---
_id: '11657'
abstract:
- lang: eng
text: The minimum cut problem for an undirected edge-weighted graph asks us to divide
its set of nodes into two blocks while minimizing the weight sum of the cut edges.
Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm
is based on cluster contraction using label propagation and Padberg and Rinaldi’s
contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory
parallel implementations of our algorithm. Extensive experiments on both real-world
and generated instances show that our algorithm finds the optimal cut on nearly
all instances significantly faster than other state-of-the-art exact algorithms,
and our error rate is lower than that of other heuristic algorithms. In addition,
our parallel algorithm runs a factor 7.5× faster on average when using 32 threads.
To further speed up computations, we also give a version of our algorithm that
performs random edge contractions as preprocessing. This version achieves a lower
running time and better parallel scalability at the expense of a higher error
rate.
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Noe, Alexander
last_name: Noe
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Darren
full_name: Strash, Darren
last_name: Strash
citation:
ama: Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms.
ACM Journal of Experimental Algorithmics. 2018;23:1-22. doi:10.1145/3274662
apa: Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum
cut algorithms. ACM Journal of Experimental Algorithmics. Association for
Computing Machinery. https://doi.org/10.1145/3274662
chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash.
“Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics.
Association for Computing Machinery, 2018. https://doi.org/10.1145/3274662.
ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut
algorithms,” ACM Journal of Experimental Algorithmics, vol. 23. Association
for Computing Machinery, pp. 1–22, 2018.
ista: Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms.
ACM Journal of Experimental Algorithmics. 23, 1–22.
mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” ACM Journal
of Experimental Algorithmics, vol. 23, Association for Computing Machinery,
2018, pp. 1–22, doi:10.1145/3274662.
short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, ACM Journal of Experimental
Algorithmics 23 (2018) 1–22.
date_created: 2022-07-27T08:28:26Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2022-09-09T11:32:52Z
day: '01'
doi: 10.1145/3274662
extern: '1'
external_id:
arxiv:
- '1708.06127'
intvolume: ' 23'
keyword:
- Theoretical Computer Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.06127
month: '10'
oa: 1
oa_version: Preprint
page: 1-22
publication: ACM Journal of Experimental Algorithmics
publication_identifier:
eissn:
- 1084-6654
issn:
- 1084-6654
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical minimum cut algorithms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2018'
...
---
_id: '11667'
abstract:
- lang: eng
text: The focus of classic mechanism design has been on truthful direct-revelation
mechanisms. In the context of combinatorial auctions, the truthful direct-revelation
mechanism that maximizes social welfare is the Vickrey-Clarke-Groves mechanism.
For many valuation spaces, computing the allocation and payments of the VCG mechanism,
however, is a computationally hard problem. We thus study the performance of the
VCG mechanism when bidders are forced to choose bids from a subspace of the valuation
space for which the VCG outcome can be computed efficiently. We prove improved
upper bounds on the welfare loss for restrictions to additive bids and upper and
lower bounds for restrictions to non-additive bids. These bounds show that increased
expressiveness can give rise to additional equilibria of poorer efficiency.
article_number: '5'
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Dütting, Paul
last_name: Dütting
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Martin
full_name: Starnberger, Martin
last_name: Starnberger
citation:
ama: Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based
combinatorial auctions. ACM Transactions on Economics and Computation.
2018;6(2). doi:10.1145/3232860
apa: Dütting, P., Henzinger, M. H., & Starnberger, M. (2018). Valuation compressions
in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation.
Association for Computing Machinery. https://doi.org/10.1145/3232860
chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions
in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation.
Association for Computing Machinery, 2018. https://doi.org/10.1145/3232860.
ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in
VCG-based combinatorial auctions,” ACM Transactions on Economics and Computation,
vol. 6, no. 2. Association for Computing Machinery, 2018.
ista: Dütting P, Henzinger MH, Starnberger M. 2018. Valuation compressions in VCG-based
combinatorial auctions. ACM Transactions on Economics and Computation. 6(2), 5.
mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.”
ACM Transactions on Economics and Computation, vol. 6, no. 2, 5, Association
for Computing Machinery, 2018, doi:10.1145/3232860.
short: P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics
and Computation 6 (2018).
date_created: 2022-07-27T11:46:46Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2022-09-09T12:04:42Z
day: '01'
doi: 10.1145/3232860
extern: '1'
external_id:
arxiv:
- '1310.3153'
intvolume: ' 6'
issue: '2'
keyword:
- Theory of computation
- Algorithmic game theory and mechanism design
- Applied computing
- Economics
- Simplified mechanisms
- Combinatorial auctions with item bidding
- Price of anarchy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.3153
month: '05'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Economics and Computation
publication_identifier:
eissn:
- 2167-8383
issn:
- 2167-8375
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Valuation compressions in VCG-based combinatorial auctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...
---
_id: '11664'
abstract:
- lang: eng
text: "We present a deterministic incremental algorithm for exactly maintaining
the size of a minimum cut with O(log3 n log log2 n) amortized time per edge insertion
and O(1) query time. This result partially answers an open question posed by Thorup
(2007). It also stays in sharp contrast to a polynomial conditional lower bound
for the fully dynamic weighted minimum cut problem. Our algorithm is obtained
by combining a sparsification technique of Kawarabayashi and Thorup (2015) or
its recent improvement by Henzinger, Rao, and Wang (2017), and an exact incremental
algorithm of Henzinger (1997).\r\n\r\nWe also study space-efficient incremental
algorithms for the minimum cut problem. Concretely, we show that there exists
an O(nlog n/ε2) space Monte Carlo algorithm that can process a stream of edge
insertions starting from an empty graph, and with high probability, the algorithm
maintains a (1+ε)-approximation to the minimum cut. The algorithm has O((α (n)
log3 n)/ε 2) amortized update time and constant query time, where α (n) stands
for the inverse of Ackermann function."
acknowledgement: "We thank the two anonymous reviewers for their suggestions and comments,
which improved the\r\nquality of the article."
article_number: '17'
article_processing_charge: No
article_type: original
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Mikkel
full_name: Thorup, Mikkel
last_name: Thorup
citation:
ama: Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in polylogarithmic
amortized update time. ACM Transactions on Algorithms. 2018;14(2). doi:10.1145/3174803
apa: Goranci, G., Henzinger, M. H., & Thorup, M. (2018). Incremental exact min-cut
in polylogarithmic amortized update time. ACM Transactions on Algorithms.
Association for Computing Machinery. https://doi.org/10.1145/3174803
chicago: Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact
Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms.
Association for Computing Machinery, 2018. https://doi.org/10.1145/3174803.
ieee: G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in
polylogarithmic amortized update time,” ACM Transactions on Algorithms,
vol. 14, no. 2. Association for Computing Machinery, 2018.
ista: Goranci G, Henzinger MH, Thorup M. 2018. Incremental exact min-cut in polylogarithmic
amortized update time. ACM Transactions on Algorithms. 14(2), 17.
mla: Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Polylogarithmic Amortized
Update Time.” ACM Transactions on Algorithms, vol. 14, no. 2, 17, Association
for Computing Machinery, 2018, doi:10.1145/3174803.
short: G. Goranci, M.H. Henzinger, M. Thorup, ACM Transactions on Algorithms 14
(2018).
date_created: 2022-07-27T11:29:39Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2022-09-09T11:38:14Z
day: '01'
doi: 10.1145/3174803
extern: '1'
external_id:
arxiv:
- '1611.06500'
intvolume: ' 14'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.06500
month: '04'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Algorithms
publication_identifier:
eissn:
- 1549-6333
issn:
- 1549-6325
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incremental exact min-cut in polylogarithmic amortized update time
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2018'
...
---
_id: '11757'
abstract:
- lang: eng
text: We develop a dynamic version of the primal-dual method for optimization problems,
and apply it to obtain the following results. (1) For the dynamic set-cover problem,
we maintain an O ( f 2)-approximately optimal solution in O ( f · log(m + n))
amortized update time, where f is the maximum “frequency” of an element, n is
the number of sets, and m is the maximum number of elements in the universe at
any point in time. (2) For the dynamic b-matching problem, we maintain an O (1)-approximately
optimal solution in O (log3 n) amortized update time, where n is the number of
nodes in the graph.
article_processing_charge: No
article_type: original
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Giuseppe
full_name: Italiano, Giuseppe
last_name: Italiano
citation:
ama: Bhattacharya S, Henzinger MH, Italiano G. Dynamic algorithms via the primal-dual
method. Information and Computation. 2018;261(08):219-239. doi:10.1016/j.ic.2018.02.005
apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. (2018). Dynamic algorithms
via the primal-dual method. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2018.02.005
chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe Italiano. “Dynamic
Algorithms via the Primal-Dual Method.” Information and Computation. Elsevier,
2018. https://doi.org/10.1016/j.ic.2018.02.005.
ieee: S. Bhattacharya, M. H. Henzinger, and G. Italiano, “Dynamic algorithms via
the primal-dual method,” Information and Computation, vol. 261, no. 08.
Elsevier, pp. 219–239, 2018.
ista: Bhattacharya S, Henzinger MH, Italiano G. 2018. Dynamic algorithms via the
primal-dual method. Information and Computation. 261(08), 219–239.
mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms via the Primal-Dual Method.”
Information and Computation, vol. 261, no. 08, Elsevier, 2018, pp. 219–39,
doi:10.1016/j.ic.2018.02.005.
short: S. Bhattacharya, M.H. Henzinger, G. Italiano, Information and Computation
261 (2018) 219–239.
date_created: 2022-08-08T11:20:03Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-02-10T07:27:39Z
day: '01'
doi: 10.1016/j.ic.2018.02.005
extern: '1'
intvolume: ' 261'
issue: '08'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ic.2018.02.005
month: '08'
oa: 1
oa_version: Published Version
page: 219-239
publication: Information and Computation
publication_identifier:
issn:
- 0890-5401
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic algorithms via the primal-dual method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2018'
...
---
_id: '11828'
abstract:
- lang: eng
text: "We consider the problem of dynamically maintaining (approximate) all-pairs
effective resistances in separable graphs, which are those that admit an n^{c}-separator
theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations
of the all-pairs effective resistances of an n-vertex graph G undergoing edge
insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and
O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable
(i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its
separator can be computed in O~(n) time. Our algorithm is built upon a dynamic
algorithm for maintaining approximate Schur complement that approximately preserves
pairwise effective resistances among a set of terminals for separable graphs,
which might be of independent interest.\r\nWe complement our result by proving
that for any two fixed vertices s and t, no incremental or decremental algorithm
can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case
update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless
the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further
show that for general graphs, no incremental or decremental algorithm can maintain
the s-t effective resistance problem with worst-case update time O(n^{1-delta})
and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false."
alternative_title:
- LIPIcs
article_number: '40'
article_processing_charge: No
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Pan
full_name: Peng, Pan
last_name: Peng
citation:
ama: 'Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate
schur complement on separable graphs. In: 26th Annual European Symposium on
Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018.
doi:10.4230/LIPICS.ESA.2018.40'
apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2018). Dynamic effective resistances
and approximate schur complement on separable graphs. In 26th Annual European
Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl -
Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.40'
chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances
and Approximate Schur Complement on Separable Graphs.” In 26th Annual European
Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.40.
ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and
approximate schur complement on separable graphs,” in 26th Annual European
Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112.
ista: 'Goranci G, Henzinger MH, Peng P. 2018. Dynamic effective resistances and
approximate schur complement on separable graphs. 26th Annual European Symposium
on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112,
40.'
mla: Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur
Complement on Separable Graphs.” 26th Annual European Symposium on Algorithms,
vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.40.
short: G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
conference:
end_date: 2018-08-22
location: Helsinki, Finland
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2018-08-20
date_created: 2022-08-12T08:26:42Z
date_published: 2018-08-14T00:00:00Z
date_updated: 2023-02-16T11:08:08Z
day: '14'
doi: 10.4230/LIPICS.ESA.2018.40
extern: '1'
external_id:
arxiv:
- '1802.09111'
intvolume: ' 112'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2018.40
month: '08'
oa: 1
oa_version: Published Version
publication: 26th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959770811'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic effective resistances and approximate schur complement on separable
graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2018'
...
---
_id: '11827'
abstract:
- lang: eng
text: We study the metric facility location problem with client insertions and deletions.
This setting differs from the classic dynamic facility location problem, where
the set of clients remains the same, but the metric space can change over time.
We show a deterministic algorithm that maintains a constant factor approximation
to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion
or deletion in metric spaces while answering queries about the cost in O(1) time,
where kappa denotes the doubling dimension of the metric. For metric spaces with
bounded doubling dimension, the update time is polylogarithmic in the parameters
of the problem.
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
author:
- first_name: 'Gramoz '
full_name: 'Goranci, Gramoz '
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Dariusz
full_name: Leniowski, Dariusz
last_name: Leniowski
citation:
ama: 'Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility
location. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.39'
apa: 'Goranci, G., Henzinger, M. H., & Leniowski, D. (2018). A tree structure
for dynamic facility location. In 26th Annual European Symposium on Algorithms
(Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ESA.2018.39'
chicago: Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure
for Dynamic Facility Location.” In 26th Annual European Symposium on Algorithms,
Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.39.
ieee: G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic
facility location,” in 26th Annual European Symposium on Algorithms, Helsinki,
Finland, 2018, vol. 112.
ista: 'Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic
facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European
Symposium on Algorithms, LIPIcs, vol. 112, 39.'
mla: Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” 26th
Annual European Symposium on Algorithms, vol. 112, 39, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.39.
short: G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
conference:
end_date: 2018-08-22
location: Helsinki, Finland
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2018-08-20
date_created: 2022-08-12T08:20:57Z
date_published: 2018-08-14T00:00:00Z
date_updated: 2023-02-16T10:50:51Z
day: '14'
doi: 10.4230/LIPICS.ESA.2018.39
extern: '1'
external_id:
arxiv:
- '1909.06653'
intvolume: ' 112'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2018.39
month: '08'
oa: 1
oa_version: Published Version
publication: 26th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959770811'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A tree structure for dynamic facility location
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2018'
...
---
_id: '11768'
abstract:
- lang: eng
text: "In the decremental single-source shortest paths (SSSP) problem, we want to
maintain the distances between a given source node s and every other node in an
n-node m-edge graph G undergoing edge deletions. While its static counterpart
can be solved in near-linear time, this decremental problem is much more challenging
even in the undirected unweighted case. In this case, the classic O(mn) total
update time of Even and Shiloach [16] has been the fastest known algorithm for
three decades. At the cost of a (1+ϵ)-approximation factor, the running time was
recently improved to n2+o(1) by Bernstein and Roditty [9]. In this article, we
bring the running time down to near-linear: We give a (1+ϵ)-approximation algorithm
with m1+o(1) expected total update time, thus obtaining near-linear time. Moreover,
we obtain m1+o(1) log W time for the weighted case, where the edge weights are
integers from 1 to W. The only prior work on weighted graphs in o(mn) time is
the mn0.9 + o(1)-time algorithm by Henzinger et al. [18, 19], which works for
directed graphs with quasi-polynomial edge weights. The expected running time
bound of our algorithm holds against an oblivious adversary.\r\n\r\nIn contrast
to the previous results, which rely on maintaining a sparse emulator, our algorithm
relies on maintaining a so-called sparse (h, ϵ)-hop set introduced by Cohen [12]
in the PRAM literature. An (h, ϵ)-hop set of a graph G=(V, E) is a set F of weighted
edges such that the distance between any pair of nodes in G can be (1+ϵ)-approximated
by their h-hop distance (given by a path containing at most h edges) on G′=(V,
E ∪ F). Our algorithm can maintain an (no(1), ϵ)-hop set of near-linear size in
near-linear time under edge deletions. It is the first of its kind to the best
of our knowledge. To maintain approximate distances using this hop set, we extend
the monotone Even-Shiloach tree of Henzinger et al. [20] and combine it with the
bounded-hop SSSP technique of Bernstein [4, 5] and Mądry [27]. These two new tools
might be of independent interest."
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest
paths on undirected graphs in near-linear total update time. Journal of the
ACM. 2018;65(6):1-40. doi:10.1145/3218657
apa: Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2018). Decremental single-source
shortest paths on undirected graphs in near-linear total update time. Journal
of the ACM. Association for Computing Machinery. https://doi.org/10.1145/3218657
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental
Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update
Time.” Journal of the ACM. Association for Computing Machinery, 2018. https://doi.org/10.1145/3218657.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source
shortest paths on undirected graphs in near-linear total update time,” Journal
of the ACM, vol. 65, no. 6. Association for Computing Machinery, pp. 1–40,
2018.
ista: Henzinger MH, Krinninger S, Nanongkai D. 2018. Decremental single-source shortest
paths on undirected graphs in near-linear total update time. Journal of the ACM.
65(6), 1–40.
mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected
Graphs in near-Linear Total Update Time.” Journal of the ACM, vol. 65,
no. 6, Association for Computing Machinery, 2018, pp. 1–40, doi:10.1145/3218657.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, Journal of the ACM 65 (2018)
1–40.
date_created: 2022-08-08T12:33:17Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-02-21T16:30:41Z
day: '01'
doi: 10.1145/3218657
extern: '1'
external_id:
arxiv:
- '1512.08148'
intvolume: ' 65'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.08148
month: '12'
oa: 1
oa_version: Preprint
page: 1-40
publication: Journal of the ACM
publication_identifier:
eissn:
- 1557-735X
issn:
- 0004-5411
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '11855'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Decremental single-source shortest paths on undirected graphs in near-linear
total update time
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 65
year: '2018'
...
---
_id: '11872'
abstract:
- lang: eng
text: We design fast dynamic algorithms for proper vertex and edge colorings in
a graph undergoing edge insertions and deletions. In the static setting, there
are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge
coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently
maintain such colorings in the dynamic setting as well. We get the following three
results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex
coloring with O(log Δ) expected amortized update time. (2) We present a deterministic
algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized
update time. (3) We present a simple, deterministic algorithm which maintains
a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the
recent O(Δ)-edge coloring algorithm with worst-case update time [4].
article_processing_charge: No
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Deeparnab
full_name: Chakrabarty, Deeparnab
last_name: Chakrabarty
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms
for graph coloring. In: 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
Society for Industrial and Applied Mathematics; 2018:1-20. doi:10.1137/1.9781611975031.1'
apa: 'Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., & Nanongkai, D. (2018).
Dynamic algorithms for graph coloring. In 29th Annual ACM-SIAM Symposium on
Discrete Algorithms (pp. 1–20). New Orleans, LA, United States: Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975031.1'
chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon
Nanongkai. “Dynamic Algorithms for Graph Coloring.” In 29th Annual ACM-SIAM
Symposium on Discrete Algorithms, 1–20. Society for Industrial and Applied
Mathematics, 2018. https://doi.org/10.1137/1.9781611975031.1.
ieee: S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic
algorithms for graph coloring,” in 29th Annual ACM-SIAM Symposium on Discrete
Algorithms, New Orleans, LA, United States, 2018, pp. 1–20.
ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms
for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA:
Symposium on Discrete Algorithms, 1–20.'
mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” 29th
Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and
Applied Mathematics, 2018, pp. 1–20, doi:10.1137/1.9781611975031.1.
short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th
Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied
Mathematics, 2018, pp. 1–20.
conference:
end_date: 2018-01-10
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2022-08-16T12:07:14Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-02-17T11:39:01Z
day: '01'
doi: 10.1137/1.9781611975031.1
extern: '1'
external_id:
arxiv:
- '1711.04355'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.04355
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 20
publication: 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- 978-161197503-1
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic algorithms for graph coloring
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '11882'
abstract:
- lang: eng
text: The minimum cut problem for an undirected edge-weighted graph asks us to divide
its set of nodes into two blocks while minimizing the weight sum of the cut edges.
Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm
is based on cluster contraction using label propagation and Padberg and Rinaldi's
contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory
parallel implementations of our algorithm. Extensive experiments on both real-world
and generated instances show that our algorithm finds the optimal cut on nearly
all instances significantly faster than other state-of-the-art exact algorithms,
and our error rate is lower than that of other heuristic algorithms. In addition,
our parallel algorithm shows good scalability.
article_processing_charge: No
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Noe, Alexander
last_name: Noe
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Darren
full_name: Strash, Darren
last_name: Strash
citation:
ama: 'Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms.
In: 20th Workshop on Algorithm Engineering and Experiments. Society for
Industrial and Applied Mathematics; 2018:48-61. doi:10.1137/1.9781611975055.5'
apa: 'Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical
minimum cut algorithms. In 20th Workshop on Algorithm Engineering and Experiments
(pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/1.9781611975055.5'
chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash.
“Practical Minimum Cut Algorithms.” In 20th Workshop on Algorithm Engineering
and Experiments, 48–61. Society for Industrial and Applied Mathematics, 2018.
https://doi.org/10.1137/1.9781611975055.5.
ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut
algorithms,” in 20th Workshop on Algorithm Engineering and Experiments,
New Orleans, LA, United States, 2018, pp. 48–61.
ista: 'Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms.
