---
_id: '10360'
abstract:
- lang: eng
text: Mapping free-energy landscapes has proved to be a powerful tool for studying
reaction mechanisms. Many complex biomolecular assembly processes, however, have
remained challenging to access using this approach, including the aggregation
of peptides and proteins into amyloid fibrils implicated in a range of disorders.
Here, we generalize the strategy used to probe free-energy landscapes in protein
folding to determine the activation energies and entropies that characterize each
of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which
is associated with Alzheimer’s disease. Our results reveal that interactions between
monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation
fundamentally reverse the thermodynamic signature of this process relative to
primary nucleation, even though both processes generate aggregates from soluble
peptides. By mapping the energetic and entropic contributions along the reaction
trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results
from the enthalpic stabilization of adsorbing peptides in conformations amenable
to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.
acknowledgement: We thank B. Jönsson and I. André for helpful discussions. We acknowledge
financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge
(S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of
Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus
Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden
(S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg
Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science
Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust
(A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the
Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases
(C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).
article_processing_charge: No
article_type: original
author:
- first_name: Samuel I. A.
full_name: Cohen, Samuel I. A.
last_name: Cohen
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Mattias
full_name: Törnquist, Mattias
last_name: Törnquist
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature
Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x
apa: Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist,
M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of
oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
Springer Nature. https://doi.org/10.1038/s41557-018-0023-x
chicago: Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić,
Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell,
Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry.
Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.
ieee: S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer
generation in the aggregation of the amyloid-β peptide,” Nature Chemistry,
vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.
ista: Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M,
Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
10(5), 523–531.
mla: Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry,
vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.
short: S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M.
Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry
10 (2018) 523–531.
date_created: 2021-11-26T12:41:38Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2021-11-26T15:14:00Z
day: '26'
doi: 10.1038/s41557-018-0023-x
extern: '1'
external_id:
pmid:
- '29581486'
fulldoi: https://doi.org/10.1038/s41557-018-0023-x
intvolume: ' 10'
issue: '5'
keyword:
- general chemical engineering
- general chemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 523-531
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct thermodynamic signatures of oligomer generation in the aggregation
of the amyloid-β peptide
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10
year: '2018'
...
---
_id: '10361'
abstract:
- lang: eng
text: Understanding how normally soluble peptides and proteins aggregate to form
amyloid fibrils is central to many areas of modern biomolecular science, ranging
from the development of functional biomaterials to the design of rational therapeutic
strategies against increasingly prevalent medical conditions such as Alzheimer's
and Parkinson's diseases. As such, there is a great need to develop models to
mechanistically describe how amyloid fibrils are formed from precursor peptides
and proteins. Here we review and discuss how ideas and concepts from chemical
reaction kinetics can help to achieve this objective. In particular, we show how
a combination of theory, experiments, and computer simulations, based on chemical
kinetics, provides a general formalism for uncovering, at the molecular level,
the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
acknowledgement: "We acknowledge support from the Swiss National Science Foundation
(T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy
of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.);
the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology
and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances
and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results
has received funding from the European Research Council (ERC) under the\r\nEuropean
Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt
(337969)."
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Johnny
full_name: Habchi, Johnny
last_name: Habchi
- first_name: Sean
full_name: Chia, Sean
last_name: Chia
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation. Annual
Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322
apa: Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo,
M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms
and macroscopic measurements of amyloid fibril formation. Annual Review of
Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322
chicago: Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl,
Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical
Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid
Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews,
2018. https://doi.org/10.1146/annurev-physchem-050317-021322.
ieee: T. C. T. Michaels et al., “Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation,” Annual
Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298,
2018.
ista: Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM,
Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic
measurements of amyloid fibril formation. Annual Review of Physical Chemistry.
69(1), 273–298.
mla: Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms
and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of
Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.
short: T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo,
C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.
date_created: 2021-11-26T12:52:12Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-11-26T15:58:19Z
day: '28'
doi: 10.1146/annurev-physchem-050317-021322
extern: '1'
external_id:
pmid:
- '29490200'
fulldoi: https://doi.org/10.1146/annurev-physchem-050317-021322
intvolume: ' 69'
issue: '1'
keyword:
- physical and theoretical chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 273-298
pmid: 1
publication: Annual Review of Physical Chemistry
publication_identifier:
eissn:
- 1545-1593
issn:
- 0066-426X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chemical kinetics for bridging molecular mechanisms and macroscopic measurements
of amyloid fibril formation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 69
year: '2018'
...
---
_id: '10362'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) form gateways that control molecular exchange
between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules
and enable the selective transport of nuclear transport receptors with bound cargo.
