---
_id: '749'
abstract:
- lang: eng
text: 'Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous
transmitter release and facilitation at synapses. However, Syt7 is strongly expressed
in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output
synapses of these neurons produce only minimal asynchronous release and show depression
rather than facilitation. To resolve this apparent contradiction, we examined
the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic
basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate
that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment,
and facilitation. In combination, these three effects ensure efficient transmitter
release during high-frequency activity and guarantee frequency independence of
inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency
of high-frequency inhibitory synaptic transmission'
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Rachel
full_name: Satterfield, Rachel
last_name: Satterfield
- first_name: Samuel
full_name: Young, Samuel
last_name: Young
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen C, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses.
Cell Reports. 2017;21(8):2082-2089. doi:10.1016/j.celrep.2017.10.122
apa: Chen, C., Satterfield, R., Young, S., & Jonas, P. M. (2017). Triple function
of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central
GABAergic synapses. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.10.122
chicago: Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple
Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission
at Central GABAergic Synapses.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.10.122.
ieee: C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses,”
Cell Reports, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017.
ista: Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses.
Cell Reports. 21(8), 2082–2089.
mla: Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency
of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports,
vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:10.1016/j.celrep.2017.10.122.
short: C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089.
date_created: 2018-12-11T11:48:18Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2023-09-27T12:26:04Z
day: '21'
ddc:
- '570'
- '571'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2017.10.122
ec_funded: 1
external_id:
isi:
- '000416216700007'
file:
- access_level: open_access
checksum: a6afa3764909bf6edafa07982d8e1cee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:14Z
date_updated: 2020-07-14T12:47:59Z
file_id: '4737'
file_name: IST-2017-874-v1+1_PIIS2211124717316029.pdf
file_size: 2759195
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2082 - 2089
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
publication: Cell Reports
publication_identifier:
issn:
- '22111247'
publication_status: published
publisher: Cell Press
publist_id: '6907'
pubrep_id: '874'
quality_controlled: '1'
related_material:
record:
- id: '324'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission
at central GABAergic synapses
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2017'
...
---
_id: '750'
abstract:
- lang: eng
text: Modern communication technologies allow first responders to contact thousands
of potential volunteers simultaneously for support during a crisis or disaster
event. However, such volunteer efforts must be well coordinated and monitored,
in order to offer an effective relief to the professionals. In this paper we extend
earlier work on optimally assigning volunteers to selected landmark locations.
In particular, we emphasize the aspect that obtaining good assignments requires
not only advanced computational tools, but also a realistic measure of distance
between volunteers and landmarks. Specifically, we propose the use of the Open
Street Map (OSM) driving distance instead of he previously used flight distance.
We find the OSM driving distance to be better aligned with the interests of volunteers
and first responders. Furthermore, we show that relying on the flying distance
leads to a substantial underestimation of the number of required volunteers, causing
negative side effects in case of an actual crisis situation.
author:
- first_name: Jasmin
full_name: Pielorz, Jasmin
id: 49BC895A-F248-11E8-B48F-1D18A9856A87
last_name: Pielorz
- first_name: Matthias
full_name: Prandtstetter, Matthias
last_name: Prandtstetter
- first_name: Markus
full_name: Straub, Markus
last_name: Straub
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer
allocation needs realistic distances. In: 2017 IEEE International Conference
on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375'
apa: 'Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal
geospatial volunteer allocation needs realistic distances. In 2017 IEEE International
Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375'
chicago: Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert.
“Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017
IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.
ieee: J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial
volunteer allocation needs realistic distances,” in 2017 IEEE International
Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.
ista: Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial
volunteer allocation needs realistic distances. 2017 IEEE International Conference
on Big Data. Big Data, 3760–3763.
mla: Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic
Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017,
pp. 3760–63, doi:10.1109/BigData.2017.8258375.
short: J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International
Conference on Big Data, IEEE, 2017, pp. 3760–3763.
conference:
end_date: 2017-12-14
location: Boston, MA, United States
name: Big Data
start_date: 2017-12-11
date_created: 2018-12-11T11:48:18Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:55Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/BigData.2017.8258375
language:
- iso: eng
month: '12'
oa_version: None
page: 3760 - 3763
publication: 2017 IEEE International Conference on Big Data
publication_identifier:
isbn:
- 978-153862714-3
publication_status: published
publisher: IEEE
publist_id: '6906'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal geospatial volunteer allocation needs realistic distances
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '751'
abstract:
- lang: eng
text: The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath
nearly all epithelial cell types that is critical for cellular and tissue function.
It is composed of numerous components conserved among all bilaterians [1]; however,
it is unknown how all of these components are generated and subsequently constructed
to form a fully mature BM in the living animal. Although BM formation is thought
to simply involve a process of self-assembly [2], this concept suffers from a
number of logistical issues when considering its construction in vivo. First,
incorporation of BM components appears to be hierarchical [3-5], yet it is unclear
whether their production during embryogenesis must also be regulated in a temporal
fashion. Second, many BM proteins are produced not only by the cells residing
on the BM but also by surrounding cell types [6-9], and it is unclear how large,
possibly insoluble protein complexes [10] are delivered into the matrix. Here
we exploit our ability to live image and genetically dissect de novo BM formation
during Drosophila development. This reveals that there is a temporal hierarchy
of BM protein production that is essential for proper component incorporation.
Furthermore, we show that BM components require secretion by migrating macrophages
(hemocytes) during their developmental dispersal, which is critical for embryogenesis.
Indeed, hemocyte migration is essential to deliver a subset of ECM components
evenly throughout the embryo. This reveals that de novo BM construction requires
a combination of both production and distribution logistics allowing for the timely
delivery of core components.
article_processing_charge: No
author:
- first_name: Yutaka
full_name: Matsubayashi, Yutaka
last_name: Matsubayashi
- first_name: Adam
full_name: Louani, Adam
last_name: Louani
- first_name: Anca
full_name: Dragu, Anca
last_name: Dragu
- first_name: Besaiz
full_name: Sanchez Sanchez, Besaiz
last_name: Sanchez Sanchez
- first_name: Eduardo
full_name: Serna Morales, Eduardo
last_name: Serna Morales
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Gema
full_name: Vizcay, Gema
last_name: Vizcay
- first_name: Roland
full_name: Fleck, Roland
last_name: Fleck
- first_name: John
full_name: Heddleston, John
last_name: Heddleston
- first_name: Teng
full_name: Chew, Teng
last_name: Chew
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Brian
full_name: Stramer, Brian
last_name: Stramer
citation:
ama: Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components
is essential for De Novo basement membrane formation. Current Biology.