20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm
Engineering and Experiments, 48–61.'
mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” 20th Workshop
on Algorithm Engineering and Experiments, Society for Industrial and Applied
Mathematics, 2018, pp. 48–61, doi:10.1137/1.9781611975055.5.
short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm
Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018,
pp. 48–61.
conference:
end_date: 2018-01-08
location: New Orleans, LA, United States
name: 'ALENEX: Symposium on Algorithm Engineering and Experiments'
start_date: 2018-01-07
date_created: 2022-08-17T07:04:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-02-17T14:03:39Z
day: '01'
doi: 10.1137/1.9781611975055.5
extern: '1'
external_id:
arxiv:
- '1708.06127'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.06127
month: '01'
oa: 1
oa_version: Preprint
page: 48-61
publication: 20th Workshop on Algorithm Engineering and Experiments
publication_identifier:
eisbn:
- 978-1-61197-505-5
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical minimum cut algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '11890'
abstract:
- lang: eng
text: "We present the first deterministic data structures for maintaining approximate
minimum vertex cover and maximum matching in a fully dynamic graph \U0001D43A=(\U0001D449,\U0001D438),
with |\U0001D449|=\U0001D45B and |\U0001D438|=\U0001D45A, in \U0001D45C(\U0001D45A‾‾√)
time per update. In particular, for minimum vertex cover, we provide deterministic
data structures for maintaining a (2+\U0001D716) approximation in \U0001D442(log\U0001D45B/\U0001D7162)
amortized time per update. For maximum matching, we show how to maintain a (3+\U0001D716)
approximation in \U0001D442(min(\U0001D45B√/\U0001D716,\U0001D45A1/3/\U0001D7162)
amortized time per update and a (4+\U0001D716) approximation in \U0001D442(\U0001D45A1/3/\U0001D7162)
worst-case time per update. Our data structure for fully dynamic minimum vertex
cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld
[in 42nd ACM Symposium on Theory of Computing, Cambridge, MA, ACM, 2010, pp. 457--464]."
article_processing_charge: No
article_type: original
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Giuseppe F.
full_name: Italiano, Giuseppe F.
last_name: Italiano
citation:
ama: Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data
structures for vertex cover and matching. SIAM Journal on Computing. 2018;47(3):859-887.
doi:10.1137/140998925
apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2018). Deterministic
fully dynamic data structures for vertex cover and matching. SIAM Journal on
Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140998925
chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic
Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal
on Computing. Society for Industrial & Applied Mathematics, 2018. https://doi.org/10.1137/140998925.
ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully
dynamic data structures for vertex cover and matching,” SIAM Journal on Computing,
vol. 47, no. 3. Society for Industrial & Applied Mathematics, pp. 859–887,
2018.
ista: Bhattacharya S, Henzinger MH, Italiano GF. 2018. Deterministic fully dynamic
data structures for vertex cover and matching. SIAM Journal on Computing. 47(3),
859–887.
mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for
Vertex Cover and Matching.” SIAM Journal on Computing, vol. 47, no. 3,
Society for Industrial & Applied Mathematics, 2018, pp. 859–87, doi:10.1137/140998925.
short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, SIAM Journal on Computing
47 (2018) 859–887.
date_created: 2022-08-17T08:21:23Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-21T16:31:30Z
day: '01'
doi: 10.1137/140998925
extern: '1'
external_id:
arxiv:
- '1412.1318'
intvolume: ' 47'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1318
month: '05'
oa: 1
oa_version: Preprint
page: 859-887
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '11875'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Deterministic fully dynamic data structures for vertex cover and matching
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2018'
...
---
_id: '11911'
abstract:
- lang: eng
text: It is common knowledge that there is no single best strategy for graph clustering,
which justifies a plethora of existing approaches. In this paper, we present a
general memetic algorithm, VieClus, to tackle the graph clustering problem. This
algorithm can be adapted to optimize different objective functions. A key component
of our contribution are natural recombine operators that employ ensemble clusterings
as well as multi-level techniques. Lastly, we combine these techniques with a
scalable communication protocol, producing a system that is able to compute high-quality
solutions in a short amount of time. We instantiate our scheme with local search
for modularity and show that our algorithm successfully improves or reproduces
all entries of the 10th DIMACS implementation challenge under consideration using
a small amount of time.
alternative_title:
- LIPIcs
article_number: '3'
article_processing_charge: No
author:
- first_name: Sonja
full_name: Biedermann, Sonja
last_name: Biedermann
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Bernhard
full_name: Schuster, Bernhard
last_name: Schuster
citation:
ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Memetic graph clustering.
In: 17th International Symposium on Experimental Algorithms. Vol 103. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.SEA.2018.3'
apa: 'Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2018). Memetic
graph clustering. In 17th International Symposium on Experimental Algorithms
(Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.SEA.2018.3'
chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster.
“Memetic Graph Clustering.” In 17th International Symposium on Experimental
Algorithms, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
https://doi.org/10.4230/LIPICS.SEA.2018.3.
ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Memetic graph
clustering,” in 17th International Symposium on Experimental Algorithms,
L’Aquila, Italy, 2018, vol. 103.
ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2018. Memetic graph clustering.
17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental
Algorithms, LIPIcs, vol. 103, 3.'
mla: Biedermann, Sonja, et al. “Memetic Graph Clustering.” 17th International
Symposium on Experimental Algorithms, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018, doi:10.4230/LIPICS.SEA.2018.3.
short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, 17th International
Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018.
conference:
end_date: 2018-07-29
location: L'Aquila, Italy
name: 'SEA: Symposium on Experimental Algorithms'
start_date: 2018-07-27
date_created: 2022-08-18T06:49:40Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-02-16T11:45:14Z
day: '01'
doi: 10.4230/LIPICS.SEA.2018.3
extern: '1'
external_id:
arxiv:
- '1802.07034'
intvolume: ' 103'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPICS.SEA.2018.3
month: '07'
oa: 1
oa_version: Published Version
publication: 17th International Symposium on Experimental Algorithms
publication_identifier:
isbn:
- '9783959770705'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Memetic graph clustering
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 103
year: '2018'
...
---
_id: '11958'
abstract:
- lang: eng
text: Solid reagents, leaching catalysts, and heterogeneous photocatalysts are commonly
employed in batch processes but are ill-suited for continuous-flow chemistry.
Heterogeneous catalysts for thermal reactions are typically used in packed-bed
reactors, which cannot be penetrated by light and thus are not suitable for photocatalytic
reactions involving solids. We demonstrate that serial micro-batch reactors (SMBRs)
allow for the continuous utilization of solid materials together with liquids
and gases in flow. This technology was utilized to develop selective and efficient
fluorination reactions using a modified graphitic carbon nitride heterogeneous
catalyst instead of costly homogeneous metal polypyridyl complexes. The merger
of this inexpensive, recyclable catalyst and the SMBR approach enables sustainable
and scalable photocatalysis.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Menny
full_name: Shalom, Menny
last_name: Shalom
- first_name: Markus
full_name: Antonietti, Markus
last_name: Antonietti
- first_name: Peter H.
full_name: Seeberger, Peter H.
last_name: Seeberger
- first_name: Kerry
full_name: Gilmore, Kerry
last_name: Gilmore
citation:
ama: Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous
photocatalysis in serial micro-batch reactors. Angewandte Chemie International
Edition. 2018;57(31):9976-9979. doi:10.1002/anie.201712568
apa: Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., & Gilmore, K.
(2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201712568
chicago: Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger,
and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch
Reactors.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201712568.
ieee: B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous
heterogeneous photocatalysis in serial micro-batch reactors,” Angewandte Chemie
International Edition, vol. 57, no. 31. Wiley, pp. 9976–9979, 2018.
ista: Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. 2018. Continuous
heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie
International Edition. 57(31), 9976–9979.
mla: Pieber, Bartholomäus, et al. “Continuous Heterogeneous Photocatalysis in Serial
Micro-Batch Reactors.” Angewandte Chemie International Edition, vol. 57,
no. 31, Wiley, 2018, pp. 9976–79, doi:10.1002/anie.201712568.
short: B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte
Chemie International Edition 57 (2018) 9976–9979.
date_created: 2022-08-24T10:57:25Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-02-21T10:09:18Z
day: '26'
doi: 10.1002/anie.201712568
extern: '1'
external_id:
pmid:
- '29377383'
intvolume: ' 57'
issue: '31'
language:
- iso: eng
month: '07'
oa_version: None
page: 9976-9979
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- ' 1521-3773'
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous heterogeneous photocatalysis in serial micro-batch reactors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2018'
...
---
_id: '1215'
abstract:
- lang: eng
text: "Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe
first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations
when they occur in examples and it is applied to the case of a group\r\ngenerator.
The second one, based on the previous one and a limit procedure, is an Itô\r\nformula
in a special class of Banach spaces having a product structure with the noise\r\nin
a Hilbert component; again the key point is the extension due to a cancellation.
This\r\nextension to Banach spaces and in particular the specific cancellation
are motivated\r\nby path-dependent Itô calculus."
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The second named author benefited partially from the support of the
“FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H).
He is also grateful for the invitation to the Department of Mathematics of the University
of Pisa. The third named author is grateful for the invitation to ENSTA.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Franco
full_name: Flandoli, Franco
last_name: Flandoli
- first_name: Francesco
full_name: Russo, Francesco
last_name: Russo
- first_name: Giovanni A
full_name: Zanco, Giovanni A
id: 47491882-F248-11E8-B48F-1D18A9856A87
last_name: Zanco
citation:
ama: Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial
regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826.
doi:10.1007/s10959-016-0724-2
apa: Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus
under weak spatial regularity of the processes. Journal of Theoretical Probability.
Springer. https://doi.org/10.1007/s10959-016-0724-2
chicago: Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional
Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical
Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.
ieee: F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under
weak spatial regularity of the processes,” Journal of Theoretical Probability,
vol. 31, no. 2. Springer, pp. 789–826, 2018.
ista: Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak
spatial regularity of the processes. Journal of Theoretical Probability. 31(2),
789–826.
mla: Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial
Regularity of the Processes.” Journal of Theoretical Probability, vol.
31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.
short: F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31
(2018) 789–826.
date_created: 2018-12-11T11:50:45Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:09Z
day: '01'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1007/s10959-016-0724-2
file:
- access_level: open_access
checksum: 47686d58ec21c164540f1a980ff2163f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:13Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5266'
file_name: IST-2016-712-v1+1_s10959-016-0724-2.pdf
file_size: 671125
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 789-826
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Theoretical Probability
publication_status: published
publisher: Springer
publist_id: '6119'
pubrep_id: '712'
quality_controlled: '1'
scopus_import: 1
status: public
title: Infinite-dimensional calculus under weak spatial regularity of the processes
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '124'
abstract:
- lang: eng
text: By investigating the in situ chemical and O-isotope compositions of olivine
in lightly sintered dust agglomerates from the early Solar System, we constrain
their origins and the retention of dust in the protoplanetary disk. The grain
sizes of silicates in these agglomeratic olivine (AO) chondrules indicate that
the grain sizes of chondrule precursors in the Renazzo-like carbonaceous (CR)
chondrites ranged from <1 to 80 µm. We infer this grain size range to be equivalent
to the size range for dust in the early Solar System. AO chondrules may contain,
but are not solely composed of, recycled fragments of earlier formed chondrules.
They also contain 16O-rich olivine related to amoeboid olivine aggregates and
represent the best record of chondrule-precursor materials. AO chondrules contain
one or more large grains, sometimes similar to FeO-poor (type I) and/or FeO-rich
(type II) chondrules, while others contain a type II chondrule core. These morphologies
are consistent with particle agglomeration by electrostatic charging of grains
during collision, a process that may explain solid agglomeration in the protoplanetary
disk in the micrometer size regime. The petrographic, isotopic, and chemical compositions
of AO chondrules are consistent with chondrule formation by large-scale shocks,
bow shocks, and current sheets. The petrographic, isotopic, and chemical similarities
between AO chondrules in CR chondrites and chondrule-like objects from comet 81P/Wild
2 indicate that comets contain AO chondrules. We infer that these AO chondrules
likely formed in the inner Solar System and migrated to the comet forming region
at least 3 Ma after the formation of the first Solar System solids. Observations
made in this study imply that the protoplanetary disk retained a dusty disk at
least ∼3.7 Ma after the formation of the first Solar System solids, longer than
half of the dusty accretion disks observed around other stars.
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Devin
full_name: Schrader, Devin
last_name: Schrader
- first_name: Kazuhide
full_name: Nagashima, Kazuhide
last_name: Nagashima
- first_name: Jemma
full_name: Davidson, Jemma
last_name: Davidson
- first_name: Timothy
full_name: Mccoy, Timothy
last_name: Mccoy
- first_name: Harold
full_name: Conolly Jr, Harold
last_name: Conolly Jr
- first_name: Dante
full_name: Lauretta, Dante
last_name: Lauretta
citation:
ama: 'Waitukaitis SR, Schrader D, Nagashima K, et al. The retention of dust in protoplanetary
disks: evidence from agglomeration olivine chondrules from the outer solar system.
Geochimica et Cosmochimica Acta. 2018;223:405-421. doi:10.1016/j.gca.2017.12.014'
apa: 'Waitukaitis, S. R., Schrader, D., Nagashima, K., Davidson, J., Mccoy, T.,
Conolly Jr, H., & Lauretta, D. (2018). The retention of dust in protoplanetary
disks: evidence from agglomeration olivine chondrules from the outer solar system.
Geochimica et Cosmochimica Acta. Elsevier. https://doi.org/10.1016/j.gca.2017.12.014'
chicago: 'Waitukaitis, Scott R, Devin Schrader, Kazuhide Nagashima, Jemma Davidson,
Timothy Mccoy, Harold Conolly Jr, and Dante Lauretta. “The Retention of Dust in
Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the
Outer Solar System.” Geochimica et Cosmochimica Acta. Elsevier, 2018. https://doi.org/10.1016/j.gca.2017.12.014.'
ieee: 'S. R. Waitukaitis et al., “The retention of dust in protoplanetary
disks: evidence from agglomeration olivine chondrules from the outer solar system,”
Geochimica et Cosmochimica Acta, vol. 223. Elsevier, pp. 405–421, 2018.'
ista: 'Waitukaitis SR, Schrader D, Nagashima K, Davidson J, Mccoy T, Conolly Jr
H, Lauretta D. 2018. The retention of dust in protoplanetary disks: evidence from
agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica
Acta. 223, 405–421.'
mla: 'Waitukaitis, Scott R., et al. “The Retention of Dust in Protoplanetary Disks:
Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica
et Cosmochimica Acta, vol. 223, Elsevier, 2018, pp. 405–21, doi:10.1016/j.gca.2017.12.014.'
short: S.R. Waitukaitis, D. Schrader, K. Nagashima, J. Davidson, T. Mccoy, H. Conolly
Jr, D. Lauretta, Geochimica et Cosmochimica Acta 223 (2018) 405–421.
date_created: 2018-12-11T11:44:45Z
date_published: 2018-02-15T00:00:00Z
date_updated: 2021-01-12T06:49:19Z
day: '15'
doi: 10.1016/j.gca.2017.12.014
extern: '1'
intvolume: ' 223'
language:
- iso: eng
month: '02'
oa_version: None
page: 405 - 421
publication: Geochimica et Cosmochimica Acta
publication_status: published
publisher: Elsevier
publist_id: '7930'
quality_controlled: '1'
status: public
title: 'The retention of dust in protoplanetary disks: evidence from agglomeration
olivine chondrules from the outer solar system'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 223
year: '2018'
...
---
_id: '125'
abstract:
- lang: eng
text: Many fields of study, including medical imaging, granular physics, colloidal
physics, and active matter, require the precise identification and tracking of
particle-like objects in images. While many algorithms exist to track particles
in diffuse conditions, these often perform poorly when particles are densely packed
together—as in, for example, solid-like systems of granular materials. Incorrect
particle identification can have significant effects on the calculation of physical
quantities, which makes the development of more precise and faster tracking algorithms
a worthwhile endeavor. In this work, we present a new tracking algorithm to identify
particles in dense systems that is both highly accurate and fast. We demonstrate
the efficacy of our approach by analyzing images of dense, solid-state granular
media, where we achieve an identification error of 5% in the worst evaluated cases.
Going further, we propose a parallelization strategy for our algorithm using a
GPU, which results in a speedup of up to 10× when compared to a sequential CPU
implementation in C and up to 40× when compared to the reference MATLAB library
widely used for particle tracking. Our results extend the capabilities of state-of-the-art
particle tracking methods by allowing fast, high-fidelity detection in dense media
at high resolutions.
author:
- first_name: Mauricio
full_name: Cerda, Mauricio
last_name: Cerda
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Cristóbal
full_name: Navarro, Cristóbal
last_name: Navarro
- first_name: Juan
full_name: Silva, Juan
last_name: Silva
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Nancy
full_name: Hitschfeld, Nancy
last_name: Hitschfeld
citation:
ama: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. A high-speed
tracking algorithm for dense granular media. Computer Physics Communications.
2018;227:8-16. doi:10.1016/j.cpc.2018.02.010
apa: Cerda, M., Waitukaitis, S. R., Navarro, C., Silva, J., Mujica, N., & Hitschfeld,
N. (2018). A high-speed tracking algorithm for dense granular media. Computer
Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.02.010
chicago: Cerda, Mauricio, Scott R Waitukaitis, Cristóbal Navarro, Juan Silva, Nicolás
Mujica, and Nancy Hitschfeld. “A High-Speed Tracking Algorithm for Dense Granular
Media.” Computer Physics Communications. Elsevier, 2018. https://doi.org/10.1016/j.cpc.2018.02.010.
ieee: M. Cerda, S. R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, and N. Hitschfeld,
“A high-speed tracking algorithm for dense granular media,” Computer Physics
Communications, vol. 227. Elsevier, pp. 8–16, 2018.
ista: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. 2018.
A high-speed tracking algorithm for dense granular media. Computer Physics Communications.
227, 8–16.
mla: Cerda, Mauricio, et al. “A High-Speed Tracking Algorithm for Dense Granular
Media.” Computer Physics Communications, vol. 227, Elsevier, 2018, pp.
8–16, doi:10.1016/j.cpc.2018.02.010.
short: M. Cerda, S.R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, N. Hitschfeld,
Computer Physics Communications 227 (2018) 8–16.
date_created: 2018-12-11T11:44:45Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:23Z
day: '01'
doi: 10.1016/j.cpc.2018.02.010
extern: '1'
intvolume: ' 227'
language:
- iso: eng
month: '06'
oa_version: None
page: 8 - 16
publication: Computer Physics Communications
publication_status: published
publisher: Elsevier
publist_id: '7928'
quality_controlled: '1'
status: public
title: A high-speed tracking algorithm for dense granular media
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 227
year: '2018'
...
---
_id: '126'
abstract:
- lang: eng
text: The Leidenfrost effect occurs when a liquid or stiff sublimable solid near
a hot surface creates enough vapor beneath it to lift itself up and float. In
contrast, vaporizable soft solids, e.g., hydrogels, have been shown to exhibit
persistent bouncing - the elastic Leidenfrost effect. By carefully lowering hydrogel
spheres towards a hot surface, we discover that they are also capable of floating.
The bounce-to-float transition is controlled by the approach velocity and temperature,
analogously to the "dynamic Leidenfrost effect." For the floating regime,
we measure power-law scalings for the gap geometry, which we explain with a model
that couples the vaporization rate to the spherical shape. Our results reveal
that hydrogels are a promising pathway for controlling floating Leidenfrost objects
through shape.
acknowledgement: We acknowledge funding from the Netherlands Organization for Scientific
Research through Grants VICI No. NWO- 680-47-609 (M. v. H. and S. W.) and VENI No.
NWO-680- 47-453 (S. W.), and from the German Science Foundation through Grant No.
HA8467/1-1 (K. H.).
article_number: '048001 '
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Kirsten
full_name: Harth, Kirsten
last_name: Harth
- first_name: Martin
full_name: Van Hecke, Martin
last_name: Van Hecke
citation:
ama: 'Waitukaitis SR, Harth K, Van Hecke M. From bouncing to floating: the Leidenfrost
effect with hydrogel spheres. Physical Review Letters. 2018;121(4). doi:10.1103/PhysRevLett.121.048001'
apa: 'Waitukaitis, S. R., Harth, K., & Van Hecke, M. (2018). From bouncing to
floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.121.048001'
chicago: 'Waitukaitis, Scott R, Kirsten Harth, and Martin Van Hecke. “From Bouncing
to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review
Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.048001.'
ieee: 'S. R. Waitukaitis, K. Harth, and M. Van Hecke, “From bouncing to floating:
the Leidenfrost effect with hydrogel spheres,” Physical Review Letters,
vol. 121, no. 4. American Physical Society, 2018.'
ista: 'Waitukaitis SR, Harth K, Van Hecke M. 2018. From bouncing to floating: the
Leidenfrost effect with hydrogel spheres. Physical Review Letters. 121(4), 048001.'
mla: 'Waitukaitis, Scott R., et al. “From Bouncing to Floating: The Leidenfrost
Effect with Hydrogel Spheres.” Physical Review Letters, vol. 121, no. 4,
048001, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.048001.'
short: S.R. Waitukaitis, K. Harth, M. Van Hecke, Physical Review Letters 121 (2018).
date_created: 2018-12-11T11:44:46Z
date_published: 2018-07-25T00:00:00Z
date_updated: 2021-01-12T06:49:27Z
day: '25'
doi: 10.1103/PhysRevLett.121.048001
extern: '1'
intvolume: ' 121'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7927'
quality_controlled: '1'
status: public
title: 'From bouncing to floating: the Leidenfrost effect with hydrogel spheres'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '127'
abstract:
- lang: eng
text: The ideas of topology are breaking ground in origami-based metamaterials.