The underlying mechanisms that establish these permeability properties remain
to be fully elucidated but require unstructured nuclear pore proteins rich in
Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical
modeling and in vitro approaches have provided a framework for explaining how
the FG network contributes to the barrier and transport properties of the NPC,
it remains unknown whether the number and/or the spatial positioning of different
FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes
to their collective properties and function. To begin to answer these questions,
we have used DNA origami to build a cylinder that mimics the dimensions of the
central transport channel and can house a specified number of FG-domains at specific
positions with easily tunable design parameters, such as grafting density and
topology. We find the overall morphology of the FG-domain assemblies to be dependent
on their chemical composition, determined by the type and density of FG-repeat,
and on their architectural confinement provided by the DNA cylinder, largely consistent
with here presented molecular dynamics simulations based on a coarse-grained polymer
model. In addition, high-speed atomic force microscopy reveals local and reversible
FG-domain condensation that transiently occludes the lumen of the DNA central
channel mimics, suggestive of how the NPC might establish its permeability properties.
acknowledgement: We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab
for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out
the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and
TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK
Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1,
and EP/M028100/1).
article_processing_charge: No
article_type: original
author:
- first_name: Patrick D. Ellis
full_name: Fisher, Patrick D. Ellis
last_name: Fisher
- first_name: Qi
full_name: Shen, Qi
last_name: Shen
- first_name: Bernice
full_name: Akpinar, Bernice
last_name: Akpinar
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Kenny Kwok Hin
full_name: Chung, Kenny Kwok Hin
last_name: Chung
- first_name: David
full_name: Baddeley, David
last_name: Baddeley
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas J.
full_name: Melia, Thomas J.
last_name: Melia
- first_name: Bart W.
full_name: Hoogenboom, Bart W.
last_name: Hoogenboom
- first_name: Chenxiang
full_name: Lin, Chenxiang
last_name: Lin
- first_name: C. Patrick
full_name: Lusk, C. Patrick
last_name: Lusk
citation:
ama: Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044
apa: Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley,
D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically
disordered nucleoporins within nanopore confinement. ACS Nano. American
Chemical Society. https://doi.org/10.1021/acsnano.7b08044
chicago: Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny
Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami
Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore
Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.
ieee: P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing
intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano,
vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.
ista: Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia
TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 12(2), 1508–1518.
mla: Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing
Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano,
vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.
short: P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley,
A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.
date_created: 2021-11-26T15:15:00Z
date_published: 2018-01-19T00:00:00Z
date_updated: 2021-11-26T15:57:02Z
day: '19'
doi: 10.1021/acsnano.7b08044
extern: '1'
external_id:
pmid:
- '29350911'
fulldoi: https://doi.org/10.1021/acsnano.7b08044
intvolume: ' 12'
issue: '2'
keyword:
- general physics and astronomy
language:
- iso: eng
month: '01'
oa_version: None
page: 1508-1518
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Programmable DNA origami platform for organizing intrinsically disordered
nucleoporins within nanopore confinement
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2018'
...
---
_id: '104'
abstract:
- lang: eng
text: The biotrophic pathogen Ustilago maydis, the causative agent of corn smut
disease, infects one of the most important crops worldwide – Zea mays. To successfully
colonize its host, U. maydis secretes proteins, known as effectors, that suppress
plant defense responses and facilitate the establishment of biotrophy. In this
work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence
and is upregulated during infection. Through microscopic analysis and in vitro
assays, we show that Cce1 is secreted from hyphae during filamentous growth of
the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection
and induce callose deposition as a plant defense response. Cce1 is highly conserved
among smut fungi and the Ustilago bromivora ortholog complemented the virulence
defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core
effector with apoplastic localization that is essential for U. maydis to infect
its host.
acknowledgement: 'the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22],
and the Austrian Academy of Science (OEAW).'
article_processing_charge: No
author:
- first_name: Denise
full_name: Seitner, Denise
last_name: Seitner
- first_name: Simon
full_name: Uhse, Simon
last_name: Uhse
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Armin
full_name: Djamei, Armin
last_name: Djamei
citation:
ama: Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required
for early infection of maize by Ustilago maydis. Molecular Plant Pathology.
2018;19(10):2277-2287. doi:10.1111/mpp.12698
apa: Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector
Cce1 is required for early infection of maize by Ustilago maydis. Molecular
Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698
chicago: Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The
Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.”
Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.
ieee: D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1
is required for early infection of maize by Ustilago maydis,” Molecular Plant
Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.
ista: Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required
for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10),
2277–2287.
mla: Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection
of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10,
Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.
short: D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19
(2018) 2277–2287.
date_created: 2018-12-11T11:44:39Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T10:06:42Z
day: '01'
ddc:
- '580'
department:
- _id: GradSch
doi: 10.1111/mpp.12698
external_id:
isi:
- '000445624100006'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:46:00Z
date_updated: 2018-12-18T09:46:00Z
file_id: '5740'
file_name: 2018_MolecPlantPath_Seitner.pdf
file_size: 682335
relation: main_file
success: 1
file_date_updated: 2018-12-18T09:46:00Z
fulldoi: https://doi.org/10.1111/mpp.12698
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2277 - 2287
publication: Molecular Plant Pathology
publication_status: published
publisher: Wiley
publist_id: '7950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The core effector Cce1 is required for early infection of maize by Ustilago
maydis
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: 19
year: '2018'
...