2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001
apa: Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales,
E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is
essential for De Novo basement membrane formation. Current Biology. Cell
Press. https://doi.org/10.1016/j.cub.2017.10.001
chicago: Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez,
Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source
of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current
Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001.
ieee: Y. Matsubayashi et al., “A moving source of matrix components is essential
for De Novo basement membrane formation,” Current Biology, vol. 27, no.
22. Cell Press, p. 3526–3534e.4, 2017.
ista: Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland
L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B.
2017. A moving source of matrix components is essential for De Novo basement membrane
formation. Current Biology. 27(22), 3526–3534e.4.
mla: Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential
for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no.
22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001.
short: Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales,
L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus,
B. Stramer, Current Biology 27 (2017) 3526–3534e.4.
date_created: 2018-12-11T11:48:18Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2023-09-27T12:25:31Z
day: '09'
ddc:
- '570'
- '576'
department:
- _id: DaSi
doi: 10.1016/j.cub.2017.10.001
external_id:
isi:
- '000415815800031'
file:
- access_level: open_access
checksum: 264cf6c6c3551486ba5ea786850e000a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:45Z
date_updated: 2020-07-14T12:47:59Z
file_id: '4770'
file_name: IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf
file_size: 4770657
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3526 - 3534e.4
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
publist_id: '6905'
pubrep_id: '875'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A moving source of matrix components is essential for De Novo basement membrane
formation
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 27
year: '2017'
...
---
_id: '7725'
abstract:
- lang: eng
text: Phenotypic plasticity is the ability of an individual genotype to alter aspects
of its phenotype depending on the current environment. It is central to the persistence,
resistance and resilience of populations facing variation in physical or biological
factors. Genetic variation in plasticity is pervasive, which suggests its local
adaptation is plausible. Existing studies on the adaptation of plasticity typically
focus on single traits and a few populations, while theory about interactions
among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale
(for example, multiple populations) perspective is required. We present data from
a landscape scale, replicated, multi-trait experiment using a classic predator–prey
system centred on the water flea Daphnia pulex. We find predator regime-driven
differences in genetic variation of multivariate plasticity. These differences
are associated with strong divergent selection linked to a predation regime. Our
findings are evidence for local adaptation of plasticity, suggesting that responses
of populations to environmental variation depend on the conditions in which they
evolved in the past.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Reger, Julia
last_name: Reger
- first_name: Martin I.
full_name: Lind, Martin I.
last_name: Lind
- 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: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation
of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107.
doi:10.1038/s41559-017-0373-6
apa: Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation
drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution.
Springer Nature. https://doi.org/10.1038/s41559-017-0373-6
chicago: Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman.
“Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology
& Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6.
ieee: J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives
local adaptation of phenotypic plasticity,” Nature Ecology & Evolution,
vol. 2. Springer Nature, pp. 100–107, 2017.
ista: Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local
adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107.
mla: Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.”
Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07,
doi:10.1038/s41559-017-0373-6.
short: J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology &
Evolution 2 (2017) 100–107.
date_created: 2020-04-30T10:46:02Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2021-01-12T08:15:07Z
day: '27'
doi: 10.1038/s41559-017-0373-6
extern: '1'
intvolume: ' 2'
language:
- iso: eng
month: '11'
oa_version: None
page: 100-107
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Predation drives local adaptation of phenotypic plasticity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '7727'
abstract:
- lang: eng
text: Genes of the major histocompatibility complex (MHC) have been shown to influence
social signalling and mate preferences in many species, including humans. First
observations suggest that MHC signalling may also affect female fertility. To
test this hypothesis, we exposed 191 female horses (Equus caballus) to either
an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation
and conception. A within-subject experimental design controlled for non-MHC-linked
male characteristics, and instrumental insemination with semen of other males
(n = 106) controlled for potential confounding effects of semen or embryo characteristics.
We found that females were more likely to become pregnant if exposed to an MHC-dissimilar
than to an MHC-similar male, while overall genetic distance to the stimulus males
(based on microsatellite markers on 20 chromosomes) had no effect. Our results
demonstrate that early pregnancy failures can be due to maternal life-history
decisions (cryptic female choice) influenced by MHC-linked social signalling.
article_number: '20171824'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Burger, D.
last_name: Burger
- first_name: S.
full_name: Thomas, S.
last_name: Thomas
- first_name: H.
full_name: Aepli, H.
last_name: Aepli
- first_name: M.
full_name: Dreyer, M.
last_name: Dreyer
- first_name: G.
full_name: Fabre, G.
last_name: Fabre
- first_name: E.
full_name: Marti, E.
last_name: Marti
- first_name: H.
full_name: Sieme, H.
last_name: Sieme
- 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: C.
full_name: Wedekind, C.
last_name: Wedekind
citation:
ama: 'Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked
social signalling affects female fertility. Proceedings of the Royal Society
B: Biological Sciences. 2017;284(1868). doi:10.1098/rspb.2017.1824'
apa: 'Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind,
C. (2017). Major histocompatibility complex-linked social signalling affects female
fertility. Proceedings of the Royal Society B: Biological Sciences. The
Royal Society. https://doi.org/10.1098/rspb.2017.1824'
chicago: 'Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme,
Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked
Social Signalling Affects Female Fertility.” Proceedings of the Royal Society
B: Biological Sciences. The Royal Society, 2017. https://doi.org/10.1098/rspb.2017.1824.'
ieee: 'D. Burger et al., “Major histocompatibility complex-linked social
signalling affects female fertility,” Proceedings of the Royal Society B: Biological
Sciences, vol. 284, no. 1868. The Royal Society, 2017.'
ista: 'Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson
MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling
affects female fertility. Proceedings of the Royal Society B: Biological Sciences.
284(1868), 20171824.'
mla: 'Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling
Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences,
vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:10.1098/rspb.2017.1824.'
short: 'D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme,
M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences
284 (2017).'
date_created: 2020-04-30T10:46:43Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2021-01-12T08:15:08Z
day: '06'
doi: 10.1098/rspb.2017.1824
extern: '1'
external_id:
pmid:
- '29212724'
intvolume: ' 284'
issue: '1868'
language:
- iso: eng
month: '12'
oa_version: None
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: Major histocompatibility complex-linked social signalling affects female fertility
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 284
year: '2017'
...
---
_id: '7728'
abstract:
- lang: eng
text: 'Meta-analyses of genome-wide association studies, which dominate genetic
discovery, are based on data from diverse historical time periods and populations.