Experiments now show that certain shapes — doughnuts included — exhibit topological
bistability, and can be made to click between different topologically stable states.
author:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Waitukaitis SR. Clicks for doughnuts. Nature Physics. 2018;14(8):777-778.
doi:10.1038/s41567-018-0160-6
apa: Waitukaitis, S. R. (2018). Clicks for doughnuts. Nature Physics. Nature
Publishing Group. https://doi.org/10.1038/s41567-018-0160-6
chicago: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0160-6.
ieee: S. R. Waitukaitis, “Clicks for doughnuts,” Nature Physics, vol. 14,
no. 8. Nature Publishing Group, pp. 777–778, 2018.
ista: Waitukaitis SR. 2018. Clicks for doughnuts. Nature Physics. 14(8), 777–778.
mla: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics, vol. 14,
no. 8, Nature Publishing Group, 2018, pp. 777–78, doi:10.1038/s41567-018-0160-6.
short: S.R. Waitukaitis, Nature Physics 14 (2018) 777–778.
date_created: 2018-12-11T11:44:46Z
date_published: 2018-05-28T00:00:00Z
date_updated: 2021-01-12T06:49:31Z
day: '28'
doi: 10.1038/s41567-018-0160-6
extern: '1'
intvolume: ' 14'
issue: '8'
language:
- iso: eng
month: '05'
oa_version: None
page: 777 - 778
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7926'
status: public
title: Clicks for doughnuts
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2018'
...
---
_id: '174'
abstract:
- lang: eng
text: We survey recent efforts to quantify failures of the Hasse principle in families
of rationally connected varieties.
alternative_title:
- Proceedings of Symposia in Pure Mathematics
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: 'Browning TD. How often does the Hasse principle hold? In: Vol 97. American
Mathematical Society; 2018:89-102. doi:10.1090/pspum/097.2/01700'
apa: 'Browning, T. D. (2018). How often does the Hasse principle hold? (Vol. 97,
pp. 89–102). Presented at the Algebraic Geometry, Salt Lake City, Utah, USA: American
Mathematical Society. https://doi.org/10.1090/pspum/097.2/01700'
chicago: Browning, Timothy D. “How Often Does the Hasse Principle Hold?,” 97:89–102.
American Mathematical Society, 2018. https://doi.org/10.1090/pspum/097.2/01700.
ieee: T. D. Browning, “How often does the Hasse principle hold?,” presented at the
Algebraic Geometry, Salt Lake City, Utah, USA, 2018, vol. 97, no. 2, pp. 89–102.
ista: Browning TD. 2018. How often does the Hasse principle hold? Algebraic Geometry,
Proceedings of Symposia in Pure Mathematics, vol. 97, 89–102.
mla: Browning, Timothy D. How Often Does the Hasse Principle Hold? Vol. 97,
no. 2, American Mathematical Society, 2018, pp. 89–102, doi:10.1090/pspum/097.2/01700.
short: T.D. Browning, in:, American Mathematical Society, 2018, pp. 89–102.
conference:
end_date: 2015-07-10
location: Salt Lake City, Utah, USA
name: Algebraic Geometry
start_date: 2015-07-06
date_created: 2018-12-11T11:45:01Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:54Z
day: '01'
doi: 10.1090/pspum/097.2/01700
extern: '1'
intvolume: ' 97'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 89 - 102
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: How often does the Hasse principle hold?
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 97
year: '2018'
...
---
_id: '176'
abstract:
- lang: eng
text: For a general class of non-negative functions defined on integral ideals of
number fields, upper bounds are established for their average over the values
of certain principal ideals that are associated to irreducible binary forms with
integer coefficients.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Efthymios
full_name: Sofos, Efthymios
last_name: Sofos
citation:
ama: Browning TD, Sofos E. Averages of arithmetic functions over principal ideals.
International Journal of Nuber Theory. 2018;15(3):547-567. doi:10.1142/S1793042119500283
apa: Browning, T. D., & Sofos, E. (2018). Averages of arithmetic functions over
principal ideals. International Journal of Nuber Theory. World Scientific
Publishing. https://doi.org/10.1142/S1793042119500283
chicago: Browning, Timothy D, and Efthymios Sofos. “Averages of Arithmetic Functions
over Principal Ideals.” International Journal of Nuber Theory. World Scientific
Publishing, 2018. https://doi.org/10.1142/S1793042119500283.
ieee: T. D. Browning and E. Sofos, “Averages of arithmetic functions over principal
ideals,” International Journal of Nuber Theory, vol. 15, no. 3. World Scientific
Publishing, pp. 547–567, 2018.
ista: Browning TD, Sofos E. 2018. Averages of arithmetic functions over principal
ideals. International Journal of Nuber Theory. 15(3), 547–567.
mla: Browning, Timothy D., and Efthymios Sofos. “Averages of Arithmetic Functions
over Principal Ideals.” International Journal of Nuber Theory, vol. 15,
no. 3, World Scientific Publishing, 2018, pp. 547–67, doi:10.1142/S1793042119500283.
short: T.D. Browning, E. Sofos, International Journal of Nuber Theory 15 (2018)
547–567.
date_created: 2018-12-11T11:45:01Z
date_published: 2018-11-16T00:00:00Z
date_updated: 2021-01-12T06:53:01Z
day: '16'
doi: 10.1142/S1793042119500283
extern: '1'
external_id:
arxiv:
- '1706.04331'
intvolume: ' 15'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.04331
month: '11'
oa: 1
oa_version: Preprint
page: 547-567
publication: International Journal of Nuber Theory
publication_status: published
publisher: World Scientific Publishing
status: public
title: Averages of arithmetic functions over principal ideals
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 15
year: '2018'
...
---
_id: '178'
abstract:
- lang: eng
text: We give an upper bound for the number of rational points of height at most
B, lying on a surface defined by a quadratic form Q. The bound shows an explicit
dependence on Q. It is optimal with respect to B, and is also optimal for typical
forms Q.
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath-Brown
citation:
ama: Browning TD, Heath-Brown R. Counting rational points on quadric surfaces. Discrete
Analysis. 2018;15:1-29. doi:10.19086/da.4375
apa: Browning, T. D., & Heath-Brown, R. (2018). Counting rational points on
quadric surfaces. Discrete Analysis. Alliance of Diamond Open Access Journals.
https://doi.org/10.19086/da.4375
chicago: Browning, Timothy D, and Roger Heath-Brown. “Counting Rational Points on
Quadric Surfaces.” Discrete Analysis. Alliance of Diamond Open Access Journals,
2018. https://doi.org/10.19086/da.4375.
ieee: T. D. Browning and R. Heath-Brown, “Counting rational points on quadric surfaces,”
Discrete Analysis, vol. 15. Alliance of Diamond Open Access Journals, pp.
1–29, 2018.
ista: Browning TD, Heath-Brown R. 2018. Counting rational points on quadric surfaces.
Discrete Analysis. 15, 1–29.
mla: Browning, Timothy D., and Roger Heath-Brown. “Counting Rational Points on Quadric
Surfaces.” Discrete Analysis, vol. 15, Alliance of Diamond Open Access
Journals, 2018, pp. 1–29, doi:10.19086/da.4375.
short: T.D. Browning, R. Heath-Brown, Discrete Analysis 15 (2018) 1–29.
date_created: 2018-12-11T11:45:02Z
date_published: 2018-09-07T00:00:00Z
date_updated: 2022-08-26T09:13:02Z
day: '07'
ddc:
- '512'
doi: 10.19086/da.4375
extern: '1'
external_id:
arxiv:
- '1801.00979'
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.00979
month: '09'
oa: 1
oa_version: Preprint
page: 1 - 29
publication: Discrete Analysis
publication_identifier:
eissn:
- 2397-3129
publication_status: published
publisher: Alliance of Diamond Open Access Journals
quality_controlled: '1'
status: public
title: Counting rational points on quadric surfaces
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '185'
abstract:
- lang: eng
text: We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998),
and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the
setting of approximating maps of graphs on 2-dimensional surfaces by embeddings.
Our proof of this result is constructive and almost immediately implies an efficient
algorithm for testing whether a given piecewise linear map of a graph in a surface
is approximable by an embedding. More precisely, an instance of this problem consists
of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster
edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact
surface M given as the union of a set of pairwise disjoint discs corresponding
to the clusters and a set of pairwise disjoint "pipes" corresponding
to the bundles, connecting certain pairs of these discs. We are to decide whether
G can be embedded inside M so that the vertices in every cluster are drawn in
the corresponding disc, the edges in every bundle pass only through its corresponding
pipe, and every edge crosses the boundary of each disc at most once.
alternative_title:
- Leibniz International Proceedings in Information, LIPIcs
article_number: '39'
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: 'Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39'
apa: 'Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of
graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry,
Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39'
chicago: Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of
Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.
ieee: 'R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented
at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol.
99.'
ista: 'Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG:
Symposium on Computational Geometry, Leibniz International Proceedings in Information,
LIPIcs, vol. 99, 39.'
mla: Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs.
Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.
short: R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:36Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2018.39
file:
- access_level: open_access
checksum: f1b94f1a75b37c414a1f61d59fb2cd4c
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:33:52Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5701'
file_name: 2018_LIPIcs_Fulek.pdf
file_size: 718857
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_identifier:
isbn:
- 978-3-95977-066-8
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hanani-Tutte for approximating maps of graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '188'
abstract:
- lang: eng
text: Smallest enclosing spheres of finite point sets are central to methods in
topological data analysis. Focusing on Bregman divergences to measure dissimilarity,
we prove bounds on the location of the center of a smallest enclosing sphere.
These bounds depend on the range of radii for which Bregman balls are convex.
acknowledgement: This research is partially supported by the Office of Naval Research,
through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR
109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of
the Austrian Science Fund
alternative_title:
- Leibniz International Proceedings in Information, LIPIcs
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff
points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35'
apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres
and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at
the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35'
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing
Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.
ieee: 'H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and
Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational
Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.'
ista: 'Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff
points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz
International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.'
mla: Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points
in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.
short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018, p. 35:1-35:13.
conference:
end_date: 2018-06-14
location: Budapest, Hungary
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2018-06-11
date_created: 2018-12-11T11:45:05Z
date_published: 2018-06-11T00:00:00Z
date_updated: 2021-01-12T06:53:48Z
day: '11'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.4230/LIPIcs.SoCG.2018.35
file:
- access_level: open_access
checksum: 7509403803b3ac1aee94bbc2ad293d21
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:31:31Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5724'
file_name: 2018_LIPIcs_Edelsbrunner.pdf
file_size: 489080
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 35:1 - 35:13
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7733'
quality_controlled: '1'
scopus_import: 1
status: public
title: Smallest enclosing spheres and Chernoff points in Bregman geometry
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2018'
...
---
_id: '2015'
abstract:
- lang: eng
text: We consider the problem of learning a Bayesian network or directed acyclic
graph model from observational data. A number of constraint‐based, score‐based
and hybrid algorithms have been developed for this purpose. Statistical consistency
guarantees of these algorithms rely on the faithfulness assumption, which has
been shown to be restrictive especially for graphs with cycles in the skeleton.
We here propose the sparsest permutation (SP) algorithm, showing that learning
Bayesian networks is possible under strictly weaker assumptions than faithfulness.
This comes at a computational price, thereby indicating a statistical‐computational
trade‐off for causal inference algorithms. In the Gaussian noiseless setting,
we prove that the SP algorithm boils down to finding the permutation of the variables
with the sparsest Cholesky decomposition of the inverse covariance matrix, which
is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation
study showing that in line with the proven stronger consistency guarantees, and
the SP algorithm compares favourably to standard causal inference algorithms in
terms of accuracy for a given sample size.
article_number: e183
article_processing_charge: No
article_type: original
author:
- first_name: Garvesh
full_name: Raskutti, Garvesh
last_name: Raskutti
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations.
STAT. 2018;7(1). doi:10.1002/sta4.183
apa: Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based
on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183
chicago: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs
Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183.
ieee: G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest
permutations,” STAT, vol. 7, no. 1. Wiley, 2018.
ista: Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest
permutations. STAT. 7(1), e183.
mla: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based
on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183.
short: G. Raskutti, C. Uhler, STAT 7 (2018).
date_created: 2018-12-11T11:55:13Z
date_published: 2018-04-17T00:00:00Z
date_updated: 2021-01-12T06:54:44Z
day: '17'
doi: 10.1002/sta4.183
extern: '1'
external_id:
arxiv:
- '1307.0366'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0366
month: '04'
oa: 1
oa_version: Preprint
publication: STAT
publication_status: published
publisher: Wiley
publist_id: '5061'
quality_controlled: '1'
status: public
title: Learning directed acyclic graphs based on sparsest permutations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2018'
...
---
_id: '306'
abstract:
- lang: eng
text: A cornerstone of statistical inference, the maximum entropy framework is being
increasingly applied to construct descriptive and predictive models of biological
systems, especially complex biological networks, from large experimental data
sets. Both its broad applicability and the success it obtained in different contexts
hinge upon its conceptual simplicity and mathematical soundness. Here we try to
concisely review the basic elements of the maximum entropy principle, starting
from the notion of ‘entropy’, and describe its usefulness for the analysis of
biological systems. As examples, we focus specifically on the problem of reconstructing
gene interaction networks from expression data and on recent work attempting to
expand our system-level understanding of bacterial metabolism. Finally, we highlight
some extensions and potential limitations of the maximum entropy approach, and
point to more recent developments that are likely to play a key role in the upcoming
challenges of extracting structures and information from increasingly rich, high-throughput
biological data.
article_number: e00596
author:
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino A, De Martino D. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 2018;4(4).
doi:10.1016/j.heliyon.2018.e00596
apa: De Martino, A., & De Martino, D. (2018). An introduction to the maximum
entropy approach and its application to inference problems in biology. Heliyon.
Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596
chicago: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon.
Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.
ieee: A. De Martino and D. De Martino, “An introduction to the maximum entropy approach
and its application to inference problems in biology,” Heliyon, vol. 4,
no. 4. Elsevier, 2018.
ista: De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach
and its application to inference problems in biology. Heliyon. 4(4), e00596.
mla: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum
Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon,
vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.
short: A. De Martino, D. De Martino, Heliyon 4 (2018).
date_created: 2018-12-11T11:45:44Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '01'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1016/j.heliyon.2018.e00596
ec_funded: 1
file:
- access_level: open_access
checksum: 67010cf5e3b3e0637c659371714a715a
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:36:24Z
date_updated: 2020-07-14T12:45:59Z
file_id: '5929'
file_name: 2018_Heliyon_DeMartino.pdf
file_size: 994490
relation: main_file
file_date_updated: 2020-07-14T12:45:59Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Heliyon
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: 1
status: public
title: An introduction to the maximum entropy approach and its application to inference
problems in biology
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: 4
year: '2018'
...
---
_id: '3300'
abstract:
- lang: eng
text: "This book first explores the origins of this idea, grounded in theoretical
work on temporal logic and automata. The editors and authors are among the world's
leading researchers in this domain, and they contributed 32 chapters representing
a thorough view of the development and application of the technique. Topics covered
include binary decision diagrams, symbolic model checking, satisfiability modulo
theories, partial-order reduction, abstraction, interpolation, concurrency, security
protocols, games, probabilistic model checking, and process algebra, and chapters
on the transfer of theory to industrial practice, property specification languages
for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe
book will be valuable for researchers and graduate students engaged with the development
of formal methods and verification tools."
article_processing_charge: No
author:
- first_name: Edmund M.
full_name: Clarke, Edmund M.
last_name: Clarke
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
citation:
ama: 'Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking.
1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8'
apa: 'Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook
of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8'
chicago: 'Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem.
Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.'
ieee: 'E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model
Checking, 1st ed. Cham: Springer Nature, 2018.'
ista: 'Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking
1st ed., Cham: Springer Nature, XLVIII, 1212p.'
mla: Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer
Nature, 2018, doi:10.1007/978-3-319-10575-8.
short: E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking,
1st ed., Springer Nature, Cham, 2018.
date_created: 2018-12-11T12:02:32Z
date_published: 2018-06-08T00:00:00Z
date_updated: 2021-12-21T10:49:36Z
day: '08'
department:
- _id: ToHe
doi: 10.1007/978-3-319-10575-8
edition: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: XLVIII, 1212
place: Cham
publication_identifier:
eisbn:
- 978-3-319-10575-8
isbn:
- 978-3-319-10574-1
publication_status: published
publisher: Springer Nature
publist_id: '3340'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Handbook of Model Checking
type: book
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2018'
...
---
_id: '37'
abstract:
- lang: eng
text: Developmental processes are inherently dynamic and understanding them requires
quantitative measurements of gene and protein expression levels in space and time.
While live imaging is a powerful approach for obtaining such data, it is still
a challenge to apply it over long periods of time to large tissues, such as the
embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression
and signaling activity patterns in this organ can be studied by collecting tissue
sections at different developmental stages. In combination with immunohistochemistry,
this allows for measuring the levels of multiple developmental regulators in a
quantitative manner with high spatiotemporal resolution. The mean protein expression
levels over time, as well as embryo-to-embryo variability can be analyzed. A key
aspect of the approach is the ability to compare protein levels across different
samples. This requires a number of considerations in sample preparation, imaging
and data analysis. Here we present a protocol for obtaining time course data of
dorsoventral expression patterns from mouse and chick neural tube in the first
3 days of neural tube development. The described workflow starts from embryo dissection
and ends with a processed dataset. Software scripts for data analysis are included.
The protocol is adaptable and instructions that allow the user to modify different
steps are provided. Thus, the procedure can be altered for analysis of time-lapse
images and applied to systems other than the neural tube.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: 'Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling
profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863.
MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4'
apa: Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and
morphogen signaling profiles in the growing neural tube. In Morphogen Gradients
(Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4
chicago: Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients
, 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.
ieee: M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube,” in Morphogen Gradients ,
vol. 1863, Springer Nature, 2018, pp. 47–63.
ista: 'Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods
in Molecular Biology, vol. 1863, 47–63.'
mla: Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients
, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.
short: M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018,
pp. 47–63.
date_created: 2018-12-11T11:44:17Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2021-01-12T07:49:03Z
day: '16'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1007/978-1-4939-8772-6_4
ec_funded: 1
file:
- access_level: open_access
checksum: 2a97d0649fdcfcf1bdca7c8ad1dce71b
content_type: application/pdf
creator: dernst
date_created: 2020-10-13T14:20:37Z
date_updated: 2020-10-13T14:20:37Z
file_id: '8656'
file_name: 2018_MIMB_Zagorski.pdf
file_size: 4906815
relation: main_file
success: 1
file_date_updated: 2020-10-13T14:20:37Z
has_accepted_license: '1'
intvolume: ' 1863'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 47 - 63
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: 'Morphogen Gradients '
publication_identifier:
isbn:
- 978-1-4939-8771-9
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
publist_id: '8018'
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Measuring dorsoventral pattern and morphogen signaling profiles in the growing
neural tube
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1863
year: '2018'
...
---
_id: '305'
abstract:
- lang: eng
text: The hanging-drop network (HDN) is a technology platform based on a completely
open microfluidic network at the bottom of an inverted, surface-patterned substrate.
The platform is predominantly used for the formation, culturing, and interaction
of self-assembled spherical microtissues (spheroids) under precisely controlled
flow conditions. Here, we describe design, fabrication, and operation of microfluidic
hanging-drop networks.
acknowledgement: This work was financially supported by FP7 of the EU through the
project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS”
(contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss
National Science Foundation for Olivier Frey. The research leading to these results
also received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.
[291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise
and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE,
ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members
of the Guet and Tkačik groups, IST Austria, for valuable comments and support.
alternative_title:
- MIMB
author:
- first_name: Patrick
full_name: Misun, Patrick
last_name: Misun
- first_name: Axel
full_name: Birchler, Axel
last_name: Birchler
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Andreas
full_name: Hierlemann, Andreas
last_name: Hierlemann
- first_name: Olivier
full_name: Frey, Olivier
last_name: Frey
citation:
ama: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation
of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202.
doi:10.1007/978-1-4939-7792-5_15
apa: Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication
and operation of microfluidic hanging drop networks. Methods in Molecular Biology.
Springer. https://doi.org/10.1007/978-1-4939-7792-5_15
chicago: Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier
Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods
in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.
ieee: P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and
operation of microfluidic hanging drop networks,” Methods in Molecular Biology,
vol. 1771. Springer, pp. 183–202, 2018.
ista: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation
of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.
mla: Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop
Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp.
183–202, doi:10.1007/978-1-4939-7792-5_15.
short: P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular
Biology 1771 (2018) 183–202.
date_created: 2018-12-11T11:45:43Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:42Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1007/978-1-4939-7792-5_15
ec_funded: 1
intvolume: ' 1771'
language:
- iso: eng
month: '01'
oa_version: None
page: 183 - 202
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '7574'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fabrication and operation of microfluidic hanging drop networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1771
year: '2018'
...