---
OA_place: publisher
OA_type: hybrid
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2018;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2018). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2018. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2018.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2018, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2018).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-05-20T09:45:10Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
file:
- access_level: open_access
checksum: b27ab1745f6dba2387deb785798a657c
content_type: application/pdf
creator: dernst
date_created: 2025-05-20T09:44:47Z
date_updated: 2025-05-20T09:44:47Z
file_id: '19716'
file_name: 2018_ACM_Chalupa.pdf
file_size: 388891
relation: main_file
success: 1
file_date_updated: 2025-05-20T09:44:47Z
fulldoi: https://doi.org/10.1145/3158119
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
fulldoi: https://doi.org/10.1007/s00283-018-9795-5
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '10626'
abstract:
- lang: eng
text: "Owing to their wide tunability, multiple internal degrees of freedom, and
low disorder, graphene heterostructures are emerging as a promising experimental
platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal
activation gap measurements in dual graphite-gated monolayer graphene devices
fabricated in an edgeless Corbino geometry. In devices with substrate-induced
sublattice splitting, we find a tunable crossover between single- and multicomponent
FQH states in the zero energy Landau level. Activation gaps in the single-component
regime show excellent agreement with numerical calculations using a single broadening
parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps
are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered
state at integer filling ν=−4."
acknowledgement: We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for
discussing their unpublished data and for sharing the stack inversion technique.
The authors acknowledge further discussions of the results with I. Sodemann, M.
Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported
by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work
was performed at the National High Magnetic Field Laboratory, which is supported
by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State
of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative
conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges
the support of the Elings Prize Fellowship in Science of the California Nanosystems
Institute at the University of California, Santa Barbara. A. F. Y. acknowledges
the support of the David and Lucile Packard Foundation.
article_number: '226801'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: H.
full_name: Zhou, H.
last_name: Zhou
- first_name: E. M.
full_name: Spanton, E. M.
last_name: Spanton
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: A. F.
full_name: Young, A. F.
last_name: Young
citation:
ama: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801
apa: Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young,
A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy
gaps in edgeless graphene devices. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.121.226801
chicago: Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and
A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy
Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical
Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.
ieee: H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young,
“Quantitative transport measurements of fractional quantum Hall energy gaps in
edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22.
American Physical Society, 2018.
ista: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 121(22), 226801.
mla: Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional
Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters,
vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.
short: H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young,
Physical Review Letters 121 (2018).
date_created: 2022-01-14T12:15:47Z
date_published: 2018-11-28T00:00:00Z
date_updated: 2022-01-14T13:48:35Z
day: '28'
doi: 10.1103/physrevlett.121.226801
extern: '1'
external_id:
arxiv:
- '1805.04199'
fulldoi: https://doi.org/10.1103/physrevlett.121.226801
intvolume: ' 121'
issue: '22'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.04199
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative transport measurements of fractional quantum Hall energy gaps
in edgeless graphene devices
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 121
year: '2018'
...
---
_id: '10627'
abstract:
- lang: eng
text: We present a scanning probe technique for measuring the dynamics of individual
fluxoid transitions in multiply connected superconducting structures. In these
measurements, a small magnetic particle attached to the tip of a silicon cantilever
is scanned over a micron-size superconducting ring fabricated from a thin aluminum
film. We find that near the superconducting transition temperature of the aluminum,
the dissipation and frequency of the cantilever changes significantly at particular
locations where the tip-induced magnetic flux penetrating the ring causes the
two lowest-energy fluxoid states to become nearly degenerate. In this regime,
we show that changes in the cantilever frequency and dissipation are well-described
by a stochastic resonance (SR) process, wherein small oscillations of the cantilever
in the presence of thermally activated phase slips (TAPS) in the ring give rise
to a dynamical force that modifies the mechanical properties of the cantilever.
Using the SR model, we calculate the average fluctuation rate of the TAPS as a
function of temperature over a 32-dB range in frequency, and we compare it to
the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting
structures.
acknowledgement: "We are grateful to Nadya Mason for useful discussions. This work
was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649,
the Department of Physics and the Frederick Seitz Materials Research Laboratory
Central Facilities at the University of Illinois.\r\n"
article_number: '184501'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler R.
full_name: Naibert, Tyler R.
last_name: Naibert
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501
apa: Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip
dynamics in micron-size superconducting rings. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.97.184501
chicago: Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase
Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B.
American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.
ieee: H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in
micron-size superconducting rings,” Physical Review B, vol. 97, no. 18.
American Physical Society, 2018.
ista: Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 97(18), 184501.
mla: Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting
Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society,
2018, doi:10.1103/physrevb.97.184501.
short: H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).
date_created: 2022-01-14T13:48:47Z
date_published: 2018-05-08T00:00:00Z
date_updated: 2022-01-14T13:58:24Z
day: '08'
doi: 10.1103/physrevb.97.184501
extern: '1'
external_id:
arxiv:
- '1703.08184'
fulldoi: https://doi.org/10.1103/physrevb.97.184501
intvolume: ' 97'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.08184
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imaging phase slip dynamics in micron-size superconducting rings
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 97
year: '2018'
...
---
_id: '1064'
abstract:
- lang: eng
text: 'In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by
P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it
is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot
be separated into two subfamilies by a straight line disjoint from the disks.
In this note we show that essentially the same idea may work for different analogues
and generalizations of their result. In particular, we prove the following: Given
a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety
coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate
of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane
disjoint from the homothets.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Mikhail
full_name: Grigorev, Mikhail
last_name: Grigorev
citation:
ama: Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W.
Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009.
doi:10.1007/s00454-017-9883-x
apa: Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering
theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-017-9883-x
chicago: Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle
Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational
Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.
ieee: A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem
by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry,
vol. 59, no. 4. Springer, pp. 1001–1009, 2018.
ista: Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by
A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.
mla: Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and
R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer,
2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.
short: A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry
59 (2018) 1001–1009.
corr_author: '1'
date_created: 2018-12-11T11:49:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2026-05-20T10:19:33Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-017-9883-x
ec_funded: 1
external_id:
isi:
- '000432205500011'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:27:36Z
date_updated: 2019-01-18T09:27:36Z
file_id: '5844'
file_name: 2018_DiscreteComp_Akopyan.pdf
file_size: 482518
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:27:36Z
fulldoi: https://doi.org/10.1007/s00454-017-9883-x
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1001-1009
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer
publist_id: '6324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the circle covering theorem by A.W. Goodman and R.E. Goodman
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2018'
...
---
_id: '107'
abstract:
- lang: eng
text: 'We introduce the notion of “non-malleable codes” which relaxes the notion
of error correction and error detection. Informally, a code is non-malleable if
the message contained in a modified codeword is either the original message, or
a completely unrelated value. In contrast to error correction and error detection,
non-malleability can be achieved for very rich classes of modifications. We construct
an efficient code that is non-malleable with respect to modifications that affect
each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set
it to either 0 or 1), but independently of the value of the other bits of the
codeword. Using the probabilistic method, we also show a very strong and general
statement: there exists a non-malleable code for every “small enough” family F
of functions via which codewords can be modified. Although this probabilistic
method argument does not directly yield efficient constructions, it gives us efficient
non-malleable codes in the random-oracle model for very general classes of tampering
functions—e.g., functions where every bit in the tampered codeword can depend
arbitrarily on any 99% of the bits in the original codeword. As an application
of non-malleable codes, we show that they provide an elegant algorithmic solution
to the task of protecting functionalities implemented in hardware (e.g., signature
cards) against “tampering attacks.” In such attacks, the secret state of a physical
system is tampered, in the hopes that future interaction with the modified system
will reveal some secret information. This problem was previously studied in the
work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security”
(ATP). We show that non-malleable codes can be used to achieve important improvements
over the prior work. In particular, we show that any functionality can be made
secure against a large class of tampering attacks, simply by encoding the secret
state with a non-malleable code while it is stored in memory.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the
ACM. 2018;65(4). doi:10.1145/3178432
apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes.
Journal of the ACM. ACM. https://doi.org/10.1145/3178432
chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable
Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.
ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal
of the ACM, vol. 65, no. 4. ACM, 2018.
ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of
the ACM. 65(4), 20.
mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM,
vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.
short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2025-04-14T07:22:06Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3178432
ec_funded: 1
external_id:
isi:
- '000442938200004'
fulldoi: https://doi.org/10.1145/3178432
intvolume: ' 65'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2009/608
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7947'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-malleable codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
fulldoi: https://doi.org/10.1109/ISIT.2018.8437654
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '76'
abstract:
- lang: eng
text: 'Consider a fully-connected synchronous distributed system consisting of n
nodes, where up to f nodes may be faulty and every node starts in an arbitrary
initial state. In the synchronous C-counting problem, all nodes need to eventually
agree on a counter that is increased by one modulo C in each round for given C>1.
In the self-stabilising firing squad problem, the task is to eventually guarantee
that all non-faulty nodes have simultaneous responses to external inputs: if a
subset of the correct nodes receive an external “go” signal as input, then all
correct nodes should agree on a round (in the not-too-distant future) in which
to jointly output a “fire” signal. Moreover, no node should generate a “fire”
signal without some correct node having previously received a “go” signal as input.
We present a framework reducing both tasks to binary consensus at very small cost.
For example, we obtain a deterministic algorithm for self-stabilising Byzantine
firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation
and response time O(f), and message size O(log f). As our framework does not restrict
the type of consensus routines used, we also obtain efficient randomised solutions.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads.
Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6
apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting
and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6
chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.
ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing
squads,” Distributed Computing. Springer, 2018.
ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing
squads. Distributed Computing.
mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.
short: C. Lenzen, J. Rybicki, Distributed Computing (2018).
corr_author: '1'
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-12T00:00:00Z
date_updated: 2025-04-15T06:53:15Z
day: '12'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-018-0342-6
external_id:
isi:
- '000475627800005'
file:
- access_level: open_access
checksum: 872db70bba9b401500abe3c6ae2f1a61
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:21:22Z
date_updated: 2020-07-14T12:48:01Z
file_id: '5711'
file_name: 2018_DistributedComputing_Lenzen.pdf
file_size: 799337
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
fulldoi: https://doi.org/10.1007/s00446-018-0342-6
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_status: published
publisher: Springer
publist_id: '7978'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-optimal self-stabilising counting and firing squads
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
year: '2018'
...
---
_id: '7698'
abstract:
- lang: eng
text: Motor output varies along the rostro-caudal axis of the tetrapod spinal cord.