Genetic scores derived from genome-wide association studies explain only a fraction
of the heritability estimates obtained from whole-genome studies on single populations,
known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062),
we test whether hidden heritability is attributed to heterogeneity across sampling
populations and time, showing that estimates are substantially smaller across
populations compared with within populations. We show that the hidden heritability
varies substantially: from zero for height to 20% for body mass index, 37% for
education, 40% for age at first birth and up to 75% for number of children. Simulations
demonstrate that our results are more likely to reflect heterogeneity in phenotypic
measurement or gene–environment interactions than genetic heterogeneity. These
findings have substantial implications for genetic discovery, suggesting that
large homogenous datasets are required for behavioural phenotypes and that gene–environment
interaction may be a central challenge for genetic discovery.'
article_processing_charge: No
article_type: original
author:
- first_name: Felix C.
full_name: Tropf, Felix C.
last_name: Tropf
- first_name: S. Hong
full_name: Lee, S. Hong
last_name: Lee
- first_name: Renske M.
full_name: Verweij, Renske M.
last_name: Verweij
- first_name: Gert
full_name: Stulp, Gert
last_name: Stulp
- first_name: Peter J.
full_name: van der Most, Peter J.
last_name: van der Most
- first_name: Ronald
full_name: de Vlaming, Ronald
last_name: de Vlaming
- first_name: Andrew
full_name: Bakshi, Andrew
last_name: Bakshi
- first_name: Daniel A.
full_name: Briley, Daniel A.
last_name: Briley
- first_name: Charles
full_name: Rahal, Charles
last_name: Rahal
- first_name: Robert
full_name: Hellpap, Robert
last_name: Hellpap
- first_name: Anastasia N.
full_name: Iliadou, Anastasia N.
last_name: Iliadou
- first_name: Tõnu
full_name: Esko, Tõnu
last_name: Esko
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Sarah E.
full_name: Medland, Sarah E.
last_name: Medland
- first_name: Nicholas G.
full_name: Martin, Nicholas G.
last_name: Martin
- first_name: Nicola
full_name: Barban, Nicola
last_name: Barban
- first_name: Harold
full_name: Snieder, Harold
last_name: Snieder
- 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: Melinda C.
full_name: Mills, Melinda C.
last_name: Mills
citation:
ama: Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity
across seven populations. Nature Human Behaviour. 2017;1(10):757-765. doi:10.1038/s41562-017-0195-1
apa: Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de
Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across
seven populations. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-017-0195-1
chicago: Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van
der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to
Heterogeneity across Seven Populations.” Nature Human Behaviour. Springer
Nature, 2017. https://doi.org/10.1038/s41562-017-0195-1.
ieee: F. C. Tropf et al., “Hidden heritability due to heterogeneity across
seven populations,” Nature Human Behaviour, vol. 1, no. 10. Springer Nature,
pp. 757–765, 2017.
ista: Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi
A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE,
Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability
due to heterogeneity across seven populations. Nature Human Behaviour. 1(10),
757–765.
mla: Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven
Populations.” Nature Human Behaviour, vol. 1, no. 10, Springer Nature,
2017, pp. 757–65, doi:10.1038/s41562-017-0195-1.
short: F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming,
A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu,
S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature
Human Behaviour 1 (2017) 757–765.
date_created: 2020-04-30T10:47:02Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:15:08Z
day: '11'
doi: 10.1038/s41562-017-0195-1
extern: '1'
intvolume: ' 1'
issue: '10'
language:
- iso: eng
month: '09'
oa_version: None
page: 757-765
publication: Nature Human Behaviour
publication_identifier:
issn:
- 2397-3374
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Hidden heritability due to heterogeneity across seven populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2017'
...
---
_id: '7729'
abstract:
- lang: eng
text: Quantifying the effects of inbreeding is critical to characterizing the genetic
architecture of complex traits. This study highlights through theory and simulations
the strengths and shortcomings of three SNP-based inbreeding measures commonly
used to estimate inbreeding depression (ID). We demonstrate that heterogeneity
in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates,
and we develop an approach to correct this bias using LD and minor allele frequency
stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000
participants of the UK Biobank, using LDMS, and confirmed previously published
ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip
ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs
for complete inbreeding; P<0.001). Our results illustrate that a careful choice
of the measure of inbreeding combined with LDMS stratification improves both detection
and quantification of ID using SNP data.
article_processing_charge: No
article_type: original
author:
- first_name: Loic
full_name: Yengo, Loic
last_name: Yengo
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Bruce S.
full_name: Weir, Bruce S.
last_name: Weir
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- 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: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding
depression for complex traits from SNP data. Proceedings of the National Academy
of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114
apa: Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., &
Visscher, P. M. (2017). Detection and quantification of inbreeding depression
for complex traits from SNP data. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114
chicago: Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew
Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding
Depression for Complex Traits from SNP Data.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114.
ieee: L. Yengo et al., “Detection and quantification of inbreeding depression
for complex traits from SNP data,” Proceedings of the National Academy of Sciences,
vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607,
2017.
ista: Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017.
Detection and quantification of inbreeding depression for complex traits from
SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.
mla: Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression
for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences,
vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07,
doi:10.1073/pnas.1621096114.
short: L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher,
Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.
date_created: 2020-04-30T10:47:19Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2021-01-12T08:15:09Z
day: '08'
doi: 10.1073/pnas.1621096114
extern: '1'
intvolume: ' 114'
issue: '32'
language:
- iso: eng
month: '08'
oa_version: None
page: 8602-8607
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'
related_material:
link:
- relation: other
url: https://doi.org/10.1073/pnas.1718598115
status: public
title: Detection and quantification of inbreeding depression for complex traits from
SNP data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7731'
abstract:
- lang: eng
text: 'Genetic association studies in admixed populations are underrepresented in
the genomics literature, with a key concern for researchers being the adequate
control of spurious associations due to population structure. Linear mixed models
(LMMs) are well suited for genome-wide association studies (GWAS) because they
account for both population stratification and cryptic relatedness and achieve
increased statistical power by jointly modeling all genotyped markers. Additionally,
Bayesian LMMs allow for more flexible assumptions about the underlying distribution
of genetic effects, and can concurrently estimate the proportion of phenotypic
variance explained by genetic markers. Using three recently published Bayesian
LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye
(n = 625) and skin (n = 684) color from Cape Verde, an island nation off West
Africa that is home to individuals with a broad range of phenotypic values for
eye and skin color due to the mix of West African and European ancestry. We use
simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying
the genetic architecture of quantitative traits in admixed populations. The Bayesian
LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR)
and one for skin color (DDB1).'
article_processing_charge: No
article_type: original
author:
- first_name: Luke R.
full_name: Lloyd-Jones, Luke R.
last_name: Lloyd-Jones
- 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: Gerhard
full_name: Moser, Gerhard
last_name: Moser
- first_name: Jian
full_name: Zeng, Jian
last_name: Zeng
- first_name: Sandra
full_name: Beleza, Sandra
last_name: Beleza
- first_name: Gregory S.
full_name: Barsh, Gregory S.
last_name: Barsh
- first_name: Hua
full_name: Tang, Hua
last_name: Tang
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis
of eye and skin color in an admixed population via Bayesian linear mixed models.
Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383
apa: Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh,
G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin
color in an admixed population via Bayesian linear mixed models. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.116.193383
chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng,
Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on
the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian
Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383.
ieee: L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and
skin color in an admixed population via Bayesian linear mixed models,” Genetics,
vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017.
ista: Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H,
Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an
admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126.
mla: Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin
Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics,
vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383.
short: L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh,
H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126.
date_created: 2020-04-30T10:47:50Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:15:10Z
day: '01'
doi: 10.1534/genetics.116.193383
extern: '1'
intvolume: ' 206'
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 1113-1126
publication: Genetics
publication_identifier:
issn:
- 0016-6731
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Inference on the genetic basis of eye and skin color in an admixed population
via Bayesian linear mixed models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2017'
...
---
_id: '7733'
abstract:
- lang: eng
text: "Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery
has provided remarkable biological insights into amyotrophic lateral sclerosis
(ALS). One challenge for clinical application of genetic testing is critical evaluation
of the significance of reported variants.\r\nMethods: We use whole exome sequencing
(WES) to develop a clinically relevant approach to identify a subset of ALS patients
harboring likely pathogenic mutations. In parallel, we assess if DNA methylation
can be used to screen for pathogenicity of novel variants since a methylation
signature has been shown to associate with the pathogenic C9orf72 expansion, but
has not been explored for other ALS mutations. Australian patients identified
with ALS‐relevant variants were cross‐checked with population databases and case
reports to critically assess whether they were “likely causal,” “uncertain significance,”
or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10%
of patients; however, in only 3% of patients (4/120) could these be confidently
considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential
DNA methylation signature in these mutation carriers.\r\nConclusions: The use
of WES in a typical ALS clinic demonstrates a critical approach to variant assessment
with the capability to combine cohorts to enhance the largely unknown genetic
basis of ALS."
article_processing_charge: No
article_type: original
author:
- first_name: Fleur C.
full_name: Garton, Fleur C.
last_name: Garton
- first_name: Beben
full_name: Benyamin, Beben
last_name: Benyamin
- first_name: Qiongyi
full_name: Zhao, Qiongyi
last_name: Zhao
- first_name: Zhijun
full_name: Liu, Zhijun
last_name: Liu
- first_name: Jacob
full_name: Gratten, Jacob
last_name: Gratten
- first_name: Anjali K.
full_name: Henders, Anjali K.
last_name: Henders
- first_name: Zong-Hong
full_name: Zhang, Zong-Hong
last_name: Zhang
- first_name: Janette
full_name: Edson, Janette
last_name: Edson
- first_name: Sarah
full_name: Furlong, Sarah
last_name: Furlong
- first_name: Sarah
full_name: Morgan, Sarah
last_name: Morgan
- first_name: Susan
full_name: Heggie, Susan
last_name: Heggie
- first_name: Kathryn
full_name: Thorpe, Kathryn
last_name: Thorpe
- first_name: Casey
full_name: Pfluger, Casey
last_name: Pfluger
- first_name: Karen A.
full_name: Mather, Karen A.
last_name: Mather
- first_name: Perminder S.
full_name: Sachdev, Perminder S.
last_name: Sachdev
- first_name: Allan F.
full_name: McRae, Allan F.
last_name: McRae
- 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: Sonia
full_name: Shah, Sonia
last_name: Shah
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Marie
full_name: Mangelsdorf, Marie
last_name: Mangelsdorf
- first_name: Robert D.
full_name: Henderson, Robert D.
last_name: Henderson
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Pamela A.
full_name: McCombe, Pamela A.
last_name: McCombe
citation:
ama: Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation
analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics
& Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302
apa: Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K.,
… McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in
a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic
Medicine. Wiley. https://doi.org/10.1002/mgg3.302
chicago: Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten,
Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation
Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics
& Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302.
ieee: F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis
in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics &
Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017.
ista: Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson
J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS,
McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray
NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a
clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic
Medicine. 5(4), 418–428.
mla: Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis
in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics &
Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302.
short: F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H.
Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A.
Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf,
R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine
5 (2017) 418–428.
date_created: 2020-04-30T10:48:25Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:10Z
day: '01'
doi: 10.1002/mgg3.302
extern: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/mgg3.302
month: '07'
oa: 1
oa_version: Published Version
page: 418-428
publication: Molecular Genetics & Genomic Medicine
publication_identifier:
issn:
- 2324-9269
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic
lateral sclerosis cohort
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2017'
...
---
_id: '7755'
abstract:
- lang: eng
text: We give a bird's-eye view of the plastic deformation of crystals aimed at
the statistical physics community, as well as a broad introduction to the statistical
theories of forced rigid systems aimed at the plasticity community. Memory effects
in magnets, spin glasses, charge density waves, and dilute colloidal suspensions
are discussed in relation to the onset of plastic yielding in crystals. Dislocation
avalanches and complex dislocation tangles are discussed via a brief introduction
to the renormalization group and scaling. Analogies to emergent scale invariance
in fracture, jamming, coarsening, and a variety of depinning transitions are explored.
Dislocation dynamics in crystals challenge nonequilibrium statistical physics.
Statistical physics provides both cautionary tales of subtle memory effects in
nonequilibrium systems and systematic tools designed to address complex scale-invariant
behavior on multiple length scales and timescales.
article_processing_charge: No
article_type: original
author:
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
- first_name: Matthew K.
full_name: Bierbaum, Matthew K.
last_name: Bierbaum
- first_name: Karin A.
full_name: Dahmen, Karin A.
last_name: Dahmen
- 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: Julia R.
full_name: Greer, Julia R.
last_name: Greer
- first_name: Lorien X.
full_name: Hayden, Lorien X.
last_name: Hayden
- first_name: Jaron P.
full_name: Kent-Dobias, Jaron P.
last_name: Kent-Dobias
- first_name: Edward D.
full_name: Lee, Edward D.
last_name: Lee
- first_name: Danilo B.
full_name: Liarte, Danilo B.
last_name: Liarte
- first_name: Xiaoyue
full_name: Ni, Xiaoyue
last_name: Ni
- first_name: Katherine N.
full_name: Quinn, Katherine N.
last_name: Quinn
- first_name: Archishman
full_name: Raju, Archishman
last_name: Raju
- first_name: D. Zeb
full_name: Rocklin, D. Zeb
last_name: Rocklin
- first_name: Ashivni
full_name: Shekhawat, Ashivni
last_name: Shekhawat
- first_name: Stefano
full_name: Zapperi, Stefano
last_name: Zapperi
citation:
ama: 'Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections
with statistical physics. Annual Review of Materials Research. 2017;47:217-246.
doi:10.1146/annurev-matsci-070115-032036'
apa: 'Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J.