---
_id: '325'
abstract:
- lang: eng
text: Probabilistic programs extend classical imperative programs with real-valued
random variables and random branching. The most basic liveness property for such
programs is the termination property. The qualitative (aka almost-sure) termination
problem asks whether a given program program terminates with probability 1. While
ranking functions provide a sound and complete method for non-probabilistic programs,
the extension of them to probabilistic programs is achieved via ranking supermartingales
(RSMs). Although deep theoretical results have been established about RSMs, their
application to probabilistic programs with nondeterminism has been limited only
to programs of restricted control-flow structure. For non-probabilistic programs,
lexicographic ranking functions provide a compositional and practical approach
for termination analysis of real-world programs. In this work we introduce lexicographic
RSMs and show that they present a sound method for almost-sure termination of
probabilistic programs with nondeterminism. We show that lexicographic RSMs provide
a tool for compositional reasoning about almost-sure termination, and for probabilistic
programs with linear arithmetic they can be synthesized efficiently (in polynomial
time). We also show that with additional restrictions even asymptotic bounds on
expected termination time can be obtained through lexicographic RSMs. Finally,
we present experimental results on benchmarks adapted from previous work to demonstrate
the effectiveness of our approach.
article_number: '34'
author:
- first_name: Sheshansh
full_name: Agrawal, Sheshansh
last_name: Agrawal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
citation:
ama: 'Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs. In: Vol 2. ACM;
2018. doi:10.1145/3158122'
apa: 'Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking
supermartingales: an efficient approach to termination of probabilistic programs
(Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles,
CA, USA: ACM. https://doi.org/10.1145/3158122'
chicago: 'Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic
Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic
Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.'
ieee: 'S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs,” presented at
the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol.
2, no. POPL.'
ista: 'Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales:
an efficient approach to termination of probabilistic programs. POPL: Principles
of Programming Languages vol. 2, 34.'
mla: 'Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient
Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM,
2018, doi:10.1145/3158122.'
short: S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.
conference:
end_date: 2018-01-13
location: Los Angeles, CA, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:50Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:07Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3158122
external_id:
arxiv:
- '1709.04037'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.04037
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: ACM
publist_id: '7540'
quality_controlled: '1'
status: public
title: 'Lexicographic ranking supermartingales: an efficient approach to termination
of probabilistic programs'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
_id: '394'
abstract:
- lang: eng
text: 'The valley pseudospin in monolayer transition metal dichalcogenides (TMDs)
has been proposed as a new way to manipulate information in various optoelectronic
devices. This relies on a large valley polarization that remains stable over long
time scales (hundreds of nanoseconds). However, time-resolved measurements report
valley lifetimes of only a few picoseconds. This has been attributed to mechanisms
such as phonon-mediated intervalley scattering and a precession of the valley
pseudospin through electron-hole exchange. Here we use transient spin grating
to directly measure the valley depolarization lifetime in monolayer MoSe2. We
find a fast valley decay rate that scales linearly with the excitation density
at different temperatures. This establishes the presence of strong exciton-exciton
Coulomb exchange interactions enhancing the valley depolarization. Our work highlights
the microscopic processes inhibiting the efficient use of the exciton valley pseudospin
in monolayer TMDs. '
author:
- first_name: Fahad
full_name: Mahmood, Fahad
last_name: Mahmood
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: Yi
full_name: Lee, Yi
last_name: Lee
- first_name: Jing
full_name: Kong, Jing
last_name: Kong
- first_name: Nuh
full_name: Gedik, Nuh
last_name: Gedik
citation:
ama: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton
interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters.
2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953
apa: Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation
of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2.
Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953
chicago: Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik.
“Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in
Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.
ieee: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of
exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,”
Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.
ista: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton
interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1),
223–228.
mla: Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated
Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1,
American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953.
short: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018)
223–228.
date_created: 2018-12-11T11:46:13Z
date_published: 2018-01-10T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '10'
doi: 10.1021/acs.nanolett.7b03953
extern: '1'
external_id:
arxiv:
- '1712.07925'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.07925
month: '01'
oa: 1
oa_version: Submitted Version
page: 223 - 228
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '7435'
quality_controlled: '1'
status: public
title: Observation of exciton-exciton interaction mediated valley Depolarization in
Monolayer MoSe2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2018'
...
---
_id: '408'
abstract:
- lang: eng
text: Adventitious roots (AR) are de novo formed roots that emerge from any part
of the plant or from callus in tissue culture, except root tissue. The plant tissue
origin and the method by which they are induced determine the physiological properties
of emerged ARs. Hence, a standard method encompassing all types of AR does not
exist. Here we describe a method for the induction and analysis of AR that emerge
from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis
and shows a determined developmental pattern which usually does not involve AR
formation. However, the hypocotyl shows propensity to form de novo roots under
specific circumstances such as removal of the root system, high humidity or flooding,
or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer
surrounding the vascular tissue of the central cylinder, which is reminiscent
to the developmental program of lateral roots. Here we propose an easy protocol
for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings.
alternative_title:
- MIMB
article_processing_charge: No
author:
- first_name: Hoang
full_name: Trinh, Hoang
last_name: Trinh
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: 'Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious
rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761.
Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7'
apa: Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction
of adventitious rooting on intact arabidopsis hypocotyls. In Root Development
(Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7
chicago: Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction
of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development
, 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.
ieee: H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of
adventitious rooting on intact arabidopsis hypocotyls,” in Root Development
, vol. 1761, Springer Nature, 2018, pp. 95–102.
ista: 'Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious
rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761,
95–102.'
mla: Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting
on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer
Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.
short: H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature,
2018, pp. 95–102.
date_created: 2018-12-11T11:46:18Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2021-01-12T07:54:21Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-1-4939-7747-5_7
external_id:
pmid:
- '29525951'
intvolume: ' 1761'
language:
- iso: eng
month: '03'
oa_version: None
page: 95 - 102
pmid: 1
publication: 'Root Development '
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
publist_id: '7421'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro assay for induction of adventitious rooting on intact arabidopsis
hypocotyls
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1761
year: '2018'
...
---
_id: '411'
abstract:
- lang: eng
text: Immunolocalization is a valuable tool for cell biology research that allows
to rapidly determine the localization and expression levels of endogenous proteins.
In plants, whole-mount in situ immunolocalization remains a challenging method,
especially in tissues protected by waxy layers and complex cell wall carbohydrates.
Here, we present a robust method for whole-mount in situ immunolocalization in
primary root meristems and lateral root primordia in Arabidopsis thaliana. For
good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde
mixture. This fixative is suitable for detecting a wide range of proteins, including
integral transmembrane proteins and proteins peripherally attached to the plasma
membrane. From initiation until emergence from the primary root, lateral root
primordia are surrounded by several layers of differentiated tissues with a complex
cell wall composition that interferes with the efficient penetration of all buffers.
Therefore, immunolocalization in early lateral root primordia requires a modified
method, including a strong solvent treatment for removal of hydrophobic barriers
and a specific cocktail of cell wall-degrading enzymes. The presented method allows
for easy, reliable, and high-quality in situ detection of the subcellular localization
of endogenous proteins in primary and lateral root meristems without the need
of time-consuming crosses or making translational fusions to fluorescent proteins.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: 'Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ
immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia.
In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols.
Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10'
apa: Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized
whole mount in situ immunolocalization for Arabidopsis thaliana root meristems
and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development.
Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10
chicago: Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste.
“Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root
Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols,
edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018.
https://doi.org/10.1007/978-1-4939-7747-5_10.
ieee: M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount
in situ immunolocalization for Arabidopsis thaliana root meristems and lateral
root primordia,” in Root Development. Methods and Protocols, vol. 1761,
D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.
ista: 'Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in
situ immunolocalization for Arabidopsis thaliana root meristems and lateral root
primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology,
vol. 1761, 131–143.'
mla: Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization
for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root
Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez,
vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.
short: M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez
(Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.
date_created: 2018-12-11T11:46:20Z
date_published: 2018-03-11T00:00:00Z
date_updated: 2021-01-12T07:54:34Z
day: '11'
department:
- _id: JiFr
doi: 10.1007/978-1-4939-7747-5_10
editor:
- first_name: Daniela
full_name: Ristova, Daniela
last_name: Ristova
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
intvolume: ' 1761'
language:
- iso: eng
month: '03'
oa_version: None
page: 131 - 143
publication: Root Development. Methods and Protocols
publication_status: published
publisher: Springer
publist_id: '7418'
quality_controlled: '1'
scopus_import: 1
series_title: MIMB
status: public
title: Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root
meristems and lateral root primordia
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1761
year: '2018'
...
---
_id: '456'
abstract:
- lang: eng
text: 'Inhibition of the endoplasmic reticulum stress pathway may hold the key to
Zika virus-associated microcephaly treatment. '
article_number: eaar7514
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Novarino G. Zika-associated microcephaly: Reduce the stress and race for the
treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514'
apa: 'Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race
for the treatment. Science Translational Medicine. American Association
for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514'
chicago: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race
for the Treatment.” Science Translational Medicine. American Association
for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.'
ieee: 'G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for
the treatment,” Science Translational Medicine, vol. 10, no. 423. American
Association for the Advancement of Science, 2018.'
ista: 'Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race
for the treatment. Science Translational Medicine. 10(423), eaar7514.'
mla: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race
for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514,
American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.'
short: G. Novarino, Science Translational Medicine 10 (2018).
date_created: 2018-12-11T11:46:34Z
date_published: 2018-01-10T00:00:00Z
date_updated: 2021-01-12T07:59:42Z
day: '10'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aar7514
intvolume: ' 10'
issue: '423'
language:
- iso: eng
month: '01'
oa_version: None
publication: Science Translational Medicine
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7365'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Zika-associated microcephaly: Reduce the stress and race for the treatment'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...
---
_id: '53'
abstract:
- lang: eng
text: In 2013, a publication repository was implemented at IST Austria and 2015
after a thorough preparation phase a data repository was implemented - both based
on the Open Source Software EPrints. In this text, designed as field report, we
will reflect on our experiences with Open Source Software in general and specifically
with EPrints regarding technical aspects but also regarding their characteristics
of the user community. The second part is a pleading for including the end users
in the process of implementation, adaption and evaluation.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
- first_name: Jana
full_name: Porsche, Jana
id: 3252EDC2-F248-11E8-B48F-1D18A9856A87
last_name: Porsche
citation:
ama: 'Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories
at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993'
apa: 'Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional
repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993'
chicago: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The
Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.'
ieee: 'B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional
repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.'
ista: 'Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional
repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.'
mla: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional
Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.'
short: B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.
date_created: 2018-12-11T11:44:22Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2021-01-12T08:01:26Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v71i1.1993
file:
- access_level: open_access
checksum: 7ac61bade5f37db011ca435ebcf86797
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:40:27Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5702'
file_name: 2018_VOEB_Petritsch.pdf
file_size: 509434
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 71'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 199 - 206
publication: VÖB Mitteilungen
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publist_id: '8001'
scopus_import: 1
status: public
title: 'IST PubRep and IST DataRep: the institutional repositories at IST Austria'
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: 71
year: '2018'
...
---
_id: '536'
abstract:
- lang: eng
text: 'We consider the problem of consensus in the challenging classic model. In
this model, the adversary is adaptive; it can choose which processors crash at
any point during the course of the algorithm. Further, communication is via asynchronous
message passing: there is no known upper bound on the time to send a message from
one processor to another, and all messages and coin flips are seen by the adversary.
We describe a new randomized consensus protocol with expected message complexity
O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear
improvement over the best previously known protocol, and within logarithmic factors
of a known Ω(n2) message lower bound. The protocol further ensures that no process
sends more than O(nlog3n) messages in expectation, which is again within logarithmic
factors of optimal. We also present a generalization of the algorithm to an arbitrary
number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach
is to build a message-efficient, resilient mechanism for aggregating individual
processor votes, implementing the message-passing equivalent of a weak shared
coin. Roughly, in our protocol, a processor first announces its votes to small
groups, then propagates them to increasingly larger groups as it generates more
and more votes. To bound the number of messages that an individual process might
have to send or receive, the protocol progressively increases the weight of generated
votes. The main technical challenge is bounding the impact of votes that are still
“in flight” (generated, but not fully propagated) on the final outcome of the
shared coin, especially since such votes might have different weights. We achieve
this by leveraging the structure of the algorithm, and a technical argument based
on martingale concentration bounds. Overall, we show that it is possible to build
an efficient message-passing implementation of a shared coin, and in the process
(almost-optimally) solve the classic consensus problem in the asynchronous message-passing
model.'
article_processing_charge: Yes (via OA deal)
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: Valerie
full_name: King, Valerie
last_name: King
- first_name: Jared
full_name: Saia, Jared
last_name: Saia
citation:
ama: Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized
consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1
apa: Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient
randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1
chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient
Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.
ieee: D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient
randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer,
pp. 489–501, 2018.
ista: Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized
consensus. Distributed Computing. 31(6), 489–501.
mla: Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.”
Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.
short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018)
489–501.
date_created: 2018-12-11T11:47:01Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-02-23T12:23:25Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-017-0315-1
file:
- access_level: open_access
checksum: 69b46e537acdcac745237ddb853fcbb5
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T07:25:51Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5867'
file_name: 2017_DistribComp_Alistarh.pdf
file_size: 595707
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 489-501
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_identifier:
issn:
- '01782770'
publication_status: published
publisher: Springer
publist_id: '7281'
quality_controlled: '1'
scopus_import: 1
status: public
title: Communication-efficient randomized consensus
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '554'
abstract:
- lang: eng
text: We analyse the canonical Bogoliubov free energy functional in three dimensions
at low temperatures in the dilute limit. We prove existence of a first-order phase
transition and, in the limit (Formula presented.), we determine the critical temperature
to be (Formula presented.) to leading order. Here, (Formula presented.) is the
critical temperature of the free Bose gas, ρ is the density of the gas and a is
the scattering length of the pair-interaction potential V. We also prove asymptotic
expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula
in the limit (Formula presented.).
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: 'Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403.
doi:10.1007/s00220-017-3064-x'
apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov
free energy functional II: The dilute Limit. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x'
chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov
Free Energy Functional II: The Dilute Limit.” Communications in Mathematical
Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.'
ieee: 'M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy
functional II: The dilute Limit,” Communications in Mathematical Physics,
vol. 360, no. 1. Springer, pp. 347–403, 2018.'
ista: 'Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional
II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.'
mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II:
The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no.
1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.'
short: M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical
Physics 360 (2018) 347–403.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:02:35Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-017-3064-x
external_id:
arxiv:
- '1511.05953'
intvolume: ' 360'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.05953
month: '05'
oa: 1
oa_version: Submitted Version
page: 347-403
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '7260'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The Bogoliubov free energy functional II: The dilute Limit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 360
year: '2018'
...
---
_id: '562'
abstract:
- lang: eng
text: Primary neuronal cell culture preparations are widely used to investigate
synaptic functions. This chapter describes a detailed protocol for the preparation
of a neuronal cell culture in which giant calyx-type synaptic terminals are formed.
This chapter also presents detailed protocols for utilizing the main technical
advantages provided by such a preparation, namely, labeling and imaging of synaptic
organelles and electrophysiological recordings directly from presynaptic terminals.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Dimitar
full_name: Dimitrov, Dimitar
last_name: Dimitrov
- first_name: Laurent
full_name: Guillaud, Laurent
last_name: Guillaud
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central
nervous system synapses and application for imaging and electrophysiological analyses.
In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215.
doi:10.1007/978-1-4939-7571-6_15'
apa: Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture
of mouse giant central nervous system synapses and application for imaging and
electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors
(Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15
chicago: Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi.
“Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging
and Electrophysiological Analyses.” In Neurotrophic Factors, edited by
Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.
ieee: D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant
central nervous system synapses and application for imaging and electrophysiological
analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer,
2018, pp. 201–215.
ista: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant
central nervous system synapses and application for imaging and electrophysiological
analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.'
mla: Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses
and Application for Imaging and Electrophysiological Analyses.” Neurotrophic
Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15,
doi:10.1007/978-1-4939-7571-6_15.
short: D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.),
Neurotrophic Factors, Springer, 2018, pp. 201–215.
date_created: 2018-12-11T11:47:11Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:05Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1007/978-1-4939-7571-6_15
editor:
- first_name: Stephen D.
full_name: Skaper, Stephen D.
last_name: Skaper
external_id:
pmid:
- '29222783'
file:
- access_level: open_access
checksum: 8aa174ca65a56fbb19e9f88cff3ac3fd
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T07:47:43Z
date_updated: 2020-07-14T12:47:09Z
file_id: '7046'
file_name: 2018_NeurotrophicFactors_Dimitrov.pdf
file_size: 787407
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 1727'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 201 - 215
pmid: 1
publication: Neurotrophic Factors
publication_status: published
publisher: Springer
publist_id: '7252'
quality_controlled: '1'
scopus_import: 1
status: public
title: Culture of mouse giant central nervous system synapses and application for
imaging and electrophysiological analyses
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1727
year: '2018'
...
---
_id: '59'
abstract:
- lang: eng
text: Graph-based games are an important tool in computer science. They have applications
in synthesis, verification, refinement, and far beyond. We review graphbased games
with objectives on infinite plays. We give definitions and algorithms to solve
the games and to give a winning strategy. The objectives we consider are mostly
Boolean, but we also look at quantitative graph-based games and their objectives.
Synthesis aims to turn temporal logic specifications into correct reactive systems.
We explain the reduction of synthesis to graph-based games (or equivalently tree
automata) using synthesis of LTL specifications as an example. We treat the classical
approach that uses determinization of parity automata and more modern approaches.
author:
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
citation:
ama: 'Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In:
Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking.
1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27'
apa: Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive
synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.),
Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27
chicago: Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games
and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas
A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62.
Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.
ieee: R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,”
in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke,
H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.
ista: 'Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis.
In: Handbook of Model Checking. , 921–962.'
mla: Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of
Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018,
pp. 921–62, doi:10.1007/978-3-319-10575-8_27.
short: R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke,
H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018,
pp. 921–962.
date_created: 2018-12-11T11:44:24Z
date_published: 2018-05-19T00:00:00Z
date_updated: 2021-01-12T08:05:10Z
day: '19'
department:
- _id: KrCh
doi: 10.1007/978-3-319-10575-8_27
edition: '1'
editor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Edmund M.
full_name: Clarke, Edmund M.
last_name: Clarke
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
language:
- iso: eng
month: '05'
oa_version: None
page: 921 - 962
publication: Handbook of Model Checking
publication_identifier:
isbn:
- 978-3-319-10574-1
publication_status: published
publisher: Springer
publist_id: '7995'
quality_controlled: '1'
scopus_import: 1
status: public
title: Graph games and reactive synthesis
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '60'
abstract:
- lang: eng
text: Model checking is a computer-assisted method for the analysis of dynamical
systems that can be modeled by state-transition systems. Drawing from research
traditions in mathematical logic, programming languages, hardware design, and
theoretical computer science, model checking is now widely used for the verification
of hardware and software in industry. This chapter is an introduction and short
survey of model checking. The chapter aims to motivate and link the individual
chapters of the handbook, and to provide context for readers who are not familiar
with model checking.
author:
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
citation:
ama: 'Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger
TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer;
2018:1-26. doi:10.1007/978-3-319-10575-8_1'
apa: Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model
checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26).
Springer. https://doi.org/10.1007/978-3-319-10575-8_1
chicago: Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to
Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger,
1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1.
ieee: E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,”
in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp.
1–26.
ista: 'Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In:
Handbook of Model Checking. , 1–26.'
mla: Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model
Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1.
short: E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook
of Model Checking, Springer, 2018, pp. 1–26.
date_created: 2018-12-11T11:44:25Z
date_published: 2018-05-19T00:00:00Z
date_updated: 2021-01-12T08:05:35Z
day: '19'
department:
- _id: ToHe
doi: 10.1007/978-3-319-10575-8_1
editor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
last_name: Henzinger
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 26
publication: Handbook of Model Checking
publication_status: published
publisher: Springer
publist_id: '7994'
quality_controlled: '1'
scopus_import: 1
series_title: Handbook of Model Checking
status: public
title: Introduction to model checking
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '61'
abstract:
- lang: eng
text: 'We prove that there is no strongly regular graph (SRG) with parameters (460;
153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques
in a SRG and some applications of Euclidean representation of SRGs. '
article_processing_charge: No
author:
- first_name: Andriy
full_name: Bondarenko, Andriy
last_name: Bondarenko
- first_name: Anton
full_name: Mellit, Anton
id: 388D3134-F248-11E8-B48F-1D18A9856A87
last_name: Mellit
- first_name: Andriy
full_name: Prymak, Andriy
last_name: Prymak
- first_name: Danylo
full_name: Radchenko, Danylo
last_name: Radchenko
- first_name: Maryna
full_name: Viazovska, Maryna
last_name: Viazovska
citation:
ama: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly
regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational
Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7'
apa: Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M.
(2018). There is no strongly regular graph with parameters (460; 153; 32; 60).