At limb levels, ∼60 motor pools control the alternation of flexor and extensor
muscles about each joint, whereas at thoracic levels as few as 10 motor pools
supply muscle groups that support posture, inspiration, and expiration. Whether
such differences in motor neuron identity and muscle number are associated with
segmental distinctions in interneuron diversity has not been resolved. We show
that select combinations of nineteen transcription factors that specify lumbar
V1 inhibitory interneurons generate subpopulations enriched at limb and thoracic
levels. Specification of limb and thoracic V1 interneurons involves the Hox gene
Hoxc9 independently of motor neurons. Thus, early Hox patterning of the spinal
cord determines the identity of V1 interneurons and motor neurons. These studies
reveal a developmental program of V1 interneuron diversity, providing insight
into the organization of inhibitory interneurons associated with differential
motor output.
article_processing_charge: No
article_type: original
author:
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Myungin
full_name: Baek, Myungin
last_name: Baek
- first_name: Jerry H.
full_name: Yang, Jerry H.
last_name: Yang
- first_name: Esteban G.
full_name: Tabak, Esteban G.
last_name: Tabak
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Christopher R.
full_name: Kintner, Christopher R.
last_name: Kintner
- first_name: Thomas M.
full_name: Jessell, Thomas M.
last_name: Jessell
citation:
ama: Sweeney LB, Bikoff JB, Gabitto MI, et al. Origin and segmental diversity of
spinal inhibitory interneurons. Neuron. 2018;97(2):341-355.e3. doi:10.1016/j.neuron.2017.12.029
apa: Sweeney, L. B., Bikoff, J. B., Gabitto, M. I., Brenner-Morton, S., Baek, M.,
Yang, J. H., … Jessell, T. M. (2018). Origin and segmental diversity of spinal
inhibitory interneurons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.12.029
chicago: Sweeney, Lora B., Jay B. Bikoff, Mariano I. Gabitto, Susan Brenner-Morton,
Myungin Baek, Jerry H. Yang, Esteban G. Tabak, Jeremy S. Dasen, Christopher R.
Kintner, and Thomas M. Jessell. “Origin and Segmental Diversity of Spinal Inhibitory
Interneurons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2017.12.029.
ieee: L. B. Sweeney et al., “Origin and segmental diversity of spinal inhibitory
interneurons,” Neuron, vol. 97, no. 2. Elsevier, p. 341–355.e3, 2018.
ista: Sweeney LB, Bikoff JB, Gabitto MI, Brenner-Morton S, Baek M, Yang JH, Tabak
EG, Dasen JS, Kintner CR, Jessell TM. 2018. Origin and segmental diversity of
spinal inhibitory interneurons. Neuron. 97(2), 341–355.e3.
mla: Sweeney, Lora B., et al. “Origin and Segmental Diversity of Spinal Inhibitory
Interneurons.” Neuron, vol. 97, no. 2, Elsevier, 2018, p. 341–355.e3, doi:10.1016/j.neuron.2017.12.029.
short: L.B. Sweeney, J.B. Bikoff, M.I. Gabitto, S. Brenner-Morton, M. Baek, J.H.
Yang, E.G. Tabak, J.S. Dasen, C.R. Kintner, T.M. Jessell, Neuron 97 (2018) 341–355.e3.
date_created: 2020-04-30T10:35:13Z
date_published: 2018-01-04T00:00:00Z
date_updated: 2024-01-31T10:13:54Z
day: '04'
doi: 10.1016/j.neuron.2017.12.029
extern: '1'
fulldoi: https://doi.org/10.1016/j.neuron.2017.12.029
intvolume: ' 97'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 341-355.e3
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Origin and segmental diversity of spinal inhibitory interneurons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2018'
...
---
_id: '77'
abstract:
- lang: eng
text: Holes confined in quantum dots have gained considerable interest in the past
few years due to their potential as spin qubits. Here we demonstrate two-axis
control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double
quantum dot device. The Pauli spin blockade principle allowed us to demonstrate
electric dipole spin resonance by applying a radio frequency electric field to
one of the electrodes defining the double quantum dot. Coherent hole spin oscillations
with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of
130 ns are measured. The reported results emphasize the potential of Ge as a platform
for fast and electrically tunable hole spin qubit devices.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
article_processing_charge: Yes
article_type: original
author:
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Fei
full_name: Gao, Fei
last_name: Gao
- first_name: Ting
full_name: Wang, Ting
last_name: Wang
- first_name: Friedrich
full_name: Schäffler, Friedrich
last_name: Schäffler
- first_name: Jian
full_name: Zhang, Jian
last_name: Zhang
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature
Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4
apa: Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F.,
… Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4
chicago: Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich
Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature
Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.
ieee: H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications,
vol. 9, no. 3902. Nature Publishing Group, 2018.
ista: Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros
G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).
mla: Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications,
vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.
short: H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang,
G. Katsaros, Nature Communications 9 (2018).
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-25T00:00:00Z
date_updated: 2026-04-08T07:27:13Z
day: '25'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1038/s41467-018-06418-4
ec_funded: 1
external_id:
isi:
- '000445560800010'
file:
- access_level: open_access
checksum: e7148c10a64497e279c4de570b6cc544
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:28:30Z
date_updated: 2020-07-14T12:48:02Z
file_id: '5687'
file_name: 2018_NatureComm_Watzinger.pdf
file_size: 1063469
relation: main_file
file_date_updated: 2020-07-14T12:48:02Z
fulldoi: https://doi.org/10.1038/s41467-018-06418-4
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3902 '
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires
- _id: 2552F888-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y00715
name: Loch Spin-Qubits und Majorana-Fermionen in Germanium
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A germanium hole spin qubit
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: 9
year: '2018'
...