R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections
with statistical physics. Annual Review of Materials Research. Annual Reviews.
https://doi.org/10.1146/annurev-matsci-070115-032036'
chicago: 'Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich,
Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of
Crystals: Connections with Statistical Physics.” Annual Review of Materials
Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036.'
ieee: 'J. P. Sethna et al., “Deformation of crystals: Connections with statistical
physics,” Annual Review of Materials Research, vol. 47. Annual Reviews,
pp. 217–246, 2017.'
ista: 'Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias
JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi
S. 2017. Deformation of crystals: Connections with statistical physics. Annual
Review of Materials Research. 47, 217–246.'
mla: 'Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical
Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews,
2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.'
short: J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X.
Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z.
Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017)
217–246.
date_created: 2020-04-30T11:38:24Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:18Z
day: '01'
doi: 10.1146/annurev-matsci-070115-032036
extern: '1'
intvolume: ' 47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1146/annurev-matsci-070115-032036
month: '07'
oa: 1
oa_version: Published Version
page: 217-246
publication: Annual Review of Materials Research
publication_identifier:
issn:
- 1531-7331
- 1545-4118
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Deformation of crystals: Connections with statistical physics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2017'
...
---
_id: '7756'
abstract:
- lang: eng
text: We study the shear jamming of athermal frictionless soft spheres, and find
that in the thermodynamic limit, a shear-jammed state exists with different elastic
properties from the isotropically-jammed state. For example, shear-jammed states
can have a non-zero residual shear stress in the thermodynamic limit that arises
from long-range stress-stress correlations. As a result, the ratio of the shear
and bulk moduli, which in isotropically-jammed systems vanishes as the jamming
transition is approached from above, instead approaches a constant. Despite these
striking differences, we argue that in a deeper sense, the shear jamming and isotropic
jamming transitions actually have the same symmetry, and that the differences
can be fully understood by rotating the six-dimensional basis of the elastic modulus
tensor.
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Baity-Jesi, Marco
last_name: Baity-Jesi
- 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
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
ama: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry
of the frictionless shear jamming transition. Journal of Statistical Physics.
2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9
apa: Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J.
P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9
chicago: Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel,
and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming
Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9.
ieee: M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent
SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical
Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.
ista: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3)
symmetry of the frictionless shear jamming transition. Journal of Statistical
Physics. 167(3–4), 735–748.
mla: Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear
Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4,
Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9.
short: M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal
of Statistical Physics 167 (2017) 735–748.
date_created: 2020-04-30T11:38:38Z
date_published: 2017-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '03'
doi: 10.1007/s10955-016-1703-9
extern: '1'
intvolume: ' 167'
issue: 3-4
language:
- iso: eng
month: '01'
oa_version: None
page: 735-748
publication: Journal of Statistical Physics
publication_identifier:
issn:
- 0022-4715
- 1572-9613
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Emergent SO(3) symmetry of the frictionless shear jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...
---
_id: '7757'
abstract:
- lang: eng
text: Recent advances in designing metamaterials have demonstrated that global mechanical
properties of disordered spring networks can be tuned by selectively modifying
only a small subset of bonds. Here, using a computationally efficient approach,
we extend this idea to tune more general properties of networks. With nearly complete
success, we are able to produce a strain between any two target nodes in a network
in response to an applied source strain on any other pair of nodes by removing
only ∼1% of the bonds. We are also able to control multiple pairs of target nodes,
each with a different individual response, from a single source, and to tune multiple
independent source/target responses simultaneously into a network. We have fabricated
physical networks in macroscopic 2D and 3D systems that exhibit these responses.
This work is inspired by the long-range coupled conformational changes that constitute
allosteric function in proteins. The fact that allostery is a common means for
regulation in biological molecules suggests that it is a relatively easy property
to develop through evolution. In analogy, our results show that long-range coupled
mechanical responses are similarly easy to achieve in disordered networks.
article_processing_charge: No
article_type: original
author:
- first_name: Jason W.
full_name: Rocks, Jason W.
last_name: Rocks
- first_name: Nidhi
full_name: Pashine, Nidhi
last_name: Pashine
- first_name: Irmgard
full_name: Bischofberger, Irmgard
last_name: Bischofberger
- 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: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing
allostery-inspired response in mechanical networks. Proceedings of the National
Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114
apa: Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J.,
& Nagel, S. R. (2017). Designing allostery-inspired response in mechanical
networks. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114
chicago: Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich,
Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in
Mechanical Networks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114.
ieee: J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and
S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings
of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the
National Academy of Sciences, pp. 2520–2525, 2017.
ista: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017.
Designing allostery-inspired response in mechanical networks. Proceedings of the
National Academy of Sciences. 114(10), 2520–2525.
mla: Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical
Networks.” Proceedings of the National Academy of Sciences, vol. 114, no.
10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114.
short: J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel,
Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.
date_created: 2020-04-30T11:38:53Z
date_published: 2017-03-07T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '07'
doi: 10.1073/pnas.1612139114
extern: '1'
intvolume: ' 114'
issue: '10'
language:
- iso: eng
month: '03'
oa_version: None
page: 2520-2525
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: Designing allostery-inspired response in mechanical networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7758'
abstract:
- lang: eng
text: Controlling motion at the microscopic scale is a fundamental goal in the development
of biologically inspired systems. We show that the motion of active, self-propelled
colloids can be sufficiently controlled for use as a tool to assemble complex
structures such as braids and weaves out of microscopic filaments. Unlike typical
self-assembly paradigms, these structures are held together by geometric constraints
rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves
precisely controlling the 2D motion of active colloids so that their path has
a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics
simulations that, when the colloids are attached to long semiflexible filaments,
this motion causes the filaments to braid. The ability of the active particles
to provide sufficient force necessary to bend the filaments into a braid depends
on a number of factors, including the self-propulsion mechanism, the properties
of the filament, and the maximum curvature in the braid. Our work demonstrates
that nonequilibrium assembly pathways can be designed using active particles.
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: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid
on the micrometer scale. Proceedings of the National Academy of Sciences.
2017;114(2):257-262. doi:10.1073/pnas.1608838114
apa: Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines
to weave and braid on the micrometer scale. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114
chicago: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as
Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1608838114.
ieee: C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave
and braid on the micrometer scale,” Proceedings of the National Academy of
Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences,
pp. 257–262, 2017.
ista: Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave
and braid on the micrometer scale. Proceedings of the National Academy of Sciences.