In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7
chicago: Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and
Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153;
32; 60).” In Contemporary Computational Mathematics, 131–34. Springer,
2018. https://doi.org/10.1007/978-3-319-72456-0_7.
ieee: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There
is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary
Computational Mathematics, Springer, 2018, pp. 131–134.
ista: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is
no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary
Computational Mathematics. , 131–134.'
mla: Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters
(460; 153; 32; 60).” Contemporary Computational Mathematics, Springer,
2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.
short: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary
Computational Mathematics, Springer, 2018, pp. 131–134.
date_created: 2018-12-11T11:44:25Z
date_published: 2018-05-23T00:00:00Z
date_updated: 2021-01-12T08:06:06Z
day: '23'
department:
- _id: TaHa
doi: 10.1007/978-3-319-72456-0_7
extern: '1'
external_id:
arxiv:
- '1509.06286'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.06286
month: '05'
oa: 1
oa_version: Preprint
page: 131 - 134
publication: Contemporary Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '7993'
quality_controlled: '1'
status: public
title: There is no strongly regular graph with parameters (460; 153; 32; 60)
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6111'
abstract:
- lang: eng
text: 'Neurons develop elaborate morphologies that provide a model for understanding
cellular architecture. By studying C. elegans sensory dendrites, we previously
identified genes that act to promote the extension of ciliated sensory dendrites
during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing
neuron URX is not affected by these genes, suggesting it develops through a distinct
mechanism. Here, we use a visual forward genetic screen to identify mutants that
affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15
or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before:
dendrites extend normally during embryogenesis but begin to overgrow as the animals
reach adulthood, ultimately extending up to 150% of their normal length. SMA-1
is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed
in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts
at the time of overgrowth, localizes at the dendrite ending, and requires its
kinase activity, suggesting it acts locally in time and space to constrain dendrite
growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which
normally localizes at the dendrite ending, is localized throughout the overgrown
region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically
mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond
to expansion of a sensory compartment at the dendrite ending, reminiscent of the
remodeling of sensory cilia or dendritic spines. Thus, in contrast to established
pathways that promote dendrite growth during early development, our results reveal
a distinct mechanism that constrains dendrite growth throughout the life of the
animal, possibly by controlling the size of a sensory compartment at the dendrite
ending.'
article_number: e1007435
author:
- first_name: Ian G.
full_name: McLachlan, Ian G.
last_name: McLachlan
- first_name: Isabel
full_name: Beets, Isabel
last_name: Beets
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Maxwell G.
full_name: Heiman, Maxwell G.
last_name: Heiman
citation:
ama: McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains
growth of a Caenorhabditis elegans sensory dendrite throughout the life of the
organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435
apa: McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal
MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout
the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435
chicago: McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman.
“A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite
throughout the Life of the Organism.” PLOS Genetics. Public Library of
Science, 2018. https://doi.org/10.1371/journal.pgen.1007435.
ieee: I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase
constrains growth of a Caenorhabditis elegans sensory dendrite throughout the
life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of
Science, 2018.
ista: McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains
growth of a Caenorhabditis elegans sensory dendrite throughout the life of the
organism. PLOS Genetics. 14(6), e1007435.
mla: McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis
Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics,
vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435.
short: I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).
date_created: 2019-03-19T13:09:28Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '07'
ddc:
- '570'
doi: 10.1371/journal.pgen.1007435
extern: '1'
external_id:
pmid:
- '29879119'
file:
- access_level: open_access
checksum: 622036b945365dbc575bea2768aa9bc8
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:18:01Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6112'
file_name: 2018_PLOS_McLachlan.pdf
file_size: 13011506
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory
dendrite throughout the life of the organism
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2018'
...
---
_id: '6109'
abstract:
- lang: eng
text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are
packaged in specialized secretory organelles called dense core vesicles (DCVs)
that are released upon neural stimulation. Unlike synaptic vesicles, which can
be recycled and refilled close to release sites, DCVs must be replenished by de
novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in
a Caenorhabditis elegans sensory neuron whose tonic activity we can control using
a natural stimulus. We express fluorescently tagged neuropeptides in the neuron
and define parameters that describe their subcellular distribution. We measure
these parameters at high and low neural activity in 187 mutants defective in proteins
implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic
activity. Using unsupervised hierarchical clustering methods, we analyze these
data and identify 62 groups of genes with similar mutant phenotypes. We explore
the function of a subset of these groups. We recapitulate many previous findings,
validating our paradigm. We uncover a large battery of proteins involved in recycling
DCV membrane proteins, something hitherto poorly explored. We show that the unfolded
protein response promotes DCV production, which may contribute to intertissue
communication of stress. We also find evidence that different mechanisms of priming
and exocytosis may operate at high and low neural activity. Our work provides
a defined framework to study DCV biology at different neural activity levels.
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: QueeLim
full_name: Ch’ng, QueeLim
last_name: Ch’ng
- first_name: Maëlle
full_name: Jospin, Maëlle
last_name: Jospin
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Ramiro
full_name: Lorenzo, Ramiro
last_name: Lorenzo
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection
of neuropeptide cell biology at high and low activity in a defined sensory neuron.
Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899.
doi:10.1073/pnas.1714610115
apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M.
(2018). Genetic dissection of neuropeptide cell biology at high and low activity
in a defined sensory neuron. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115
chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro
Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.
ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron,” Proceedings of the National Academy of Sciences, vol.
115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.
ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic
dissection of neuropeptide cell biology at high and low activity in a defined
sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.
mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at
High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National
Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018,
pp. E6890–99, doi:10.1073/pnas.1714610115.
short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings
of the National Academy of Sciences 115 (2018) E6890–E6899.
date_created: 2019-03-19T12:41:33Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2021-01-12T08:06:09Z
day: '17'
ddc:
- '570'
doi: 10.1073/pnas.1714610115
extern: '1'
external_id:
pmid:
- '29959203'
file:
- access_level: open_access
checksum: 5e81665377441cdd8d99ab952c534319
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:01:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6110'
file_name: 2018_PNAS_Laurent.pdf
file_size: 1567765
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E6890-E6899
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Genetic dissection of neuropeptide cell biology at high and low activity in
a defined sensory neuron
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '6164'
abstract:
- lang: eng
text: In this paper, we propose an algorithm to build discrete spherical shell having
integer center and real-valued inner and outer radii on the face-centered cubic
(FCC) grid. We address the problem by mapping it to a 2D scenario and building
the shell layer by layer on hexagonal grids with additive manufacturing in mind.
The layered hexagonal grids get shifted according to need as we move from one
layer to another and forms the FCC grid in 3D. However, we restrict our computation
strictly to 2D in order to utilize symmetry and simplicity.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Girish
full_name: Koshti, Girish
last_name: Koshti
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Gaëlle
full_name: Largeteau-Skapin, Gaëlle
last_name: Largeteau-Skapin
- first_name: Rita
full_name: Zrour, Rita
last_name: Zrour
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere
construction on the FCC grid interpreted as layered hexagonal grids in 3D. In:
19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7'
apa: 'Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., &
Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered
hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp.
82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7'
chicago: 'Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric
Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted
as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96.
Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.'
ieee: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick,
“Sphere construction on the FCC grid interpreted as layered hexagonal grids in
3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255,
pp. 82–96.
ista: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018.
Sphere construction on the FCC grid interpreted as layered hexagonal grids in
3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial
Image Analysis, LNCS, vol. 11255, 82–96.'
mla: Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as
Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255,
Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7.
short: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick,
in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96.
conference:
end_date: 2018-11-24
location: Porto, Portugal
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2018-11-22
date_created: 2019-03-21T12:16:58Z
date_published: 2018-11-22T00:00:00Z
date_updated: 2022-01-27T15:26:39Z
day: '22'
doi: 10.1007/978-3-030-05288-1_7
extern: '1'
intvolume: ' 11255'
language:
- iso: eng
month: '11'
oa_version: None
page: 82-96
place: Cham
publication: 19th International Workshop
publication_identifier:
eisbn:
- 978-3-030-05288-1
eissn:
- 1611-3349
isbn:
- 978-3-030-05287-4
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Sphere construction on the FCC grid interpreted as layered hexagonal grids
in 3D
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11255
year: '2018'
...
---
_id: '6354'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis, but also play
diverse roles during immune responses. We have recently reported that platelets
migrate at sites of infection in vitro and in vivo. Importantly, platelets use
their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing
efficient intravascular bacterial trapping. Here, we describe a method that allows
analyzing platelet migration in vitro, focusing on their ability to collect bacteria
and trap bacteria under flow.
acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project
41/16 (F.G.)'
article_number: e3018
author:
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
citation:
ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping
assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018
apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration
and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018
chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet
Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol,
2018. https://doi.org/10.21769/bioprotoc.3018.
ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and
bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol,
2018.
ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial
trapping assay under flow. Bio-Protocol. 8(18), e3018.
mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under
Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.
short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).
date_created: 2019-04-29T09:40:33Z
date_published: 2018-09-20T00:00:00Z
date_updated: 2021-01-12T08:07:12Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.21769/bioprotoc.3018
ec_funded: 1
file:
- access_level: open_access
checksum: d4588377e789da7f360b553ae02c5119
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T08:04:33Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6360'
file_name: 2018_BioProtocol_Fan.pdf
file_size: 2928337
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '18'
keyword:
- Platelets
- Cell migration
- Bacteria
- Shear flow
- Fibrinogen
- E. coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Bio-Protocol
publication_identifier:
issn:
- 2331-8325
publication_status: published
publisher: Bio-Protocol
quality_controlled: '1'
status: public
title: Platelet migration and bacterial trapping assay under flow
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2018'
...
---
_id: '6368'
abstract:
- lang: eng
text: An optical network of superconducting quantum bits (qubits) is an appealing
platform for quantum communication and distributed quantum computing, but developing
a quantum-compatible link between the microwave and optical domains remains an
outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum
electrical circuits, we demonstrate a mechanically mediated microwave–optical
converter with 47% conversion efficiency, and use a classical feed-forward protocol
to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery
that noise emitted from the two converter output ports is strongly correlated
because both outputs record thermal motion of the same mechanical mode. We also
discuss a quantum feed-forward protocol that, given high system efficiencies,
would allow quantum information to be transferred even when thermal phonons enter
the mechanical element faster than the electro-optic conversion rate.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: P. S.
full_name: Burns, P. S.
last_name: Burns
- first_name: M. D.
full_name: Urmey, M. D.
last_name: Urmey
- first_name: R. W.
full_name: Peterson, R. W.
last_name: Peterson
- first_name: N. S.
full_name: Kampel, N. S.
last_name: Kampel
- first_name: B. M.
full_name: Brubaker, B. M.
last_name: Brubaker
- first_name: G.
full_name: Smith, G.
last_name: Smith
- first_name: K. W.
full_name: Lehnert, K. W.
last_name: Lehnert
- first_name: C. A.
full_name: Regal, C. A.
last_name: Regal
citation:
ama: Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations
in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042.
doi:10.1038/s41567-018-0210-0
apa: Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N.
S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations
in an efficient mechanical converter. Nature Physics. Springer Nature.
https://doi.org/10.1038/s41567-018-0210-0
chicago: Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S.
Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing
Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics.
Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0.
ieee: A. P. Higginbotham et al., “Harnessing electro-optic correlations in
an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer
Nature, pp. 1038–1042, 2018.
ista: Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM,
Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in
an efficient mechanical converter. Nature Physics. 14(10), 1038–1042.
mla: Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an
Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer
Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0.
short: A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M.
Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042.
date_created: 2019-05-03T09:17:20Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2021-01-12T08:07:15Z
day: '01'
doi: 10.1038/s41567-018-0210-0
extern: '1'
external_id:
arxiv:
- '1712.06535'
intvolume: ' 14'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.06535
month: '10'
oa: 1
oa_version: Preprint
page: 1038-1042
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Harnessing electro-optic correlations in an efficient mechanical converter
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2018'
...
---
_id: '6369'
abstract:
- lang: eng
text: We construct a metamaterial from radio-frequency harmonic oscillators, and
find two topologically distinct phases resulting from dissipation engineered into
the system. These phases are distinguished by a quantized value of bulk energy
transport. The impulse response of our circuit is measured and used to reconstruct
the band structure and winding number of circuit eigenfunctions around a dark
mode. Our results demonstrate that dissipative topological transport can occur
in a wider class of physical systems than considered before.
article_number: '220301'
author:
- first_name: Eric I.
full_name: Rosenthal, Eric I.
last_name: Rosenthal
- first_name: Nicole K.
full_name: Ehrlich, Nicole K.
last_name: Ehrlich
- first_name: Mark S.
full_name: Rudner, Mark S.
last_name: Rudner
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: K. W.
full_name: Lehnert, K. W.
last_name: Lehnert
citation:
ama: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological
phase transition measured in a dissipative metamaterial. Physical Review B.
2018;97(22). doi:10.1103/physrevb.97.220301
apa: Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., &
Lehnert, K. W. (2018). Topological phase transition measured in a dissipative
metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301
chicago: Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham,
and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.”
Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301.
ieee: E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W.
Lehnert, “Topological phase transition measured in a dissipative metamaterial,”
Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018.
ista: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological
phase transition measured in a dissipative metamaterial. Physical Review B. 97(22),
220301.
mla: Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative
Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical
Society (APS), 2018, doi:10.1103/physrevb.97.220301.
short: E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert,
Physical Review B 97 (2018).
date_created: 2019-05-03T09:29:49Z
date_published: 2018-06-04T00:00:00Z
date_updated: 2021-01-12T08:07:16Z
day: '04'
doi: 10.1103/physrevb.97.220301
extern: '1'
external_id:
arxiv:
- '1802.02243'
intvolume: ' 97'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.02243
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
issn:
- 2469-9950
- 2469-9969
publication_status: published
publisher: American Physical Society (APS)
quality_controlled: '1'
status: public
title: Topological phase transition measured in a dissipative metamaterial
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2018'
...
---
_id: '6459'
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018.
doi:10.5281/zenodo.1410279
apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented
at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279'
chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018. https://doi.org/10.5281/zenodo.1410279.
ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.
ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.
mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria,
2018, doi:10.5281/zenodo.1410279.
short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.
conference:
end_date: 2018-09-26
location: Graz, Austria
name: Open-Access-Tage
start_date: 2018-09-24
date_created: 2019-05-16T07:27:14Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2020-07-14T23:06:21Z
day: '24'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.1410279
file:
- access_level: open_access
checksum: 9063ab4d10ea93353c3a03bbf53fbcf1
content_type: application/pdf
creator: dernst
date_created: 2019-05-16T07:26:25Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6460'
file_name: Poster_Beitrag_125_Petritsch.pdf
file_size: 1967778
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
keyword:
- Open Access
- Publication Analysis
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication_status: published
publisher: IST Austria
status: public
title: Open Access at IST Austria 2009-2017
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference_poster
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6525'
abstract:
- lang: eng
text: This chapter finds an agreement of equivariant indices of semi-classical homomorphisms
between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface.
On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs
bundles, whose mirror was proposed by Hitchin to be certain even exterior powers
of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present.
The agreement arises from a mysterious functional equation. This gives strong
computational evidence for Hitchin’s proposal.
author:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Anton
full_name: Mellit, Anton
id: 388D3134-F248-11E8-B48F-1D18A9856A87
last_name: Mellit
- first_name: Du
full_name: Pei, Du
last_name: Pei
citation:
ama: 'Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde
formulas. In: Geometry and Physics: Volume I. Oxford University Press;
2018:189-218. doi:10.1093/oso/9780198802013.003.0009'
apa: 'Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes
by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp.
189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009'
chicago: 'Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes
by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218.
Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.'
ieee: 'T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant
verlinde formulas,” in Geometry and Physics: Volume I, Oxford University
Press, 2018, pp. 189–218.'
ista: 'Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant
verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.'
mla: 'Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde
Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018,
pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.'
short: 'T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford
University Press, 2018, pp. 189–218.'
date_created: 2019-06-06T12:42:01Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:52Z
day: '01'
department:
- _id: TaHa
doi: 10.1093/oso/9780198802013.003.0009
language:
- iso: eng
month: '01'
oa_version: None
page: 189-218
publication: 'Geometry and Physics: Volume I'
publication_identifier:
isbn:
- '9780198802013'
- '9780191840500'
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Mirror symmetry with branes by equivariant verlinde formulas
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6664'
abstract:
- lang: eng
text: Reed-Muller (RM) and polar codes are a class of capacity-achieving channel
coding schemes with the same factor graph representation. Low-complexity decoding
algorithms fall short in providing a good error-correction performance for RM
and polar codes. Using the symmetric group of RM and polar codes, the specific
decoding algorithm can be carried out on multiple permutations of the factor graph
to boost the error-correction performance. However, this approach results in high
decoding complexity. In this paper, we first derive the total number of factor
graph permutations on which the decoding can be performed. We further propose
a successive permutation (SP) scheme which finds the permutations on the fly,
thus the decoding always progresses on a single factor graph permutation. We show
that SP can be used to improve the error-correction performance of RM and polar
codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping
the memory requirements of the decoders unaltered. Our results for RM and polar
codes of length 128 and rate 0.5 show that when SP is used and at a target frame
error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for
RM and polar codes respectively.
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Nghia
full_name: Doan, Nghia
last_name: Doan
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: 'Warren '
full_name: 'Gross, Warren '
last_name: Gross
citation:
ama: 'Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes
by successive factor graph permutations. In: 2018 IEEE 10th International Symposium
on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281'
apa: 'Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller
and polar codes by successive factor graph permutations. In 2018 IEEE 10th
International Symposium on Turbo Codes & Iterative Information Processing
(pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281'
chicago: Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding
Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018
IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing,
1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281.
ieee: S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and
polar codes by successive factor graph permutations,” in 2018 IEEE 10th International
Symposium on Turbo Codes & Iterative Information Processing, Hong Kong,
China, 2018, pp. 1–5.
ista: 'Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar
codes by successive factor graph permutations. 2018 IEEE 10th International Symposium
on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo
Codes & Iterative Information Processing, 1–5.'
mla: Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive
Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo
Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281.
short: S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International
Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp.
1–5.
conference:
end_date: 2018-12-07
location: Hong Kong, China
name: 'ISTC: Symposium on Turbo Codes & Iterative Information Processing'
start_date: 2018-12-03
date_created: 2019-07-23T09:12:43Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:29Z
day: '01'
doi: 10.1109/istc.2018.8625281
extern: '1'
external_id:
arxiv:
- '1807.03912'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.03912
month: '12'
oa: 1
oa_version: Preprint
page: 1-5
publication: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information
Processing
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Decoding Reed-Muller and polar codes by successive factor graph permutations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6674'
abstract:
- lang: eng
text: Polar codes represent one of the major recent breakthroughs in coding theory
and, because of their attractive features, they have been selected for the incoming
5G standard. As such, a lot of attention has been devoted to the development of
decoding algorithms with good error performance and efficient hardware implementation.
One of the leading candidates in this regard is represented by successive-cancellation
list (SCL) decoding. However, its hardware implementation requires a large amount
of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly
reduce the memory consumption. In this paper, we consider the paradigm of PSCL
decoding from a practical standpoint, and we provide several improvements. First,
by changing the target signal-to-noise ratio and consequently modifying the construction
of the code, we are able to improve the performance at no additional computational,
latency, or memory cost. Second, we bridge the performance gap between SCL and
PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder.
In this way, we obtain almost the same performance of the SCL decoder with a significantly
lower memory requirement, as testified by hardware implementation results. Third,
we present an optimal scheme to allocate cyclic redundancy checks. Finally, we
provide a lower bound on the list size that guarantees optimal maximum a posteriori
performance for the binary erasure channel.
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Carlo
full_name: Condo, Carlo
last_name: Condo
- first_name: Rudiger L.
full_name: Urbanke, Rudiger L.
last_name: Urbanke
- first_name: Warren J.
full_name: Gross, Warren J.
last_name: Gross
citation:
ama: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder
partitioning: Towards practical list decoding of polar codes. IEEE Transactions
on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207'
apa: 'Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., &
Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of
polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207'
chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger
L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List
Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018.
https://doi.org/10.1109/tcomm.2018.2832207.'
ieee: 'S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W.
J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,”
IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759,
2018.'
ista: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018.
Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions
on Communications. 66(9), 3749–3759.'
mla: 'Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List
Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66,
no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207.'
short: S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross,
IEEE Transactions on Communications 66 (2018) 3749–3759.
date_created: 2019-07-24T08:59:41Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:31Z
day: '01'
doi: 10.1109/tcomm.2018.2832207
extern: '1'
intvolume: ' 66'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 3749-3759
publication: IEEE Transactions on Communications
publication_identifier:
eissn:
- 1558-0857
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Decoder partitioning: Towards practical list decoding of polar codes'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2018'
...
---
_id: '6728'
abstract:
- lang: eng
text: Polar codes are a channel coding scheme for the next generation of wireless
communications standard (5G). The belief propagation (BP) decoder allows for parallel
decoding of polar codes, making it suitable for high throughput applications.
However, the error-correction performance of polar codes under BP decoding is
far from the requirements of 5G. It has been shown that the error-correction performance
of BP can be improved if the decoding is performed on multiple permuted factor
graphs of polar codes. However, a different BP decoding scheduling is required
for each factor graph permutation which results in the design of a different decoder
for each permutation. Moreover, the selection of the different factor graph permutations
is at random, which prevents the decoder to achieve a desirable error correction
performance with a small number of permutations. In this paper, we first show
that the permutations on the factor graph can be mapped into suitable permutations
on the codeword positions. As a result, we can make use of a single decoder for
all the permutations. In addition, we introduce a method to construct a set of
predetermined permutations which can provide the correct codeword if the decoding
fails on the original permutation. We show that for the 5G polar code of length
1024, the error-correction performance of the proposed decoder is more than 0.25
dB better than that of the BP decoder with the same number of random permutations
at the frame error rate of 10 -4 .
author:
- first_name: Nghia
full_name: Doan, Nghia
last_name: Doan
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Warren J.
full_name: Gross, Warren J.
last_name: Gross
citation:
ama: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on
permuted factor graphs. In: 2018 IEEE Global Communications Conference .
IEEE; 2018. doi:10.1109/glocom.2018.8647308'
apa: 'Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the
decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications
Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308'
chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On
the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global
Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308.
ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of
polar codes on permuted factor graphs,” in 2018 IEEE Global Communications
Conference , Abu Dhabi, United Arab Emirates, 2018.
ista: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar
codes on permuted factor graphs. 2018 IEEE Global Communications Conference .
GLOBECOM: Global Communications Conference.'
mla: Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.”