---
_id: '7712'
abstract:
- lang: eng
text: 'Male pattern baldness (MPB) is a sex-limited, age-related, complex trait.
We study MPB genetics in 205,327 European males from the UK Biobank. Here we show
that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62
(SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01)
from conventionally-unrelated males. We detect 624 near-independent genome-wide
loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome
loci explain 11.6%. Autosomal genetic variance is enriched for common variants
and regions of lower linkage disequilibrium. We identify plausible genetic correlations
between MPB and multiple sex-limited markers of earlier puberty, increased bone
mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations
with reproductive traits imply an effect on fitness, consistent with an estimated
linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide
genetic insights into MPB: a phenotype of interest in its own right, with value
as a model sex-limited, complex trait.'
article_number: '5407'
article_processing_charge: No
article_type: original
author:
- first_name: Chloe X.
full_name: Yap, Chloe X.
last_name: Yap
- first_name: Julia
full_name: Sidorenko, Julia
last_name: Sidorenko
- first_name: Yang
full_name: Wu, Yang
last_name: Wu
- first_name: Kathryn E.
full_name: Kemper, Kathryn E.
last_name: Kemper
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- 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: Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence
for pleiotropy in male pattern baldness. Nature Communications. 2018;9.
doi:10.1038/s41467-018-07862-y
apa: Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., …
Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy
in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y
chicago: Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang,
Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of
Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature
Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y.
ieee: C. X. Yap et al., “Dissection of genetic variation and evidence for
pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher
PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male
pattern baldness. Nature Communications. 9, 5407.
mla: Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy
in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer
Nature, 2018, doi:10.1038/s41467-018-07862-y.
short: C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson,
P.M. Visscher, Nature Communications 9 (2018).
date_created: 2020-04-30T10:41:19Z
date_published: 2018-12-20T00:00:00Z
date_updated: 2021-01-12T08:15:02Z
day: '20'
doi: 10.1038/s41467-018-07862-y
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-018-07862-y
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-07862-y
month: '12'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Dissection of genetic variation and evidence for pleiotropy in male pattern
baldness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7713'
abstract:
- lang: eng
text: There are mean differences in complex traits among global human populations.
We hypothesize that part of the phenotypic differentiation is due to natural selection.
To address this hypothesis, we assess the differentiation in allele frequencies
of trait-associated SNPs among African, Eastern Asian, and European populations
for ten complex traits using data of large sample size (up to ~405,000). We show
that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4),
and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations
than matched “control” SNPs, suggesting that these trait-associated SNPs have
undergone natural selection. We further find that SNPs associated with height
(P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance
in linkage disequilibrium (LD) scores across populations than control SNPs. Our
results support the hypothesis that natural selection has shaped the genetic differentiation
of complex traits, such as height and schizophrenia, among worldwide populations.
article_number: '1865'
article_processing_charge: No
article_type: original
author:
- first_name: Jing
full_name: Guo, Jing
last_name: Guo
- first_name: Yang
full_name: Wu, Yang
last_name: Wu
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Zhili
full_name: Zheng, Zhili
last_name: Zheng
- first_name: Maciej
full_name: Trzaskowski, Maciej
last_name: Trzaskowski
- first_name: Jian
full_name: Zeng, Jian
last_name: Zeng
- 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
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
citation:
ama: Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits
shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y
apa: Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J.
(2018). Global genetic differentiation of complex traits shaped by natural selection
in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y
chicago: Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian
Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic
Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature
Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y.
ieee: J. Guo et al., “Global genetic differentiation of complex traits shaped
by natural selection in humans,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher
PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural
selection in humans. Nature Communications. 9, 1865.
mla: Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped
by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer
Nature, 2018, doi:10.1038/s41467-018-04191-y.
short: J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson,
P.M. Visscher, J. Yang, Nature Communications 9 (2018).
date_created: 2020-04-30T10:41:36Z
date_published: 2018-05-14T00:00:00Z
date_updated: 2021-01-12T08:15:02Z
day: '14'
doi: 10.1038/s41467-018-04191-y
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-018-04191-y
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-04191-y
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Global genetic differentiation of complex traits shaped by natural selection
in humans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7714'
abstract:
- lang: eng
text: Health risk factors such as body mass index (BMI) and serum cholesterol are
associated with many common diseases. It often remains unclear whether the risk
factors are cause or consequence of disease, or whether the associations are the
result of confounding. We develop and apply a method (called GSMR) that performs
a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide
association studies to test the causal associations of BMI, waist-to-hip ratio,
serum cholesterols, blood pressures, height, and years of schooling (EduYears)
with common diseases (sample sizes of up to 405,072). We identify a number of
causal associations including a protective effect of LDL-cholesterol against type-2
diabetes (T2D) that might explain the side effects of statins on T2D, a protective
effect of EduYears against Alzheimer’s disease, and bidirectional associations
with opposite effects (e.g., higher BMI increases the risk of T2D but the effect
of T2D on BMI is negative).
article_number: '224'
article_processing_charge: No
article_type: original
author:
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Zhili
full_name: Zheng, Zhili
last_name: Zheng
- first_name: Futao
full_name: Zhang, Futao
last_name: Zhang
- first_name: Yang
full_name: Wu, Yang
last_name: Wu
- first_name: Maciej
full_name: Trzaskowski, Maciej
last_name: Trzaskowski
- first_name: Robert
full_name: Maier, Robert
last_name: Maier
- 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 J.
full_name: McGrath, John J.
last_name: McGrath
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
citation:
ama: Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and
common diseases inferred from GWAS summary data. Nature Communications.