114(2), 257–262.
mla: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines
to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy
of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences,
2017, pp. 257–62, doi:10.1073/pnas.1608838114.
short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences
114 (2017) 257–262.
date_created: 2020-04-30T11:39:09Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:15:20Z
day: '10'
doi: 10.1073/pnas.1608838114
extern: '1'
intvolume: ' 114'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 257-262
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: Using active colloids as machines to weave and braid on the micrometer scale
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '787'
abstract:
- lang: eng
text: 'Population protocols are a popular model of distributed computing, in which
randomly-interacting agents with little computational power cooperate to jointly
perform computational tasks. Inspired by developments in molecular computation,
and in particular DNA computing, recent algorithmic work has focused on the complexity
of solving simple yet fundamental tasks in the population model, such as leader
election (which requires convergence to a single agent in a special "leader"
state), and majority (in which agents must converge to a decision as to which
of two possible initial states had higher initial count). Known results point
towards an inherent trade-off between the time complexity of such algorithms,
and the space complexity, i.e. size of the memory available to each agent. In
this paper, we explore this trade-off and provide new upper and lower bounds for
majority and leader election. First, we prove a unified lower bound, which relates
the space available per node with the time complexity achievable by a protocol:
for instance, our result implies that any protocol solving either of these tasks
for n agents using O(log log n) states must take (n=polylogn) expected time. This
is the first result to characterize time complexity for protocols which employ
super-constant number of states per node, and proves that fast, poly-logarithmic
running times require protocols to have relatively large space costs. On the positive
side, we give algorithms showing that fast, poly-logarithmic convergence time
can be achieved using O(log2 n) space per node, in the case of both tasks. Overall,
our results highlight a time complexity separation between O(log log n) and (log2
n) state space size for both majority and leader election in population protocols,
and introduce new techniques, which should be applicable more broadly.'
acknowledgement: "Dan Alistarh was supported by a Swiss National Science\r\nFoundation
Ambizione Fellowship. James Aspnes was supported by the National Science Foundation
\ under grants\r\nCCF-1637385 and CCF-1650596. Rati Gelashvili was supported by
\ the National Science Foundation under grants\r\nCCF-1217921, CCF-1301926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and\r\nOracle
and Intel corporations.\r\nThe authors would like to thank David Doty, David\r\nSoloveichik,
\ and Milan Vojnovic for insightful discussions\r\nand feedback during the development
of this work."
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: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: David
full_name: Eisenstat, David
last_name: Eisenstat
- first_name: Ronald
full_name: Rivest, Ronald
last_name: Rivest
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. Time-space trade-offs
in population protocols. In: SIAM; 2017:2560-2579. doi:doi.org/10.1137/1.9781611974782.169'
apa: 'Alistarh, D.-A., Aspnes, J., Eisenstat, D., Rivest, R., & Gelashvili,
R. (2017). Time-space trade-offs in population protocols (pp. 2560–2579). Presented
at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/doi.org/10.1137/1.9781611974782.169'
chicago: Alistarh, Dan-Adrian, James Aspnes, David Eisenstat, Ronald Rivest, and
Rati Gelashvili. “Time-Space Trade-Offs in Population Protocols,” 2560–79. SIAM,
2017. https://doi.org/doi.org/10.1137/1.9781611974782.169.
ieee: 'D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, and R. Gelashvili, “Time-space
trade-offs in population protocols,” presented at the SODA: Symposium on Discrete
Algorithms, 2017, pp. 2560–2579.'
ista: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. 2017. Time-space
trade-offs in population protocols. SODA: Symposium on Discrete Algorithms, 2560–2579.'
mla: Alistarh, Dan-Adrian, et al. Time-Space Trade-Offs in Population Protocols.
SIAM, 2017, pp. 2560–79, doi:doi.org/10.1137/1.9781611974782.169.
short: D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, R. Gelashvili, in:, SIAM,
2017, pp. 2560–2579.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-02-23T13:19:13Z
day: '01'
doi: doi.org/10.1137/1.9781611974782.169
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.08032
month: '01'
oa: 1
oa_version: None
page: 2560 - 2579
publication_status: published
publisher: SIAM
publist_id: '6869'
status: public
title: Time-space trade-offs in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '788'
abstract:
- lang: eng
text: In contrast to electronic computation, chemical computation is noisy and susceptible
to a variety of sources of error, which has prevented the construction of robust
complex systems. To be effective, chemical algorithms must be designed with an
appropriate error model in mind. Here we consider the model of chemical reaction
networks that preserve molecular count (population protocols), and ask whether
computation can be made robust to a natural model of unintended “leak” reactions.
Our definition of leak is motivated by both the particular spurious behavior seen
when implementing chemical reaction networks with DNA strand displacement cascades,
as well as the unavoidable side reactions in any implementation due to the basic
laws of chemistry. We develop a new “Robust Detection” algorithm for the problem
of fast (logarithmic time) single molecule detection, and prove that it is robust
to this general model of leaks. Besides potential applications in single molecule
detection, the error-correction ideas developed here might enable a new class
of robust-by-design chemical algorithms. Our analysis is based on a non-standard
hybrid argument, combining ideas from discrete analysis of population protocols
with classic Markov chain techniques.
acknowledgement: "D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski
— Supported by Inria project GANG, ANR project DESCARTES, and\r\nNCN grant 2015/17/B/ST6/01897.
D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.\r\n\r\n"
alternative_title:
- LNCS
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: Bartłomiej
full_name: Dudek, Bartłomiej
last_name: Dudek
- first_name: Adrian
full_name: Kosowski, Adrian
last_name: Kosowski
- first_name: David
full_name: Soloveichik, David
last_name: Soloveichik
- first_name: Przemysław
full_name: Uznański, Przemysław
last_name: Uznański
citation:
ama: 'Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection
in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171.
doi:10.1007/978-3-319-66799-7_11'
apa: Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., & Uznański,
P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS,
pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer.
https://doi.org/10.1007/978-3-319-66799-7_11
chicago: Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik,
and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,”
10467 LNCS:155–71. Springer, 2017. https://doi.org/10.1007/978-3-319-66799-7_11.
ieee: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust
detection in leak-prone population protocols,” presented at the DNA Computing
and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171.
ista: Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust
detection in leak-prone population protocols. DNA Computing and Molecular Programming,
LNCS, vol. 10467 LNCS, 155–171.
mla: Alistarh, Dan-Adrian, et al. Robust Detection in Leak-Prone Population Protocols.
Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:10.1007/978-3-319-66799-7_11.
short: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, P. Uznański, in:,
Springer, 2017, pp. 155–171.
conference:
name: DNA Computing and Molecular Programming
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-03-18T12:48:02Z
day: '01'
doi: 10.1007/978-3-319-66799-7_11
extern: '1'
external_id:
arxiv:
- '1706.09937'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09937
month: '01'
oa: 1
oa_version: None
page: 155 - 171
publication_status: published
publisher: Springer
publist_id: '6868'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Robust detection in leak-prone population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10467 LNCS
year: '2017'
...