2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308.
short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications
Conference , IEEE, 2018.
conference:
end_date: 2018-12-13
location: Abu Dhabi, United Arab Emirates
name: 'GLOBECOM: Global Communications Conference'
start_date: 2018-12-09
date_created: 2019-07-30T06:43:15Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:42Z
day: '01'
doi: 10.1109/glocom.2018.8647308
extern: '1'
external_id:
arxiv:
- '1806.11195'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.11195
month: '12'
oa: 1
oa_version: Preprint
publication: '2018 IEEE Global Communications Conference '
publication_identifier:
isbn:
- '9781538647271'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: On the decoding of polar codes on permuted factor graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6678'
abstract:
- lang: eng
text: We survey coding techniques that enable reliable transmission at rates that
approach the capacity of an arbitrary discrete memoryless channel. In particular,
we take the point of view of modern coding theory and discuss how recent advances
in coding for symmetric channels help provide more efficient solutions for the
asymmetric case. We consider, in more detail, three basic coding paradigms. The
first one is Gallager's scheme that consists of concatenating a linear code with
a non-linear mapping so that the input distribution can be appropriately shaped.
We explicitly show that both polar codes and spatially coupled codes can be employed
in this scenario. Furthermore, we derive a scaling law between the gap to capacity,
the cardinality of the input and output alphabets, and the required size of the
mapper. The second one is an integrated scheme in which the code is used both
for source coding, in order to create codewords distributed according to the capacity-achieving
input distribution, and for channel coding, in order to provide error protection.
Such a technique has been recently introduced by Honda and Yamamoto in the context
of polar codes, and we show how to apply it also to the design of sparse graph
codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates
the two tasks of source coding and channel coding by a chaining construction that
binds together several codewords. We present conditions for the source code and
the channel code, and we describe how to combine any source code with any channel
code that fulfill those conditions, in order to provide capacity-achieving schemes
for asymmetric channels. In particular, we show that polar codes, spatially coupled
codes, and homophonic codes are suitable as basic building blocks of the proposed
coding strategy. Rather than focusing on the exact details of the schemes, the
purpose of this tutorial is to present different coding techniques that can then
be implemented with many variants. There is no absolute winner and, in order to
understand the most suitable technique for a specific application scenario, we
provide a detailed comparison that takes into account several performance metrics.
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: 'Rudiger '
full_name: 'Urbanke, Rudiger '
last_name: Urbanke
citation:
ama: Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric
channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393.
doi:10.1109/tit.2018.2789885
apa: Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity
of asymmetric channels. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/tit.2018.2789885
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the
Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory.
IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric
channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE,
pp. 3371–3393, 2018.
ista: Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric
channels. IEEE Transactions on Information Theory. 64(5), 3371–3393.
mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.”
IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp.
3371–93, doi:10.1109/tit.2018.2789885.
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory
64 (2018) 3371–3393.
date_created: 2019-07-24T12:38:49Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T12:50:46Z
day: '01'
doi: 10.1109/tit.2018.2789885
extern: '1'
external_id:
arxiv:
- '1406.7373'
intvolume: ' 64'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1406.7373
month: '05'
oa: 1
oa_version: Preprint
page: 3371-3393
publication: IEEE Transactions on Information Theory
publication_identifier:
issn:
- 0018-9448
- 1557-9654
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '6740'
relation: earlier_version
status: public
status: public
title: How to achieve the capacity of asymmetric channels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2021-01-12T08:09:33Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
intvolume: ' 171'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2018'
...
---
_id: '6675'
abstract:
- lang: eng
text: 'We present a coding paradigm that provides a new achievable rate for the
primitive relay channel by combining compress-and-forward and decode-and-forward
with a chaining construction. In the primitive relay channel model, the source
broadcasts a message to the relay and to the destination; and the relay facilitates
this communication by sending an additional message to the destination through
a separate channel. Two well-known coding approaches for this setting are decode-and-forward
and compress-and-forward: in the former, the relay decodes the message and sends
some of the information to the destination; in the latter, the relay does not
attempt to decode, but it sends a compressed description of the received sequence
to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs
of blocks and we use compress-and-forward for the first block and decode-and-forward
for the second. In particular, in the first block, the relay does not attempt
to decode and it sends only a part of the compressed description of the received
sequence; in the second block, the relay decodes the message and sends this information
plus the remaining part of the compressed sequence relative to the first block.
As a result, we strictly outperform both compress-and- forward and decode-and-forward.
Furthermore, this paradigm can be implemented with a low-complexity polar coding
scheme that has the typical attractive features of polar codes, i.e., quasi-linear
encoding/decoding complexity and super-polynomial decay of the error probability.
Throughout the paper we consider as a running example the special case of the
erasure relay channel and we compare the rates achievable by our proposed scheme
with the existing upper and lower bounds.'
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: 'Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive
relay channel. In: 2018 IEEE International Symposium on Information Theory.
IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479'
apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm
for the primitive relay channel. In 2018 IEEE International Symposium on Information
Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479'
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information
Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive
relay channel,” in 2018 IEEE International Symposium on Information Theory,
Vail, CO, United States, 2018, pp. 351–355.
ista: 'Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive
relay channel. 2018 IEEE International Symposium on Information Theory. ISIT:
International Symposium on Information Theory , 351–355.'
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp.
351–55, doi:10.1109/isit.2018.8437479.
short: M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium
on Information Theory, IEEE, 2018, pp. 351–355.
conference:
end_date: 2018-06-22
location: Vail, CO, United States
name: 'ISIT: International Symposium on Information Theory '
start_date: 2018-06-17
date_created: 2019-07-24T09:10:38Z
date_published: 2018-06-16T00:00:00Z
date_updated: 2023-02-23T12:56:49Z
day: '16'
doi: 10.1109/isit.2018.8437479
extern: '1'
external_id:
arxiv:
- '1801.03153'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.03153
month: '06'
oa: 1
oa_version: Preprint
page: 351-355
publication: 2018 IEEE International Symposium on Information Theory
publication_identifier:
eissn:
- 2157-8117
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '7007'
relation: later_version
status: public
status: public
title: A new coding paradigm for the primitive relay channel
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '703'
abstract:
- lang: eng
text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical
models. We propose a polynomial time and practically efficient algorithm for finding
a part of its optimal solution. Specifically, our algorithm marks some labels
of the considered graphical model either as (i) optimal, meaning that they belong
to all optimal solutions of the inference problem; (ii) non-optimal if they provably
do not belong to any solution. With access to an exact solver of a linear programming
relaxation to the MAP-inference problem, our algorithm marks the maximal possible
(in a specified sense) number of labels. We also present a version of the algorithm,
which has access to a suboptimal dual solver only and still can ensure the (non-)optimality
for the marked labels, although the overall number of the marked labels may decrease.
We propose an efficient implementation, which runs in time comparable to a single
run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art
results on computational benchmarks from machine learning and computer vision.
author:
- first_name: Alexander
full_name: Shekhovtsov, Alexander
last_name: Shekhovtsov
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative
relaxed inference with graphical models. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884
apa: Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency
via iterative relaxed inference with graphical models. IEEE Transactions on
Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884
chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum
Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions
on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.
ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative
relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis
and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.
ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative
relaxed inference with graphical models. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 40(7), 1668–1682.
mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference
with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.
short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern
Analysis and Machine Intelligence 40 (2018) 1668–1682.
date_created: 2018-12-11T11:48:01Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2021-01-12T08:11:32Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/TPAMI.2017.2730884
external_id:
arxiv:
- '1508.07902'
intvolume: ' 40'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.07902
month: '07'
oa: 1
oa_version: Preprint
page: 1668-1682
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_identifier:
issn:
- '01628828'
publication_status: published
publisher: IEEE
publist_id: '6992'
quality_controlled: '1'
scopus_import: 1
status: public
title: Maximum persistency via iterative relaxed inference with graphical models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2018'
...
---
_id: '7063'
abstract:
- lang: eng
text: The high-pressure synthesis and incommensurately modulated structure are reported
for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of
Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations
predict a metallic character with a dominant role of the Pt d electrons. The electrical
resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly,
ρ showed a near-flat temperature dependence. This observation fits the description
of the Mooij correlation for electrical resistivity in disordered metals, originally
developed for statistically distributed point defects. The discussed material
has a long-range crystallographic order, but the high concentration of Pt vacancies,
incommensurately ordered, strongly influences the electronic conduction properties.
This result extends the range of validity of the Mooij correlation to long-range
ordered incommensurately modulated vacancies. Motivated by the layered structure,
the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated
well oriented single crystal. A low resistivity anisotropy indicates that the
layers are electrically coupled and conduction channels along different directions
are intermixed.
article_processing_charge: No
article_type: original
author:
- first_name: Edoardo
full_name: Martino, Edoardo
last_name: Martino
- first_name: Alla
full_name: Arakcheeva, Alla
last_name: Arakcheeva
- first_name: Gabriel
full_name: Autès, Gabriel
last_name: Autès
- first_name: Andrea
full_name: Pisoni, Andrea
last_name: Pisoni
- first_name: Maja D.
full_name: Bachmann, Maja D.
last_name: Bachmann
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Toni
full_name: Helm, Toni
last_name: Helm
- first_name: Oleg V.
full_name: Yazyev, Oleg V.
last_name: Yazyev
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: László
full_name: Forró, László
last_name: Forró
- first_name: Sergiy
full_name: Katrych, Sergiy
last_name: Katrych
citation:
ama: 'Martino E, Arakcheeva A, Autès G, et al. Sr2Pt8−xAs: A layered incommensurately
modulated metal with saturated resistivity. IUCrJ. 2018;5(4):470-477. doi:10.1107/s2052252518007303'
apa: 'Martino, E., Arakcheeva, A., Autès, G., Pisoni, A., Bachmann, M. D., Modic,
K. A., … Katrych, S. (2018). Sr2Pt8−xAs: A layered incommensurately modulated
metal with saturated resistivity. IUCrJ. International Union of Crystallography
(IUCr). https://doi.org/10.1107/s2052252518007303'
chicago: 'Martino, Edoardo, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja
D. Bachmann, Kimberly A Modic, Toni Helm, et al. “Sr2Pt8−xAs: A Layered Incommensurately
Modulated Metal with Saturated Resistivity.” IUCrJ. International Union
of Crystallography (IUCr), 2018. https://doi.org/10.1107/s2052252518007303.'
ieee: 'E. Martino et al., “Sr2Pt8−xAs: A layered incommensurately modulated
metal with saturated resistivity,” IUCrJ, vol. 5, no. 4. International
Union of Crystallography (IUCr), pp. 470–477, 2018.'
ista: 'Martino E, Arakcheeva A, Autès G, Pisoni A, Bachmann MD, Modic KA, Helm T,
Yazyev OV, Moll PJW, Forró L, Katrych S. 2018. Sr2Pt8−xAs: A layered incommensurately
modulated metal with saturated resistivity. IUCrJ. 5(4), 470–477.'
mla: 'Martino, Edoardo, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated
Metal with Saturated Resistivity.” IUCrJ, vol. 5, no. 4, International
Union of Crystallography (IUCr), 2018, pp. 470–77, doi:10.1107/s2052252518007303.'
short: E. Martino, A. Arakcheeva, G. Autès, A. Pisoni, M.D. Bachmann, K.A. Modic,
T. Helm, O.V. Yazyev, P.J.W. Moll, L. Forró, S. Katrych, IUCrJ 5 (2018) 470–477.
date_created: 2019-11-19T13:11:15Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2021-01-12T08:11:38Z
day: '01'
ddc:
- '530'
doi: 10.1107/s2052252518007303
extern: '1'
file:
- access_level: open_access
checksum: 5c6180c7d19da599dd50a067eb2efd50
content_type: application/pdf
creator: dernst
date_created: 2019-11-20T14:00:27Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7090'
file_name: 2018_IUCrJ_Martino.pdf
file_size: 1563353
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 470-477
publication: IUCrJ
publication_identifier:
eissn:
- 2052-2525
publication_status: published
publisher: International Union of Crystallography (IUCr)
quality_controlled: '1'
status: public
title: 'Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity'
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: 5
year: '2018'
...
---
_id: '7062'
abstract:
- lang: eng
text: 'Weyl fermions are a recently discovered ingredient for correlated states
of electronic matter. A key difficulty has been that real materials also contain
non-Weyl quasiparticles, and disentangling the experimental signatures has proven
challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal
TaAs far into its quantum limit, where only the purely chiral 0th Landau levels
of the Weyl fermions are occupied. We find the electrical resistivity to be nearly
independent of magnetic field up to 50 T: unusual for conventional metals but
consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a
two-order-of-magnitude increase in resistivity, indicating that a gap opens in
the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation
below 2 K, suggesting a mesoscopically textured state of matter. These results
point the way to inducing new correlated states of matter in the quantum limit
of Weyl semimetals.'
article_number: '2217'
article_processing_charge: No
article_type: original
author:
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Arkady
full_name: Shekhter, Arkady
last_name: Shekhter
- first_name: Yi
full_name: Zhang, Yi
last_name: Zhang
- first_name: Eun-Ah
full_name: Kim, Eun-Ah
last_name: Kim
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
- first_name: Maja D.
full_name: Bachmann, Maja D.
last_name: Bachmann
- first_name: M. K.
full_name: Chan, M. K.
last_name: Chan
- first_name: J. B.
full_name: Betts, J. B.
last_name: Betts
- first_name: F.
full_name: Balakirev, F.
last_name: Balakirev
- first_name: A.
full_name: Migliori, A.
last_name: Migliori
- first_name: N. J.
full_name: Ghimire, N. J.
last_name: Ghimire
- first_name: E. D.
full_name: Bauer, E. D.
last_name: Bauer
- first_name: F.
full_name: Ronning, F.
last_name: Ronning
- first_name: R. D.
full_name: McDonald, R. D.
last_name: McDonald
citation:
ama: Ramshaw BJ, Modic KA, Shekhter A, et al. Quantum limit transport and destruction
of the Weyl nodes in TaAs. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04542-9
apa: Ramshaw, B. J., Modic, K. A., Shekhter, A., Zhang, Y., Kim, E.-A., Moll, P.
J. W., … McDonald, R. D. (2018). Quantum limit transport and destruction of the
Weyl nodes in TaAs. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04542-9
chicago: Ramshaw, B. J., Kimberly A Modic, Arkady Shekhter, Yi Zhang, Eun-Ah Kim,
Philip J. W. Moll, Maja D. Bachmann, et al. “Quantum Limit Transport and Destruction
of the Weyl Nodes in TaAs.” Nature Communications. Springer Nature, 2018.
https://doi.org/10.1038/s41467-018-04542-9.
ieee: B. J. Ramshaw et al., “Quantum limit transport and destruction of the
Weyl nodes in TaAs,” Nature Communications, vol. 9, no. 1. Springer Nature,
2018.
ista: Ramshaw BJ, Modic KA, Shekhter A, Zhang Y, Kim E-A, Moll PJW, Bachmann MD,
Chan MK, Betts JB, Balakirev F, Migliori A, Ghimire NJ, Bauer ED, Ronning F, McDonald
RD. 2018. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature
Communications. 9(1), 2217.
mla: Ramshaw, B. J., et al. “Quantum Limit Transport and Destruction of the Weyl
Nodes in TaAs.” Nature Communications, vol. 9, no. 1, 2217, Springer Nature,
2018, doi:10.1038/s41467-018-04542-9.
short: B.J. Ramshaw, K.A. Modic, A. Shekhter, Y. Zhang, E.-A. Kim, P.J.W. Moll,
M.D. Bachmann, M.K. Chan, J.B. Betts, F. Balakirev, A. Migliori, N.J. Ghimire,
E.D. Bauer, F. Ronning, R.D. McDonald, Nature Communications 9 (2018).
date_created: 2019-11-19T13:10:33Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2021-01-12T08:11:38Z
day: '07'
ddc:
- '530'
doi: 10.1038/s41467-018-04542-9
extern: '1'
file:
- access_level: open_access
checksum: 9c53f9a1f06a4d83d5fe879d2478b7d7
content_type: application/pdf
creator: dernst
date_created: 2019-11-20T13:55:44Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7089'
file_name: 2018_NatureComm_Ramshaw.pdf
file_size: 1794797
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
month: '06'
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: Quantum limit transport and destruction of the Weyl nodes in TaAs
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: 9
year: '2018'
...
---
_id: '7059'
abstract:
- lang: eng
text: Unusual behavior in quantum materials commonly arises from their effective
low-dimensional physics, reflecting the underlying anisotropy in the spin and
charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2,
the second derivative of the free energy F with respect to the magnetic field
orientation θ in the crystal. We show that the magnetotropic coefficient can be
quantitatively determined from a shift in the resonant frequency of a commercially
available atomic force microscopy cantilever under magnetic field. This detection
method enables part per 100 million sensitivity and the ability to measure magnetic
anisotropy in nanogram-scale samples, as demonstrated on the Weyl semimetal NbP.
Measurement of the magnetotropic coefficient in the spin-liquid candidate RuCl3
highlights its sensitivity to anisotropic phase transitions and allows a quantitative
comparison to other thermodynamic coefficients via the Ehrenfest relations.
article_processing_charge: No
article_type: original
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Maja D.
full_name: Bachmann, Maja D.
last_name: Bachmann
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: F.
full_name: Arnold, F.
last_name: Arnold
- first_name: K. R.
full_name: Shirer, K. R.
last_name: Shirer
- first_name: Amelia
full_name: Estry, Amelia
last_name: Estry
- first_name: J. B.
full_name: Betts, J. B.
last_name: Betts
- first_name: Nirmal J.
full_name: Ghimire, Nirmal J.
last_name: Ghimire
- first_name: E. D.
full_name: Bauer, E. D.
last_name: Bauer
- first_name: Marcus
full_name: Schmidt, Marcus
last_name: Schmidt
- first_name: Michael
full_name: Baenitz, Michael
last_name: Baenitz
- first_name: E.
full_name: Svanidze, E.
last_name: Svanidze
- first_name: Ross D.
full_name: McDonald, Ross D.
last_name: McDonald
- first_name: Arkady
full_name: Shekhter, Arkady
last_name: Shekhter
- first_name: Philip J. W.
full_name: Moll, Philip J. W.
last_name: Moll
citation:
ama: Modic KA, Bachmann MD, Ramshaw BJ, et al. Resonant torsion magnetometry in
anisotropic quantum materials. Nature Communications. 2018;9(1):3975. doi:10.1038/s41467-018-06412-w
apa: Modic, K. A., Bachmann, M. D., Ramshaw, B. J., Arnold, F., Shirer, K. R., Estry,
A., … Moll, P. J. W. (2018). Resonant torsion magnetometry in anisotropic quantum
materials. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06412-w
chicago: Modic, Kimberly A, Maja D. Bachmann, B. J. Ramshaw, F. Arnold, K. R. Shirer,
Amelia Estry, J. B. Betts, et al. “Resonant Torsion Magnetometry in Anisotropic
Quantum Materials.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06412-w.
ieee: K. A. Modic et al., “Resonant torsion magnetometry in anisotropic quantum
materials,” Nature Communications, vol. 9, no. 1. Springer Nature, p. 3975,
2018.
ista: Modic KA, Bachmann MD, Ramshaw BJ, Arnold F, Shirer KR, Estry A, Betts JB,
Ghimire NJ, Bauer ED, Schmidt M, Baenitz M, Svanidze E, McDonald RD, Shekhter
A, Moll PJW. 2018. Resonant torsion magnetometry in anisotropic quantum materials.
Nature Communications. 9(1), 3975.
mla: Modic, Kimberly A., et al. “Resonant Torsion Magnetometry in Anisotropic Quantum
Materials.” Nature Communications, vol. 9, no. 1, Springer Nature, 2018,
p. 3975, doi:10.1038/s41467-018-06412-w.
short: K.A. Modic, M.D. Bachmann, B.J. Ramshaw, F. Arnold, K.R. Shirer, A. Estry,
J.B. Betts, N.J. Ghimire, E.D. Bauer, M. Schmidt, M. Baenitz, E. Svanidze, R.D.
McDonald, A. Shekhter, P.J.W. Moll, Nature Communications 9 (2018) 3975.
date_created: 2019-11-19T13:02:20Z
date_published: 2018-09-28T00:00:00Z
date_updated: 2021-01-12T08:11:37Z
day: '28'
ddc:
- '530'
doi: 10.1038/s41467-018-06412-w
extern: '1'
file:
- access_level: open_access
checksum: 46a313c816e66899d4dad2cf3583e5b0
content_type: application/pdf
creator: dernst
date_created: 2019-11-20T12:48:58Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7088'
file_name: 2018_NatureComm_Modic.pdf
file_size: 1257681
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '3975'
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Resonant torsion magnetometry in anisotropic quantum materials
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: 9
year: '2018'
...
---
_id: '7058'
abstract:
- lang: eng
text: We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3
and RuCl3, which have been discussed as possible realizations of the Kitaev model.
The analysis of the reported discontinuity in torque, as an external magnetic
field is rotated across the c axis in both crystals, suggests that they have a
translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the
ground state and persisting over a very wide range of magnetic field and temperature.