2018;9. doi:10.1038/s41467-017-02317-2
apa: Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang,
J. (2018). Causal associations between risk factors and common diseases inferred
from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2
chicago: Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert
Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors
and Common Diseases Inferred from GWAS Summary Data.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2.
ieee: Z. Zhu et al., “Causal associations between risk factors and common
diseases inferred from GWAS summary data,” Nature Communications, vol.
9. Springer Nature, 2018.
ista: Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath
JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors
and common diseases inferred from GWAS summary data. Nature Communications. 9,
224.
mla: Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases
Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer
Nature, 2018, doi:10.1038/s41467-017-02317-2.
short: Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson,
J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018).
date_created: 2020-04-30T10:41:55Z
date_published: 2018-01-15T00:00:00Z
date_updated: 2021-01-12T08:15:03Z
day: '15'
doi: 10.1038/s41467-017-02317-2
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-017-02317-2
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02317-2
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Causal associations between risk factors and common diseases inferred from
GWAS summary data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7715'
abstract:
- lang: eng
text: Preference for mates with similar phenotypes; that is, assortative mating,
is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8.
Under Fisher's classical theory6, assortative mating is predicted to induce a
signature in the genome at trait-associated loci that can be detected and quantified.
Here, we develop and apply a method to quantify assortative mating on a specific
trait by estimating the correlation (θ) between genetic predictors of the trait
from single nucleotide polymorphisms on odd- versus even-numbered chromosomes.
We show by theory and simulation that the effect of assortative mating can be
quantified in the presence of population stratification. We applied this approach
to 32 complex traits and diseases using single nucleotide polymorphism data from
~400,000 unrelated individuals of European ancestry. We found significant evidence
of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%),
both of which were consistent with theoretical predictions. Overall, our results
imply that assortative mating involves multiple traits and affects the genomic
architecture of loci that are associated with these traits, and that the consequence
of mate choice can be detected from a random sample of genomes.
article_processing_charge: No
article_type: original
author:
- first_name: Loic
full_name: Yengo, Loic
last_name: Yengo
- 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: Matthew C.
full_name: Keller, Matthew C.
last_name: Keller
- first_name: Kathryn E.
full_name: Kemper, Kathryn E.
last_name: Kemper
- first_name: Yuanhao
full_name: Yang, Yuanhao
last_name: Yang
- first_name: Maciej
full_name: Trzaskowski, Maciej
last_name: Trzaskowski
- first_name: Jacob
full_name: Gratten, Jacob
last_name: Gratten
- first_name: Patrick
full_name: Turley, Patrick
last_name: Turley
- first_name: David
full_name: Cesarini, David
last_name: Cesarini
- first_name: Daniel J.
full_name: Benjamin, Daniel J.
last_name: Benjamin
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- 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: Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the
human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3
apa: Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski,
M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome.
Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3
chicago: Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper,
Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative
Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018.
https://doi.org/10.1038/s41562-018-0476-3.
ieee: L. Yengo et al., “Imprint of assortative mating on the human genome,”
Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018.
ista: Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten
J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM.
2018. Imprint of assortative mating on the human genome. Nature Human Behaviour.
2(12), 948–954.
mla: Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature
Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3.
short: L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski,
J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J.
Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954.
date_created: 2020-04-30T10:42:12Z
date_published: 2018-11-26T00:00:00Z
date_updated: 2021-01-12T08:15:03Z
day: '26'
doi: 10.1038/s41562-018-0476-3
extern: '1'
fulldoi: https://doi.org/10.1038/s41562-018-0476-3
intvolume: ' 2'
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 948-954
publication: Nature Human Behaviour
publication_identifier:
issn:
- 2397-3374
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Imprint of assortative mating on the human genome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
_id: '7716'
abstract:
- lang: eng
text: Genomic prediction has the potential to contribute to precision medicine.
However, to date, the utility of such predictors is limited due to low accuracy
for most traits. Here theory and simulation study are used to demonstrate that
widespread pleiotropy among phenotypes can be utilised to improve genomic risk
prediction. We show how a genetic predictor can be created as a weighted index
that combines published genome-wide association study (GWAS) summary statistics
across many different traits. We apply this framework to predict risk of schizophrenia
and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial
heterogeneity in prediction accuracy increases across cohorts. For six additional
phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging
from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor
that combines published summary statistics from multiple traits, as compared to
a predictor based only on one trait.
article_number: '989'
article_processing_charge: No
article_type: original
author:
- first_name: Robert M.
full_name: Maier, Robert M.
last_name: Maier
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Sang Hong
full_name: Lee, Sang Hong
last_name: Lee
- first_name: Maciej
full_name: Trzaskowski, Maciej
last_name: Trzaskowski
- first_name: Douglas M.
full_name: Ruderfer, Douglas M.
last_name: Ruderfer
- first_name: Eli A.
full_name: Stahl, Eli A.
last_name: Stahl
- first_name: Stephan
full_name: Ripke, Stephan
last_name: Ripke
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging
genetic correlations among human diseases and traits. Nature Communications.