---
_id: '789'
abstract:
- lang: eng
text: 'The problem of efficient concurrent memory reclamation in unmanaged languages
such as C or C++ is one of the major challenges facing the parallelization of
billions of lines of legacy code. Garbage collectors for C/C++ can be inefficient;
thus, programmers are often forced to use finely-crafted concurrent memory reclamation
techniques. These techniques can provide good performance, but require considerable
programming effort to deploy, and have strict requirements, allowing the programmer
very little room for error. In this work, we present Forkscan, a new conservative
concurrent memory reclamation scheme which is fully automatic and surprisingly
scalable. Forkscan''s semantics place it between automatic garbage collectors
(it requires the programmer to explicitly retire nodes before they can be reclaimed),
and concurrent memory reclamation techniques (as it does not assume that nodes
are completely unlinked from the data structure for correctness). Forkscan''s
implementation exploits these new semantics for efficiency: we leverage parallelism
and optimized implementations of signaling and copy-on-write in modern operating
systems to efficiently obtain and process consistent snapshots of memory that
can be scanned concurrently with the normal program operation. Empirical evaluation
on a range of classical concurrent data structure microbenchmarks shows that Forkscan
can preserve the scalability of the original code, while maintaining an order
of magnitude lower latency than automatic garbage collection, and demonstrating
competitive performance with finely crafted memory reclamation techniques.'
acknowledgement: William Leiserson, Alexander Matveev, and Nir Shavit were supported
by the NSF under grants IIS-1447786 and CCF-1563880, and Dan Alistarh was supported
by a Swiss National Fund Ambizione Fellowship.
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: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. Forkscan: Conservative memory
reclamation for modern operating systems. In: ACM; 2017:483-498. doi:10.1145/3064176.3064214'
apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2017). Forkscan:
Conservative memory reclamation for modern operating systems (pp. 483–498). Presented
at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/3064176.3064214'
chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit.
“Forkscan: Conservative Memory Reclamation for Modern Operating Systems,” 483–98.
ACM, 2017. https://doi.org/10.1145/3064176.3064214.'
ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “Forkscan: Conservative
memory reclamation for modern operating systems,” presented at the EuroSys: European
Conference on Computer Systems, 2017, pp. 483–498.'
ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2017. Forkscan: Conservative
memory reclamation for modern operating systems. EuroSys: European Conference
on Computer Systems, 483–498.'
mla: 'Alistarh, Dan-Adrian, et al. Forkscan: Conservative Memory Reclamation
for Modern Operating Systems. ACM, 2017, pp. 483–98, doi:10.1145/3064176.3064214.'
short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, in:, ACM, 2017, pp.
483–498.
conference:
name: 'EuroSys: European Conference on Computer Systems'
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-02-23T13:19:44Z
day: '01'
doi: 10.1145/3064176.3064214
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 483 - 498
publication_status: published
publisher: ACM
publist_id: '6867'
status: public
title: 'Forkscan: Conservative memory reclamation for modern operating systems'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '790'
abstract:
- lang: eng
text: Stochastic gradient descent (SGD) is a commonly used algorithm for training
linear machine learning models. Based on vector algebra, it benefits from the
inherent parallelism available in an FPGA. In this paper, we first present a single-precision
floating-point SGD implementation on an FPGA that provides similar performance
as a 10-core CPU. We then adapt the design to make it capable of processing low-precision
data. The low-precision data is obtained from a novel compression scheme - called
stochastic quantization, specifically designed for machine learning applications.
We test both full-precision and low-precision designs on various regression and
classification data sets. We achieve up to an order of magnitude training speedup
when using low-precision data compared to a full-precision SGD on the same FPGA
and a state-of-the-art multi-core solution, while maintaining the quality of training.
We open source the designs presented in this paper.
article_processing_charge: No
author:
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- 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: Gustavo
full_name: Alonso, Gustavo
last_name: Alonso
- first_name: Onur
full_name: Mutlu, Onur
last_name: Mutlu
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. FPGA-accelerated dense linear
machine learning: A precision-convergence trade-off. In: IEEE; 2017:160-167. doi:10.1109/FCCM.2017.39'
apa: 'Kara, K., Alistarh, D.-A., Alonso, G., Mutlu, O., & Zhang, C. (2017).
FPGA-accelerated dense linear machine learning: A precision-convergence trade-off
(pp. 160–167). Presented at the FCCM: Field-Programmable Custom Computing Machines,
IEEE. https://doi.org/10.1109/FCCM.2017.39'
chicago: 'Kara, Kaan, Dan-Adrian Alistarh, Gustavo Alonso, Onur Mutlu, and Ce Zhang.
“FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off,”
160–67. IEEE, 2017. https://doi.org/10.1109/FCCM.2017.39.'
ieee: 'K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, and C. Zhang, “FPGA-accelerated
dense linear machine learning: A precision-convergence trade-off,” presented at
the FCCM: Field-Programmable Custom Computing Machines, 2017, pp. 160–167.'
ista: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. 2017. FPGA-accelerated
dense linear machine learning: A precision-convergence trade-off. FCCM: Field-Programmable
Custom Computing Machines, 160–167.'
mla: 'Kara, Kaan, et al. FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence
Trade-Off. IEEE, 2017, pp. 160–67, doi:10.1109/FCCM.2017.39.'
short: K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, C. Zhang, in:, IEEE, 2017,
pp. 160–167.
conference:
name: 'FCCM: Field-Programmable Custom Computing Machines'
date_created: 2018-12-11T11:48:31Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2023-02-23T13:19:52Z
day: '30'
doi: 10.1109/FCCM.2017.39
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 160 - 167
publication_status: published
publisher: IEEE
publist_id: '6865'
status: public
title: 'FPGA-accelerated dense linear machine learning: A precision-convergence trade-off'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '791'
abstract:
- lang: eng
text: 'Consider the following random process: we are given n queues, into which
elements of increasing labels are inserted uniformly at random. To remove an element,
we pick two queues at random, and remove the element of lower label (higher priority)
among the two. The cost of a removal is the rank of the label removed, among labels
still present in any of the queues, that is, the distance from the optimal choice
at each step. Variants of this strategy are prevalent in state-of-the-art concurrent
priority queue implementations. Nonetheless, it is not known whether such implementations
provide any rank guarantees, even in a sequential model. We answer this question,
showing that this strategy provides surprisingly strong guarantees: Although the
single-choice process, where we always insert and remove from a single randomly
chosen queue, has degrading cost, going to infinity as we increase the number
of steps, in the two choice process, the expected rank of a removed element is
O(n) while the expected worst-case cost is O(n log n). These bounds are tight,
and hold irrespective of the number of steps for which we run the process. The
argument is based on a new technical connection between "heavily loaded"
balls-into-bins processes and priority scheduling. Our analytic results inspire
a new concurrent priority queue implementation, which improves upon the state
of the art in terms of practical performance.'