An extraordinary |B|B2 dependence of the torque for small fields, beside the usual
B2 part, is predicted by the chiral spin order. Data for small fields are available
for γ−Li2IrO3 and are found to be consistent with the prediction upon further
analysis. Other experiments such as inelastic scattering and thermal Hall effect
and several questions raised by the discovery of chiral spin order, including
its topological consequences, are discussed.
article_number: '205110 '
article_processing_charge: No
article_type: original
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: A.
full_name: Shekhter, A.
last_name: Shekhter
- first_name: C. M.
full_name: Varma, C. M.
last_name: Varma
citation:
ama: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. Chiral spin order in some purported
Kitaev spin-liquid compounds. Physical Review B. 2018;98(20). doi:10.1103/physrevb.98.205110
apa: Modic, K. A., Ramshaw, B. J., Shekhter, A., & Varma, C. M. (2018). Chiral
spin order in some purported Kitaev spin-liquid compounds. Physical Review
B. APS. https://doi.org/10.1103/physrevb.98.205110
chicago: Modic, Kimberly A, B. J. Ramshaw, A. Shekhter, and C. M. Varma. “Chiral
Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review
B. APS, 2018. https://doi.org/10.1103/physrevb.98.205110.
ieee: K. A. Modic, B. J. Ramshaw, A. Shekhter, and C. M. Varma, “Chiral spin order
in some purported Kitaev spin-liquid compounds,” Physical Review B, vol.
98, no. 20. APS, 2018.
ista: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. 2018. Chiral spin order in some
purported Kitaev spin-liquid compounds. Physical Review B. 98(20), 205110.
mla: Modic, Kimberly A., et al. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid
Compounds.” Physical Review B, vol. 98, no. 20, 205110, APS, 2018, doi:10.1103/physrevb.98.205110.
short: K.A. Modic, B.J. Ramshaw, A. Shekhter, C.M. Varma, Physical Review B 98 (2018).
date_created: 2019-11-19T13:01:31Z
date_published: 2018-11-05T00:00:00Z
date_updated: 2021-01-12T08:11:36Z
day: '05'
doi: 10.1103/physrevb.98.205110
extern: '1'
external_id:
arxiv:
- '1807.06637'
intvolume: ' 98'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.06637
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Chiral spin order in some purported Kitaev spin-liquid compounds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '7060'
abstract:
- lang: eng
text: The anomalous metallic state in the high-temperature superconducting cuprates
is masked by superconductivity near a quantum critical point. Applying high magnetic
fields to suppress superconductivity has enabled detailed studies of the normal
state, yet the direct effect of strong magnetic fields on the metallic state is
poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4
cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that
the metallic state exposed by suppressing superconductivity is characterized by
magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude
of the linear-in-field resistivity mirrors the magnitude and doping evolution
of the well-known linear-in-temperature resistivity that has been associated with
quantum criticality in high-temperature superconductors.
article_processing_charge: No
article_type: original
author:
- first_name: P.
full_name: Giraldo-Gallo, P.
last_name: Giraldo-Gallo
- first_name: J. A.
full_name: Galvis, J. A.
last_name: Galvis
- first_name: Z.
full_name: Stegen, Z.
last_name: Stegen
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: F. F.
full_name: Balakirev, F. F.
last_name: Balakirev
- first_name: J. B.
full_name: Betts, J. B.
last_name: Betts
- first_name: X.
full_name: Lian, X.
last_name: Lian
- first_name: C.
full_name: Moir, C.
last_name: Moir
- first_name: S. C.
full_name: Riggs, S. C.
last_name: Riggs
- first_name: J.
full_name: Wu, J.
last_name: Wu
- first_name: A. T.
full_name: Bollinger, A. T.
last_name: Bollinger
- first_name: X.
full_name: He, X.
last_name: He
- first_name: I.
full_name: Božović, I.
last_name: Božović
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: R. D.
full_name: McDonald, R. D.
last_name: McDonald
- first_name: G. S.
full_name: Boebinger, G. S.
last_name: Boebinger
- first_name: A.
full_name: Shekhter, A.
last_name: Shekhter
citation:
ama: Giraldo-Gallo P, Galvis JA, Stegen Z, et al. Scale-invariant magnetoresistance
in a cuprate superconductor. Science. 2018;361(6401):479-481. doi:10.1126/science.aan3178
apa: Giraldo-Gallo, P., Galvis, J. A., Stegen, Z., Modic, K. A., Balakirev, F. F.,
Betts, J. B., … Shekhter, A. (2018). Scale-invariant magnetoresistance in a cuprate
superconductor. Science. AAAS. https://doi.org/10.1126/science.aan3178
chicago: Giraldo-Gallo, P., J. A. Galvis, Z. Stegen, Kimberly A Modic, F. F. Balakirev,
J. B. Betts, X. Lian, et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.”
Science. AAAS, 2018. https://doi.org/10.1126/science.aan3178.
ieee: P. Giraldo-Gallo et al., “Scale-invariant magnetoresistance in a cuprate
superconductor,” Science, vol. 361, no. 6401. AAAS, pp. 479–481, 2018.
ista: Giraldo-Gallo P, Galvis JA, Stegen Z, Modic KA, Balakirev FF, Betts JB, Lian
X, Moir C, Riggs SC, Wu J, Bollinger AT, He X, Božović I, Ramshaw BJ, McDonald
RD, Boebinger GS, Shekhter A. 2018. Scale-invariant magnetoresistance in a cuprate
superconductor. Science. 361(6401), 479–481.
mla: Giraldo-Gallo, P., et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.”
Science, vol. 361, no. 6401, AAAS, 2018, pp. 479–81, doi:10.1126/science.aan3178.
short: P. Giraldo-Gallo, J.A. Galvis, Z. Stegen, K.A. Modic, F.F. Balakirev, J.B.
Betts, X. Lian, C. Moir, S.C. Riggs, J. Wu, A.T. Bollinger, X. He, I. Božović,
B.J. Ramshaw, R.D. McDonald, G.S. Boebinger, A. Shekhter, Science 361 (2018) 479–481.
date_created: 2019-11-19T13:03:16Z
date_published: 2018-08-03T00:00:00Z
date_updated: 2021-01-12T08:11:37Z
day: '03'
doi: 10.1126/science.aan3178
extern: '1'
intvolume: ' 361'
issue: '6401'
language:
- iso: eng
month: '08'
oa_version: None
page: 479-481
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
status: public
title: Scale-invariant magnetoresistance in a cuprate superconductor
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 361
year: '2018'
...
---
_id: '7116'
abstract:
- lang: eng
text: 'Training deep learning models has received tremendous research interest recently.
In particular, there has been intensive research on reducing the communication
cost of training when using multiple computational devices, through reducing the
precision of the underlying data representation. Naturally, such methods induce
system trade-offs—lowering communication precision could de-crease communication
overheads and improve scalability; but, on the other hand, it can also reduce
the accuracy of training. In this paper, we study this trade-off space, and ask:Can
low-precision communication consistently improve the end-to-end performance of
training modern neural networks, with no accuracy loss?From the performance point
of view, the answer to this question may appear deceptively easy: compressing
communication through low precision should help when the ratio between communication
and computation is high. However, this answer is less straightforward when we
try to generalize this principle across various neural network architectures (e.g.,
AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g.,
EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL),
and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is
not clear how a realistic realization of all these factors maps to the speed up
provided by low-precision communication. In this paper, we conduct an empirical
study to answer this question and report the insights.'
article_processing_charge: No
author:
- first_name: Demjan
full_name: Grubic, Demjan
last_name: Grubic
- first_name: Leo
full_name: Tam, Leo
last_name: Tam
- 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: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for
deep learning with low-precision communications: An empirical study. In: Proceedings
of the 21st International Conference on Extending Database Technology. OpenProceedings;
2018:145-156. doi:10.5441/002/EDBT.2018.14'
apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous
multi-GPU training for deep learning with low-precision communications: An empirical
study. In Proceedings of the 21st International Conference on Extending Database
Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14'
chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous
Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical
Study.” In Proceedings of the 21st International Conference on Extending Database
Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.'
ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study,” in Proceedings
of the 21st International Conference on Extending Database Technology, Vienna,
Austria, 2018, pp. 145–156.'
ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study. Proceedings
of the 21st International Conference on Extending Database Technology. EDBT: Conference
on Extending Database Technology, 145–156.'
mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with
Low-Precision Communications: An Empirical Study.” Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings,
2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.'
short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings, 2018,
pp. 145–156.
conference:
end_date: 2018-03-29
location: Vienna, Austria
name: 'EDBT: Conference on Extending Database Technology'
start_date: 2018-03-26
date_created: 2019-11-26T14:19:11Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2023-02-23T12:59:17Z
day: '26'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5441/002/EDBT.2018.14
file:
- access_level: open_access
checksum: ec979b56abc71016d6e6adfdadbb4afe
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T14:23:04Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7118'
file_name: 2018_OpenProceedings_Grubic.pdf
file_size: 1603204
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 145-156
publication: Proceedings of the 21st International Conference on Extending Database
Technology
publication_identifier:
isbn:
- '9783893180783'
issn:
- 2367-2005
publication_status: published
publisher: OpenProceedings
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synchronous multi-GPU training for deep learning with low-precision communications:
An empirical study'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7126'
abstract:
- lang: eng
text: In the Minimum Description Length (MDL) principle, learning from the data
is equivalent to an optimal coding problem. We show that the codes that achieve
optimal compression in MDL are critical in a very precise sense. First, when they
are taken as generative models of samples, they generate samples with broad empirical
distributions and with a high value of the relevance, defined as the entropy of
the empirical frequencies. These results are derived for different statistical
models (Dirichlet model, independent and pairwise dependent spin models, and restricted
Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition
point where the symmetry between the sampled outcomes is spontaneously broken.
The order parameter controlling the phase transition is the coding cost of the
samples. The phase transition is a manifestation of the optimality of MDL codes,
and it arises because codes that achieve a higher compression do not exist. These
results suggest a clear interpretation of the widespread occurrence of statistical
criticality as a characterization of samples which are maximally informative on
the underlying generative process.
article_number: '755'
article_processing_charge: No
article_type: original
author:
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Matteo
full_name: Marsili, Matteo
last_name: Marsili
- first_name: Yasser
full_name: Roudi, Yasser
last_name: Roudi
citation:
ama: Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical.
Entropy. 2018;20(10). doi:10.3390/e20100755
apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2018). Minimum description length
codes are critical. Entropy. MDPI. https://doi.org/10.3390/e20100755
chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description
Length Codes Are Critical.” Entropy. MDPI, 2018. https://doi.org/10.3390/e20100755.
ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes
are critical,” Entropy, vol. 20, no. 10. MDPI, 2018.
ista: Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are
critical. Entropy. 20(10), 755.
mla: Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” Entropy,
vol. 20, no. 10, 755, MDPI, 2018, doi:10.3390/e20100755.
short: R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018).
date_created: 2019-11-26T22:18:05Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '01'
ddc:
- '519'
doi: 10.3390/e20100755
extern: '1'
file:
- access_level: open_access
checksum: d642b7b661e1d5066b62e6ea9986b917
content_type: application/pdf
creator: rcubero
date_created: 2019-11-26T22:23:08Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7127'
file_name: entropy-20-00755-v2.pdf
file_size: 1366813
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '10'
keyword:
- Minimum Description Length
- normalized maximum likelihood
- statistical criticality
- phase transitions
- large deviations
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Entropy
publication_identifier:
issn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Minimum description length codes are critical
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: 20
year: '2018'
...
---
_id: '7277'
abstract:
- lang: eng
text: 'Solid alkali metal carbonates are universal passivation layer components
of intercalation battery materials and common side products in metal‐O2 batteries,
and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these
cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs.
Li/Li+. However, O2 evolution, as would be expected according to the decomposition
reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted
for, which was previously ascribed to unidentified parasitic reactions. Here,
we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3
in an aprotic electrolyte and therefore does not evolve as O2. These results have
substantial implications for the long‐term cyclability of batteries: they underpin
the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility
of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and
help explain the interfacial reactivity of transition‐metal cathodes with residual
Li2CO3.'
article_processing_charge: No
article_type: original
author:
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Sara E.
full_name: Renfrew, Sara E.
last_name: Renfrew
- first_name: Bryan D.
full_name: McCloskey, Bryan D.
last_name: McCloskey
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Electrochemical oxidation
of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International
Edition. 2018;57(19):5529-5533. doi:10.1002/anie.201802277
apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018).
Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte
Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201802277
chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander
Freunberger. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet
Oxygen.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201802277.
ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Electrochemical
oxidation of Lithium Carbonate generates singlet oxygen,” Angewandte Chemie
International Edition, vol. 57, no. 19. Wiley, pp. 5529–5533, 2018.
ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Electrochemical oxidation
of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International
Edition. 57(19), 5529–5533.
mla: Mahne, Nika, et al. “Electrochemical Oxidation of Lithium Carbonate Generates
Singlet Oxygen.” Angewandte Chemie International Edition, vol. 57, no.
19, Wiley, 2018, pp. 5529–33, doi:10.1002/anie.201802277.
short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie
International Edition 57 (2018) 5529–5533.
date_created: 2020-01-15T07:20:09Z
date_published: 2018-03-15T00:00:00Z
date_updated: 2021-01-12T08:12:42Z
day: '15'
ddc:
- '540'
doi: 10.1002/anie.201802277
extern: '1'
file:
- access_level: open_access
checksum: 45868d0adc2d13a506bb9a59eb4f409c
content_type: application/pdf
creator: dernst
date_created: 2020-01-22T16:28:31Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7357'
file_name: 2018_AngewChemie_Mahne.pdf
file_size: 657963
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 57'
issue: '19'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 5529-5533
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Electrochemical oxidation of Lithium Carbonate generates singlet oxygen
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2018'
...
---
_id: '7271'
abstract:
- lang: eng
text: The recent demand of multifunctional materials and devices for advanced applications
in energy conversion and data storage resulted into a revival of multiferroics,
that is, materials characterized by the coexistence of ferromagnetism and ferroelectricity.
Despite intense efforts made in the past decade, single-phase room temperature
multiferroics are yet to be discovered/fabricated. Nanostructured ferroic materials
could potentially exhibit multiferroism since a high fraction of their atoms/ions
are superficial, thereby altering significantly the properties of the bulk phase.
Alternately, a magnetic order can be induced into ferroelectric materials upon
aliovalent doping with magnetic ions. Here, we report on the synthesis of aggregate-free
single-phase transition-metal-doped BaTiO3 quasi-monodisperse cuboidal nanocrystals
(NC) which exhibit multiferroic properties at room temperature and can be suitable
for applications in data storage. The proposed synthetic route allows the inclusion
of a high concentration of magnetic ions such as Mn+ (M = Cr, Mn, Fe, Co) up to
a nominal concentration of 4% without the formation of any secondary phase. The
size of the nanocrystals was controlled in a wide range from ∼15 up to ∼70 nm
by varying the reaction time from 48 to 144 h. The presence of unpaired electrons
and their magnetic ordering have been probed by electron paramagnetic resonance
spectroscopy (EPR), and a vibrating sample magnetometer (VSM). Likewise, an acentric
structure, associated with the existence of a dielectric polarization, was observed
by lattice dynamics analysis and piezoresponse force microscopy (PFM). These results
show that high-quality titanium-containing perovskite nanocrystals which display
multiferroic properties at room temperature can be fabricated via soft solution-based
synthetic routes, and the properties of these materials can be modulated by changing
the size of the nanocrystals and the concentration of the dopant thereby opening
the door to the design and study of single-phase multiferroic materials.
article_processing_charge: No
article_type: original
author:
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: John
full_name: McCracken, John
last_name: McCracken
- first_name: Aurelian
full_name: Rotaru, Aurelian
last_name: Rotaru
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
citation:
ama: Costanzo T, McCracken J, Rotaru A, Caruntu G. Quasi-monodisperse transition-metal-doped
BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties.
ACS Applied Nano Materials. 2018;1(9):4863-4874. doi:10.1021/acsanm.8b01036
apa: Costanzo, T., McCracken, J., Rotaru, A., & Caruntu, G. (2018). Quasi-monodisperse
transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with
multiferroic properties. ACS Applied Nano Materials. ACS. https://doi.org/10.1021/acsanm.8b01036
chicago: Costanzo, Tommaso, John McCracken, Aurelian Rotaru, and Gabriel Caruntu.
“Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal
Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials.
ACS, 2018. https://doi.org/10.1021/acsanm.8b01036.
ieee: T. Costanzo, J. McCracken, A. Rotaru, and G. Caruntu, “Quasi-monodisperse
transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with
multiferroic properties,” ACS Applied Nano Materials, vol. 1, no. 9. ACS,
pp. 4863–4874, 2018.
ista: Costanzo T, McCracken J, Rotaru A, Caruntu G. 2018. Quasi-monodisperse transition-metal-doped
BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties.
ACS Applied Nano Materials. 1(9), 4863–4874.
mla: Costanzo, Tommaso, et al. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3
(M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS
Applied Nano Materials, vol. 1, no. 9, ACS, 2018, pp. 4863–74, doi:10.1021/acsanm.8b01036.
short: T. Costanzo, J. McCracken, A. Rotaru, G. Caruntu, ACS Applied Nano Materials
1 (2018) 4863–4874.
date_created: 2020-01-13T21:58:27Z
date_published: 2018-09-28T00:00:00Z
date_updated: 2023-02-23T13:02:57Z
day: '28'
doi: 10.1021/acsanm.8b01036
extern: '1'
intvolume: ' 1'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 4863-4874
publication: ACS Applied Nano Materials
publication_identifier:
issn:
- 2574-0970
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal
nanocrystals with multiferroic properties
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2018'
...
---
_id: '7287'
abstract:
- lang: eng
text: Passivation layers on electrode materials are ubiquitous in nonaqueous battery
chemistries and strongly govern performance and lifetime. They comprise breakdown
products of the electrolyte including carbonate, alkyl carbonates, alkoxides,
carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar
products and is tied to the deviation of the O2 balance from the ideal stoichiometry
during formation/decomposition of alkaline peroxides or superoxides. Accurate
and integral quantification of carbonaceous species and peroxides or superoxides
in battery electrodes remains, however, elusive. We present a refined procedure
to quantify them accurately and sensitively by pointing out and rectifying pitfalls
of previous procedures. Carbonaceous compounds are differentiated into inorganic
and organic ones. We combine mass and UV–vis spectrometry to quantify evolved
O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid
treatment and Fenton’s reaction. The capabilities of the method are exemplified
by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2
cathodes.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bettina
full_name: Schafzahl, Bettina
last_name: Schafzahl
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Anjana R.
full_name: Raju, Anjana R.
last_name: Raju
- first_name: Musthafa Ottakam
full_name: Thotiyl, Musthafa Ottakam
last_name: Thotiyl
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Schafzahl B, Mourad E, Schafzahl L, et al. Quantifying total superoxide, peroxide,
and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase.
ACS Energy Letters. 2018;3(1):170-176. doi:10.1021/acsenergylett.7b01111
apa: Schafzahl, B., Mourad, E., Schafzahl, L., Petit, Y. K., Raju, A. R., Thotiyl,
M. O., … Freunberger, S. A. (2018). Quantifying total superoxide, peroxide, and
carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase.
ACS Energy Letters. ACS. https://doi.org/10.1021/acsenergylett.7b01111
chicago: Schafzahl, Bettina, Eléonore Mourad, Lukas Schafzahl, Yann K. Petit, Anjana
R. Raju, Musthafa Ottakam Thotiyl, Martin Wilkening, Christian Slugovc, and Stefan
Alexander Freunberger. “Quantifying Total Superoxide, Peroxide, and Carbonaceous
Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS
Energy Letters. ACS, 2018. https://doi.org/10.1021/acsenergylett.7b01111.
ieee: B. Schafzahl et al., “Quantifying total superoxide, peroxide, and carbonaceous
compounds in metal–O2 batteries and the solid electrolyte interphase,” ACS
Energy Letters, vol. 3, no. 1. ACS, pp. 170–176, 2018.
ista: Schafzahl B, Mourad E, Schafzahl L, Petit YK, Raju AR, Thotiyl MO, Wilkening
M, Slugovc C, Freunberger SA. 2018. Quantifying total superoxide, peroxide, and
carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase.
ACS Energy Letters. 3(1), 170–176.
mla: Schafzahl, Bettina, et al. “Quantifying Total Superoxide, Peroxide, and Carbonaceous
Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS
Energy Letters, vol. 3, no. 1, ACS, 2018, pp. 170–76, doi:10.1021/acsenergylett.7b01111.
short: B. Schafzahl, E. Mourad, L. Schafzahl, Y.K. Petit, A.R. Raju, M.O. Thotiyl,
M. Wilkening, C. Slugovc, S.A. Freunberger, ACS Energy Letters 3 (2018) 170–176.
date_created: 2020-01-15T12:13:52Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T08:12:46Z
day: '01'
ddc:
- '540'
- '543'
- '546'
- '547'
doi: 10.1021/acsenergylett.7b01111
extern: '1'
file:
- access_level: open_access
checksum: 461ccf575ba077af90314fe72d20521e
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T14:19:36Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8049'
file_name: O2 TIOC_fin_incl_SI.pdf
file_size: 1892355
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 170-176
publication: ACS Energy Letters
publication_identifier:
issn:
- 2380-8195
- 2380-8195
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2
batteries and the solid electrolyte interphase
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2018'
...