2018;9. doi:10.1038/s41467-017-02769-6
apa: Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl,
E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic
correlations among human diseases and traits. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-017-02769-6
chicago: Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas
M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction
by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature
Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6.
ieee: R. M. Maier et al., “Improving genetic prediction by leveraging genetic
correlations among human diseases and traits,” Nature Communications, vol.
9. Springer Nature, 2018.
ista: Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray
NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging
genetic correlations among human diseases and traits. Nature Communications. 9,
989.
mla: Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic
Correlations among Human Diseases and Traits.” Nature Communications, vol.
9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6.
short: R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl,
S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications
9 (2018).
date_created: 2020-04-30T10:42:29Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2021-01-12T08:15:03Z
day: '07'
doi: 10.1038/s41467-017-02769-6
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-017-02769-6
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02769-6
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Improving genetic prediction by leveraging genetic correlations among human
diseases and traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7717'
abstract:
- lang: eng
text: "Background: DNA methylation levels change along with age, but few studies
have examined the variation in the rate of such changes between individuals.\r\nMethods:
We performed a longitudinal analysis to quantify the variation in the rate of
change of DNA methylation between individuals using whole blood DNA methylation
array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90
years).\r\nResults: After stringent quality control, we identified 1507 DNA methylation
CpG sites (rsCpGs) with statistically significant variation in the rate of change
(random slope) of DNA methylation among individuals in a mixed linear model analysis.
Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription
factors and the Wnt signalling pathway, both of which are related to ageing processes.
Furthermore, we investigated the SNP effect on the random slope. We found that
4 out of 1507 rsCpGs had one significant (P < 5 × 10−8/1507) SNP effect and 343
rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide
significance (P < 5 × 10−8). Ninety-five percent of the significant (P < 5 × 10−8)
SNPs are on different chromosomes from their corresponding probes.\r\nConclusions:
We identified CpG sites that have variability in the rate of change of DNA methylation
between individuals, and our results suggest a genetic basis of this variation.
Genes around these CpG sites have been reported to be involved in the ageing process."
article_number: '75'
article_processing_charge: No
article_type: original
author:
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: Riccardo E
full_name: Marioni, Riccardo E
last_name: Marioni
- 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: Jon
full_name: Higham, Jon
last_name: Higham
- first_name: Duncan
full_name: Sproul, Duncan
last_name: Sproul
- first_name: Naomi R
full_name: Wray, Naomi R
last_name: Wray
- first_name: Ian J
full_name: Deary, Ian J
last_name: Deary
- first_name: Allan F
full_name: McRae, Allan F
last_name: McRae
- first_name: Peter M
full_name: Visscher, Peter M
last_name: Visscher
citation:
ama: Zhang Q, Marioni RE, Robinson MR, et al. Genotype effects contribute to variation
in longitudinal methylome patterns in older people. Genome Medicine. 2018;10(1).
doi:10.1186/s13073-018-0585-7
apa: Zhang, Q., Marioni, R. E., Robinson, M. R., Higham, J., Sproul, D., Wray, N.
R., … Visscher, P. M. (2018). Genotype effects contribute to variation in longitudinal
methylome patterns in older people. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-018-0585-7
chicago: Zhang, Qian, Riccardo E Marioni, Matthew Richard Robinson, Jon Higham,
Duncan Sproul, Naomi R Wray, Ian J Deary, Allan F McRae, and Peter M Visscher.
“Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in
Older People.” Genome Medicine. Springer Nature, 2018. https://doi.org/10.1186/s13073-018-0585-7.
ieee: Q. Zhang et al., “Genotype effects contribute to variation in longitudinal
methylome patterns in older people,” Genome Medicine, vol. 10, no. 1. Springer
Nature, 2018.
ista: Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae
AF, Visscher PM. 2018. Genotype effects contribute to variation in longitudinal
methylome patterns in older people. Genome Medicine. 10(1), 75.
mla: Zhang, Qian, et al. “Genotype Effects Contribute to Variation in Longitudinal
Methylome Patterns in Older People.” Genome Medicine, vol. 10, no. 1, 75,
Springer Nature, 2018, doi:10.1186/s13073-018-0585-7.
short: Q. Zhang, R.E. Marioni, M.R. Robinson, J. Higham, D. Sproul, N.R. Wray, I.J.
Deary, A.F. McRae, P.M. Visscher, Genome Medicine 10 (2018).
date_created: 2020-04-30T10:42:50Z
date_published: 2018-10-22T00:00:00Z
date_updated: 2021-01-12T08:15:04Z
day: '22'
doi: 10.1186/s13073-018-0585-7
extern: '1'
fulldoi: https://doi.org/10.1186/s13073-018-0585-7
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13073-018-0585-7
month: '10'
oa: 1
oa_version: Published Version
publication: Genome Medicine
publication_identifier:
issn:
- 1756-994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Genotype effects contribute to variation in longitudinal methylome patterns
in older people
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...