30T11:41:23Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '15'
doi: 10.1039/c4sm02905d
extern: '1'
intvolume: ' 11'
issue: '14'
language:
- iso: eng
month: '02'
oa_version: None
page: 2745-2751
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Disordered surface vibrations in jammed sphere packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '777'
abstract:
- lang: eng
text: 'In many applications, the data is of rich structure that can be represented
by a hypergraph, where the data items are represented by vertices and the associations
among items are represented by hyperedges. Equivalently, we are given an input
bipartite graph with two types of vertices: items, and associations (which we
refer to as topics). We consider the problem of partitioning the set of items
into a given number of components such that the maximum number of topics covered
by a component is minimized. This is a clustering problem with various applications,
e.g. partitioning of a set of information objects such as documents, images, and
videos, and load balancing in the context of modern computation platforms.Inthis
paper, we focus on the streaming computation model for this problem, in which
items arrive online one at a time and each item must be assigned irrevocably to
a component at its arrival time. Motivated by scalability requirements, we focus
on the class of streaming computation algorithms with memory limited to be at
most linear in the number of components. We show that a greedy assignment strategy
is able to recover a hidden co-clustering of items under a natural set of recovery
conditions. We also report results of an extensive empirical evaluation, which
demonstrate that this greedy strategy yields superior performance when compared
with alternative approaches.'
article_processing_charge: No
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: Jennifer
full_name: Iglesias, Jennifer
last_name: Iglesias
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning.
In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.'
apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max
hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS:
Neural Information Processing Systems, Neural Information Processing Systems.'
chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming
Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing
Systems, 2015.
ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph
partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015,
vol. 2015–January, pp. 1900–1908.'
ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph
partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.'
mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning.
Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.
short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing
Systems, 2015, pp. 1900–1908.
conference:
name: 'NIPS: Neural Information Processing Systems'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:09Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning
month: '01'
oa_version: None
page: 1900 - 1908
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6879'
status: public
title: Streaming min-max hypergraph partitioning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '778'
abstract:
- lang: eng
text: Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed
to complement the fast, but best-effort nature of Hardware Transactional Memory
(HTM) with a slow, reliable software backup. However, the costs of providing concurrency
between hardware and software transactions in HyTM are still not well understood.
In this paper, we propose a general model for HyTM implementations, which captures
the ability of hardware transactions to buffer memory accesses. The model allows
us to formally quantify and analyze the amount of overhead (instrumentation) caused
by the potential presence of software transactions.We prove that (1) it is impossible
to build a strictly serializable HyTM implementation that has both uninstrumented
reads and writes, even for very weak progress guarantees, and (2) the instrumentation
cost incurred by a hardware transaction in any progressive opaque HyTM is linear
in the size of the transaction’s data set.We further describe two implementations
which exhibit optimal instrumentation costs for two different progress conditions.
In sum, this paper proposes the first formal HyTM model and captures for the first
time the trade-off between the degree of hardware-software TM concurrency and
the amount of instrumentation overhead.
acknowledgement: P. Kuznetsov-The author is supported by the Agence Nationale de la
Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully
acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and
the Oracle and Intel corporations.
alternative_title:
- LNCS
article_processing_charge: No
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Petr
full_name: Kuznetsov, Petr
last_name: Kuznetsov
- first_name: Srivatsan
full_name: Ravi, Srivatsan
last_name: Ravi
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations
of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13'
apa: 'Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015).
Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi,
and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99.
Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.
ieee: 'D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent
limitations of hybrid transactional memory,” presented at the DISC: Distributed
Computing, 2015, vol. 9363, pp. 185–199.'
ista: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations
of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363,
185–199.'
mla: Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional
Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.
short: D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer,
2015, pp. 185–199.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:35Z
day: '01'
doi: 10.1007/978-3-662-48653-5_13
extern: '1'
external_id:
arxiv:
- '1405.5689'
intvolume: ' 9363'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5689
month: '01'
oa: 1
oa_version: None
page: 185 - 199
publication_status: published
publisher: Springer
publist_id: '6880'
quality_controlled: '1'
status: public
title: Inherent limitations of hybrid transactional memory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9363
year: '2015'
...
---
_id: '7779'
abstract:
- lang: eng
text: "The fact that a disordered material is not constrained in its properties
in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential
for novel material design. However, unlike their crystalline\r\ncounterparts,
disordered solids are not well understood. One of the primary\r\nobstacles is
the lack of a theoretical framework for thinking about disorder\r\nand its relation
to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless
athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition
with diverging length scales and clean power-law\r\nsignatures. This critical
point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the
potential to provide the essential theoretical\r\nfoundation necessary for a unified
understanding of the mechanics of disordered\r\nsolids. We begin by showing that
jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact
nonlinearities.\" We then investigate\r\nthe critical nature of the transition,
focusing on diverging length scales and\r\nfinite-size effects. Next, we argue
that jamming plays the same role for\r\ndisordered solids as the perfect crystal
plays for crystalline solids. Not only\r\ncan it be considered an idealized starting
point for understanding disordered\r\nmaterials, but it can even influence systems
that have a relatively high amount\r\nof crystalline order. The behavior of solids
can thus be thought of as existing\r\non a spectrum, with the perfect crystal
and the jamming transition at opposing\r\nends. Finally, we introduce a new principle
wherein the contribution of an\r\nindividual bond to one global property is independent
of its contribution to\r\nanother. This principle allows the different global
responses of a disordered\r\nsystem to be manipulated independently and provides
a great deal of flexibility\r\nin designing materials with unique, textured and
tunable properties."
article_processing_charge: No
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response
of disordered solids,” arXiv:1510.08820. 2015.'
ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820, .'
mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear
Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
short: C.P. Goodrich, ArXiv:1510.08820 (2015).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...