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: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority
scheduling. In: Proceedings of the ACM Symposium on Principles of Distributed
Computing. Vol Part F129314. ACM; 2017:283-292. doi:10.1145/3087801.3087810'
apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Nadiradze, G. (2017). The power
of choice in priority scheduling. In Proceedings of the ACM Symposium on Principles
of Distributed Computing (Vol. Part F129314, pp. 283–292). Washington, WA,
USA: ACM. https://doi.org/10.1145/3087801.3087810'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze.
“The Power of Choice in Priority Scheduling.” In Proceedings of the ACM Symposium
on Principles of Distributed Computing, Part F129314:283–92. ACM, 2017. https://doi.org/10.1145/3087801.3087810.
ieee: D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice
in priority scheduling,” in Proceedings of the ACM Symposium on Principles
of Distributed Computing, Washington, WA, USA, 2017, vol. Part F129314, pp.
283–292.
ista: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in
priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed
Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.'
mla: Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.”
Proceedings of the ACM Symposium on Principles of Distributed Computing,
vol. Part F129314, ACM, 2017, pp. 283–92, doi:10.1145/3087801.3087810.
short: D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the
ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.
conference:
end_date: 2017-07-27
location: Washington, WA, USA
name: 'PODC: Principles of Distributed Computing'
start_date: 2017-07-25
date_created: 2018-12-11T11:48:31Z
date_published: 2017-07-26T00:00:00Z
date_updated: 2023-09-27T12:17:59Z
day: '26'
department:
- _id: DaAl
doi: 10.1145/3087801.3087810
external_id:
isi:
- '000462995000035'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.04178
month: '07'
oa: 1
oa_version: Submitted Version
page: 283 - 292
publication: Proceedings of the ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- 978-145034992-5
publication_status: published
publisher: ACM
publist_id: '6864'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The power of choice in priority scheduling
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: Part F129314
year: '2017'
...
---
_id: '792'
abstract:
- lang: eng
text: The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler
flows, is guided by the infinity of periodic orbits embedded in their strange
attractors. Whether this is also the case for the infinite-dimensional dynamics
of Navier–Stokes equations has long been speculated, and is a topic of ongoing
study. Periodic and relative periodic solutions have been shown to be involved
in transitions to turbulence. Their relevance to turbulent dynamics – specifically,
whether periodic orbits play the same role in high-dimensional nonlinear systems
like the Navier–Stokes equations as they do in lower-dimensional systems – is
the focus of the present investigation. We perform here a detailed study of pipe
flow relative periodic orbits with energies and mean dissipations close to turbulent
values. We outline several approaches to reduction of the translational symmetry
of the system. We study pipe flow in a minimal computational cell at Re=2500,
and report a library of invariant solutions found with the aid of the method of
slices. Detailed study of the unstable manifolds of a sample of these solutions
is consistent with the picture that relative periodic orbits are embedded in the
chaotic saddle and that they guide the turbulent dynamics.
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Kimberly
full_name: Short, Kimberly
last_name: Short
- first_name: Mohammad
full_name: Farazmand, Mohammad
last_name: Farazmand
- first_name: Ashley
full_name: Willis, Ashley
last_name: Willis
- first_name: Predrag
full_name: Cvitanović, Predrag
last_name: Cvitanović
citation:
ama: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic
orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics.
2017;833:274-301. doi:10.1017/jfm.2017.699
apa: Budanur, N. B., Short, K., Farazmand, M., Willis, A., & Cvitanović, P.
(2017). Relative periodic orbits form the backbone of turbulent pipe flow. Journal
of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.699
chicago: Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and
Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe
Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.699.
ieee: N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative
periodic orbits form the backbone of turbulent pipe flow,” Journal of Fluid
Mechanics, vol. 833. Cambridge University Press, pp. 274–301, 2017.
ista: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic
orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833,
274–301.
mla: Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent
Pipe Flow.” Journal of Fluid Mechanics, vol. 833, Cambridge University
Press, 2017, pp. 274–301, doi:10.1017/jfm.2017.699.
short: N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of
Fluid Mechanics 833 (2017) 274–301.
date_created: 2018-12-11T11:48:32Z
date_published: 2017-12-25T00:00:00Z
date_updated: 2023-09-27T12:17:35Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.699
external_id:
isi:
- '000414641700001'
intvolume: ' 833'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.03720
month: '12'
oa: 1
oa_version: Submitted Version
page: 274 - 301
project:
- _id: 25636330-B435-11E9-9278-68D0E5697425
grant_number: 11-NSF-1070
name: ROOTS Genome-wide Analysis of Root Traits
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6862'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relative periodic orbits form the backbone of turbulent pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 833
year: '2017'
...
---
_id: '793'
abstract:
- lang: eng
text: 'Let P be a finite point set in the plane. A cordinary triangle in P is a
subset of P consisting of three non-collinear points such that each of the three
lines determined by the three points contains at most c points of P . Motivated
by a question of Erdös, and answering a question of de Zeeuw, we prove that there
exists a constant c > 0such that P contains a c-ordinary triangle, provided
that P is not contained in the union of two lines. Furthermore, the number of
c-ordinary triangles in P is Ω(| P |). '
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Hossein
full_name: Mojarrad, Hossein
last_name: Mojarrad
- first_name: Márton
full_name: Naszódi, Márton
last_name: Naszódi
- first_name: József
full_name: Solymosi, József
last_name: Solymosi
- first_name: Sebastian
full_name: Stich, Sebastian
last_name: Stich
- first_name: May
full_name: Szedlák, May
last_name: Szedlák
citation:
ama: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence
of ordinary triangles. Computational Geometry: Theory and Applications.
2017;66:28-31. doi:10.1016/j.comgeo.2017.07.002'
apa: 'Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., & Szedlák,
M. (2017). On the existence of ordinary triangles. Computational Geometry:
Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.07.002'
chicago: 'Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian
Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” Computational
Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.07.002.'
ieee: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák,
“On the existence of ordinary triangles,” Computational Geometry: Theory and
Applications, vol. 66. Elsevier, pp. 28–31, 2017.'
ista: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On
the existence of ordinary triangles. Computational Geometry: Theory and Applications.
66, 28–31.'
mla: 'Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” Computational
Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 28–31, doi:10.1016/j.comgeo.2017.07.002.'
short: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational
Geometry: Theory and Applications 66 (2017) 28–31.'
date_created: 2018-12-11T11:48:32Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-27T12:15:16Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.comgeo.2017.07.002
ec_funded: 1
external_id:
isi:
- '000412039700003'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.08183
month: '01'
oa: 1
oa_version: Submitted Version
page: 28 - 31
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
issn:
- '09257721'
publication_status: published
publisher: Elsevier
publist_id: '6861'
quality_controlled: '1'
status: public
title: On the existence of ordinary triangles
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2017'
...