---
_id: '7285'
abstract:
- lang: eng
text: Hydrogelation, the self-assembly of molecules into soft, water-loaded networks,
is one way to bridge the structural gap between single molecules and functional
materials. The potential of hydrogels, such as those based on perylene bisimides,
lies in their chemical, physical, optical, and electronic properties, which are
governed by the supramolecular structure of the gel. However, the structural motifs
and their precise role for long-range conductivity are yet to be explored. Here,
we present a comprehensive structural picture of a perylene bisimide hydrogel,
suggesting that its long-range conductivity is limited by charge transfer between
electronic backbones. We reveal nanocrystalline ribbon-like structures as the
electronic and structural backbone units between which charge transfer is mediated
by polar solvent bridges. We exemplify this effect with sensing, where exposure
to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the
crucial role of the interplay between structural motif and surrounding medium
for the rational design of devices based on nanocrystalline hydrogels.
article_processing_charge: No
article_type: original
author:
- first_name: Max
full_name: Burian, Max
last_name: Burian
- first_name: Francesco
full_name: Rigodanza, Francesco
last_name: Rigodanza
- first_name: Nicola
full_name: Demitri, Nicola
last_name: Demitri
- first_name: Luka
full_name: D̵ord̵ević, Luka
last_name: D̵ord̵ević
- first_name: Silvia
full_name: Marchesan, Silvia
last_name: Marchesan
- first_name: Tereza
full_name: Steinhartova, Tereza
last_name: Steinhartova
- first_name: Ilse
full_name: Letofsky-Papst, Ilse
last_name: Letofsky-Papst
- first_name: Ivan
full_name: Khalakhan, Ivan
last_name: Khalakhan
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Heinz
full_name: Amenitsch, Heinz
last_name: Amenitsch
- first_name: Maurizio
full_name: Prato, Maurizio
last_name: Prato
- first_name: Zois
full_name: Syrgiannis, Zois
last_name: Syrgiannis
citation:
ama: Burian M, Rigodanza F, Demitri N, et al. Inter-backbone charge transfer as
prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS
Nano. 2018;12(6):5800-5806. doi:10.1021/acsnano.8b01689
apa: Burian, M., Rigodanza, F., Demitri, N., D̵ord̵ević, L., Marchesan, S., Steinhartova,
T., … Syrgiannis, Z. (2018). Inter-backbone charge transfer as prerequisite for
long-range conductivity in perylene bisimide hydrogels. ACS Nano. ACS.
https://doi.org/10.1021/acsnano.8b01689
chicago: Burian, Max, Francesco Rigodanza, Nicola Demitri, Luka D̵ord̵ević, Silvia
Marchesan, Tereza Steinhartova, Ilse Letofsky-Papst, et al. “Inter-Backbone Charge
Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.”
ACS Nano. ACS, 2018. https://doi.org/10.1021/acsnano.8b01689.
ieee: M. Burian et al., “Inter-backbone charge transfer as prerequisite for
long-range conductivity in perylene bisimide hydrogels,” ACS Nano, vol.
12, no. 6. ACS, pp. 5800–5806, 2018.
ista: Burian M, Rigodanza F, Demitri N, D̵ord̵ević L, Marchesan S, Steinhartova
T, Letofsky-Papst I, Khalakhan I, Mourad E, Freunberger SA, Amenitsch H, Prato
M, Syrgiannis Z. 2018. Inter-backbone charge transfer as prerequisite for long-range
conductivity in perylene bisimide hydrogels. ACS Nano. 12(6), 5800–5806.
mla: Burian, Max, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range
Conductivity in Perylene Bisimide Hydrogels.” ACS Nano, vol. 12, no. 6,
ACS, 2018, pp. 5800–06, doi:10.1021/acsnano.8b01689.
short: M. Burian, F. Rigodanza, N. Demitri, L. D̵ord̵ević, S. Marchesan, T. Steinhartova,
I. Letofsky-Papst, I. Khalakhan, E. Mourad, S.A. Freunberger, H. Amenitsch, M.
Prato, Z. Syrgiannis, ACS Nano 12 (2018) 5800–5806.
date_created: 2020-01-15T12:13:25Z
date_published: 2018-06-05T00:00:00Z
date_updated: 2021-01-12T08:12:46Z
day: '05'
ddc:
- '540'
- '541'
doi: 10.1021/acsnano.8b01689
extern: '1'
file:
- access_level: open_access
checksum: 050f7f0ba5d845c5c71779ef14ad5ef3
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T14:56:40Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8052'
file_name: Manuscript 20092017_subm.pdf
file_size: 1333353
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 5800-5806
publication: ACS Nano
publication_identifier:
issn:
- 1936-0851
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Inter-backbone charge transfer as prerequisite for long-range conductivity
in perylene bisimide hydrogels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2018'
...
---
_id: '7286'
abstract:
- lang: eng
text: The solid electrolyte interphase (SEI) in Li and Na ion batteries forms when
highly reducing or oxidizing electrode materials come into contact with a liquid
organic electrolyte. Its ability to form a mechanically robust, ion-conducting,
and electron-insulating layer critically determines performance, cycle life, and
safety. Li or Na alkyl carbonates (LiAC and NaAC, respectively) are lead SEI components
in state-of-the-art carbonate based electrolytes, and our fundamental understanding
of their charge transport and mechanical properties may hold the key to designing
electrolytes forming an improved SEI. We synthesized a homologous series of LiACs
and NaACs from methyl to octyl analogues and characterized them with respect to
structure, ionic conductivity, and stiffness. The compounds assume layered structures
except for the lithium methyl carbonate. Room-temperature conductivities were
found to be ∼10–9 S cm–1 for lithium methyl carbonate, <10–12 S cm–1 for the other
LiACs, and <10–12 S cm–1 for the NaACs with ion transport mostly attributed to
grain boundaries. While LiACs show stiffnesses of ∼1 GPa, NaACs become significantly
softer with increasing chain lengths. These findings will help to more precisely
interpret the complex results from charge transport and mechanical characterization
of real SEIs and can give a rationale for influencing the SEI’s mechanical properties
via the electrolyte.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Heike
full_name: Ehmann, Heike
last_name: Ehmann
- first_name: Manfred
full_name: Kriechbaum, Manfred
last_name: Kriechbaum
- first_name: Jürgen
full_name: Sattelkow, Jürgen
last_name: Sattelkow
- first_name: Thomas
full_name: Ganner, Thomas
last_name: Ganner
- first_name: Harald
full_name: Plank, Harald
last_name: Plank
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: 'Schafzahl L, Ehmann H, Kriechbaum M, et al. Long-chain Li and Na alkyl carbonates
as solid electrolyte interphase components: Structure, ion transport, and mechanical
properties. Chemistry of Materials. 2018;30(10):3338-3345. doi:10.1021/acs.chemmater.8b00750'
apa: 'Schafzahl, L., Ehmann, H., Kriechbaum, M., Sattelkow, J., Ganner, T., Plank,
H., … Freunberger, S. A. (2018). Long-chain Li and Na alkyl carbonates as solid
electrolyte interphase components: Structure, ion transport, and mechanical properties.
Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.8b00750'
chicago: 'Schafzahl, Lukas, Heike Ehmann, Manfred Kriechbaum, Jürgen Sattelkow,
Thomas Ganner, Harald Plank, Martin Wilkening, and Stefan Alexander Freunberger.
“Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components:
Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials.
ACS, 2018. https://doi.org/10.1021/acs.chemmater.8b00750.'
ieee: 'L. Schafzahl et al., “Long-chain Li and Na alkyl carbonates as solid
electrolyte interphase components: Structure, ion transport, and mechanical properties,”
Chemistry of Materials, vol. 30, no. 10. ACS, pp. 3338–3345, 2018.'
ista: 'Schafzahl L, Ehmann H, Kriechbaum M, Sattelkow J, Ganner T, Plank H, Wilkening
M, Freunberger SA. 2018. Long-chain Li and Na alkyl carbonates as solid electrolyte
interphase components: Structure, ion transport, and mechanical properties. Chemistry
of Materials. 30(10), 3338–3345.'
mla: 'Schafzahl, Lukas, et al. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte
Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry
of Materials, vol. 30, no. 10, ACS, 2018, pp. 3338–45, doi:10.1021/acs.chemmater.8b00750.'
short: L. Schafzahl, H. Ehmann, M. Kriechbaum, J. Sattelkow, T. Ganner, H. Plank,
M. Wilkening, S.A. Freunberger, Chemistry of Materials 30 (2018) 3338–3345.
date_created: 2020-01-15T12:13:37Z
date_published: 2018-05-03T00:00:00Z
date_updated: 2021-01-12T08:12:46Z
day: '03'
doi: 10.1021/acs.chemmater.8b00750
extern: '1'
intvolume: ' 30'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 3338-3345
publication: Chemistry of Materials
publication_identifier:
eissn:
- 1520-5002
issn:
- 0897-4756
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: 'Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components:
Structure, ion transport, and mechanical properties'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2018'
...
---
_id: '7407'
abstract:
- lang: eng
text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems
where a prover can convince a verifier that he "wastes" disk space. PoS were introduced
as a more ecological and economical replacement for proofs of work which are currently
used to secure blockchains like Bitcoin. In this work we investigate extensions
of PoS which allow the prover to embed useful data into the dedicated space, which
later can be recovered. Our first contribution is a security proof for the original
PoS from CRYPTO''15 in the random oracle model (the original proof only applied
to a restricted class of adversaries which can store a subset of the data an honest
prover would store). When this PoS is instantiated with recent constructions of
maximally depth robust graphs, our proof implies basically optimal security. As
a second contribution we show three different extensions of this PoS where useful
data can be embedded into the space required by the prover. Our security proof
for the PoS extends (non-trivially) to these constructions. We discuss how some
of these variants can be used as proofs of catalytic space (PoCS), a notion we
put forward in this work, and which basically is a PoS where most of the space
required by the prover can be used to backup useful data. Finally we discuss how
one of the extensions is a candidate construction for a proof of replication (PoR),
a proof system recently suggested in the Filecoin whitepaper. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59'
apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations
in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25).
San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ITCS.2019.59'
chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations
in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.
ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018,
vol. 124, p. 59:1-59:25.
ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical
Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer
Science Conference, LIPIcs, vol. 124, 59:1-59:25.'
mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in
Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.
short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference
(ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.
conference:
end_date: 2019-01-12
location: San Diego, CA, United States
name: 'ITCS: Innovations in theoretical Computer Science Conference'
start_date: 2019-01-10
date_created: 2020-01-30T09:16:05Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2021-01-12T08:13:26Z
day: '31'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPICS.ITCS.2019.59
ec_funded: 1
file:
- access_level: open_access
checksum: 5cebb7f7849a3beda898f697d755dd96
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T08:17:52Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7443'
file_name: 2018_LIPIcs_Pietrzak.pdf
file_size: 822884
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 124'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/194
month: '12'
oa: 1
oa_version: Published Version
page: 59:1-59:25
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019)
publication_identifier:
isbn:
- 978-3-95977-095-8
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Proofs of catalytic space
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2018'
...
---
_id: '7458'
abstract:
- lang: eng
text: The coupling between magnetic and electric subsystems in composites of ferromagnetic
and ferroelectric phases is a product property that is facilitated by mechanical
strain that arises due to magnetostriction and the piezoelectric effect in the
constituent phases. Such multiferroic composites are of immense interests for
studies on the physics of electromagnetic coupling and for use in a variety of
applications. Here, we focus on magneto-electric (ME) coupling in nanocomposites.
Particular emphasis is on core-shell particles and coaxial fibers, thin film heterostructures,
and planar structures with a variety of mechanical connectivity. A brief review
of models that predict strong ME effects in nanostructures is followed by synthesis
and characterization. Core-shell particulate composites can be prepared by hydrothermal
processes and chemical or deoxyribonucleic acid-assisted assembly. Electrospinning
techniques have been utilized to prepare defect free core-shell nanofibers. Core-shell
particles and fibers can be assembled into superstructures with the aid of magnetic
and electric fields and characterized for possible use in advanced technologies.
Chemical-vapor deposition techniques have been shown to be effective for the preparation
of heterostructures of ferrites and ferroelectrics. Exotic planar multiferroic
structures with potential for enhancing ME coupling strengths are also considered.
Scanning probe microscopy techniques are ideal for probing the nature of direct-
and converse-ME coupling in individual nanostructures. Magnetoelectric characterization
of assemblies of nanocomposites can be done by ME voltage coefficient, magnetic
field induced polarization, and magneto-dielectric effects. We conclude with a
brief discussion on possible avenues for strengthening the product properties
in the nanocomposites.
article_number: '061101'
article_processing_charge: No
article_type: original
author:
- first_name: Dwight
full_name: Viehland, Dwight
last_name: Viehland
- first_name: Jie Fang
full_name: Li, Jie Fang
last_name: Li
- first_name: Yaodong
full_name: Yang, Yaodong
last_name: Yang
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Amin
full_name: Yourdkhani, Amin
last_name: Yourdkhani
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
- first_name: Peng
full_name: Zhou, Peng
last_name: Zhou
- first_name: Tianjin
full_name: Zhang, Tianjin
last_name: Zhang
- first_name: Tianqian
full_name: Li, Tianqian
last_name: Li
- first_name: Arunava
full_name: Gupta, Arunava
last_name: Gupta
- first_name: Maksym
full_name: Popov, Maksym
last_name: Popov
- first_name: Gopalan
full_name: Srinivasan, Gopalan
last_name: Srinivasan
citation:
ama: 'Viehland D, Li JF, Yang Y, et al. Tutorial: Product properties in multiferroic
nanocomposites. Journal of Applied Physics. 2018;124(6). doi:10.1063/1.5038726'
apa: 'Viehland, D., Li, J. F., Yang, Y., Costanzo, T., Yourdkhani, A., Caruntu,
G., … Srinivasan, G. (2018). Tutorial: Product properties in multiferroic nanocomposites.
Journal of Applied Physics. AIP. https://doi.org/10.1063/1.5038726'
chicago: 'Viehland, Dwight, Jie Fang Li, Yaodong Yang, Tommaso Costanzo, Amin Yourdkhani,
Gabriel Caruntu, Peng Zhou, et al. “Tutorial: Product Properties in Multiferroic
Nanocomposites.” Journal of Applied Physics. AIP, 2018. https://doi.org/10.1063/1.5038726.'
ieee: 'D. Viehland et al., “Tutorial: Product properties in multiferroic
nanocomposites,” Journal of Applied Physics, vol. 124, no. 6. AIP, 2018.'
ista: 'Viehland D, Li JF, Yang Y, Costanzo T, Yourdkhani A, Caruntu G, Zhou P, Zhang
T, Li T, Gupta A, Popov M, Srinivasan G. 2018. Tutorial: Product properties in
multiferroic nanocomposites. Journal of Applied Physics. 124(6), 061101.'
mla: 'Viehland, Dwight, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.”
Journal of Applied Physics, vol. 124, no. 6, 061101, AIP, 2018, doi:10.1063/1.5038726.'
short: D. Viehland, J.F. Li, Y. Yang, T. Costanzo, A. Yourdkhani, G. Caruntu, P.
Zhou, T. Zhang, T. Li, A. Gupta, M. Popov, G. Srinivasan, Journal of Applied Physics
124 (2018).
date_created: 2020-02-05T14:18:22Z
date_published: 2018-08-10T00:00:00Z
date_updated: 2023-02-23T13:08:29Z
day: '10'
doi: 10.1063/1.5038726
extern: '1'
intvolume: ' 124'
issue: '6'
language:
- iso: eng
month: '08'
oa_version: None
publication: Journal of Applied Physics
publication_identifier:
issn:
- 0021-8979
- 1089-7550
publication_status: published
publisher: AIP
quality_controlled: '1'
status: public
title: 'Tutorial: Product properties in multiferroic nanocomposites'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
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'
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'
...
---
_id: '7718'
abstract:
- lang: eng
text: Flores Island, Indonesia, was inhabited by the small-bodied hominin species
Homo floresiensis, which has an unknown evolutionary relationship to modern humans.
This island is also home to an extant human pygmy population. Here we describe
genome-scale single-nucleotide polymorphism data and whole-genome sequences from
a contemporary human pygmy population living on Flores near the cave where H.
floresiensis was found. The genomes of Flores pygmies reveal a complex history
of admixture with Denisovans and Neanderthals but no evidence for gene flow with
other archaic hominins. Modern individuals bear the signatures of recent positive
selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related
to diet, and polygenic selection acting on standing variation that contributed
to their short-stature phenotype. Thus, multiple independent instances of hominin
insular dwarfism occurred on Flores.
article_processing_charge: No
article_type: original
author:
- first_name: Serena
full_name: Tucci, Serena
last_name: Tucci
- first_name: Samuel H.
full_name: Vohr, Samuel H.
last_name: Vohr
- first_name: Rajiv C.
full_name: McCoy, Rajiv C.
last_name: McCoy
- first_name: Benjamin
full_name: Vernot, Benjamin
last_name: Vernot
- 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: Chiara
full_name: Barbieri, Chiara
last_name: Barbieri
- first_name: Brad J.
full_name: Nelson, Brad J.
last_name: Nelson
- first_name: Wenqing
full_name: Fu, Wenqing
last_name: Fu
- first_name: Gludhug A.
full_name: Purnomo, Gludhug A.
last_name: Purnomo
- first_name: Herawati
full_name: Sudoyo, Herawati
last_name: Sudoyo
- first_name: Evan E.
full_name: Eichler, Evan E.
last_name: Eichler
- first_name: Guido
full_name: Barbujani, Guido
last_name: Barbujani
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Joshua M.
full_name: Akey, Joshua M.
last_name: Akey
- first_name: Richard E.
full_name: Green, Richard E.
last_name: Green
citation:
ama: Tucci S, Vohr SH, McCoy RC, et al. Evolutionary history and adaptation of a
human pygmy population of Flores Island, Indonesia. Science. 2018;361(6401):511-516.
doi:10.1126/science.aar8486
apa: Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri,
C., … Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy
population of Flores Island, Indonesia. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aar8486
chicago: Tucci, Serena, Samuel H. Vohr, Rajiv C. McCoy, Benjamin Vernot, Matthew
Richard Robinson, Chiara Barbieri, Brad J. Nelson, et al. “Evolutionary History
and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science.
American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aar8486.
ieee: S. Tucci et al., “Evolutionary history and adaptation of a human pygmy
population of Flores Island, Indonesia,” Science, vol. 361, no. 6401. American
Association for the Advancement of Science, pp. 511–516, 2018.
ista: Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ,
Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green
RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores
Island, Indonesia. Science. 361(6401), 511–516.
mla: Tucci, Serena, et al. “Evolutionary History and Adaptation of a Human Pygmy
Population of Flores Island, Indonesia.” Science, vol. 361, no. 6401, American
Association for the Advancement of Science, 2018, pp. 511–16, doi:10.1126/science.aar8486.
short: S. Tucci, S.H. Vohr, R.C. McCoy, B. Vernot, M.R. Robinson, C. Barbieri, B.J.
Nelson, W. Fu, G.A. Purnomo, H. Sudoyo, E.E. Eichler, G. Barbujani, P.M. Visscher,
J.M. Akey, R.E. Green, Science 361 (2018) 511–516.
date_created: 2020-04-30T10:43:24Z
date_published: 2018-08-03T00:00:00Z
date_updated: 2021-01-12T08:15:04Z
day: '03'
doi: 10.1126/science.aar8486
extern: '1'
external_id:
pmid:
- '30072539'
intvolume: ' 361'
issue: '6401'
language:
- iso: eng
month: '08'
oa_version: None
page: 511-516
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Evolutionary history and adaptation of a human pygmy population of Flores Island,
Indonesia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 361
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'
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: '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'
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: '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'
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: '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'
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: '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'
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: '7721'
abstract:
- lang: eng
text: 'The availability of genome-wide genetic data on hundreds of thousands of
people has led to an equally rapid growth in methodologies available to analyse
these data. While the motivation for undertaking genome-wide association studies
(GWAS) is identification of genetic markers associated with complex traits, once
generated these data can be used for many other analyses. GWAS have demonstrated
that complex traits exhibit a highly polygenic genetic architecture, often with
shared genetic risk factors across traits. New methods to analyse data from GWAS
are increasingly being used to address a diverse set of questions about the aetiology
of complex traits and diseases, including psychiatric disorders. Here, we give
an overview of some of these methods and present examples of how they have contributed
to our understanding of psychiatric disorders. We consider: (i) estimation of
the extent of genetic influence on traits, (ii) uncovering of shared genetic control
between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering
of causal relationships between traits, (v) identifying causal single-nucleotide
polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification
helps organise the large number of recently developed methods, although some could
be placed in more than one category. While some methods require GWAS data on individual
people, others simply use GWAS summary statistics data, allowing novel well-powered
analyses to be conducted at a low computational burden.'
article_processing_charge: No
article_type: original
author:
- first_name: R. M.
full_name: Maier, R. M.
last_name: Maier
- first_name: P. M.
full_name: Visscher, P. 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
- first_name: N. R.
full_name: Wray, N. R.
last_name: Wray
citation:
ama: 'Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review
of methods and tools for psychiatric genetics research. Psychological Medicine.
2018;48(7):1055-1067. doi:10.1017/s0033291717002318'
apa: 'Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018).
Embracing polygenicity: A review of methods and tools for psychiatric genetics
research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318'
chicago: 'Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray.
“Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics
Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318.'
ieee: 'R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity:
A review of methods and tools for psychiatric genetics research,” Psychological
Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.'
ista: 'Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity:
A review of methods and tools for psychiatric genetics research. Psychological
Medicine. 48(7), 1055–1067.'
mla: 'Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools
for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no.
7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.'
short: R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine
48 (2018) 1055–1067.
date_created: 2020-04-30T10:44:35Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:15:05Z
day: '01'
doi: 10.1017/s0033291717002318
extern: '1'
intvolume: ' 48'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/s0033291717002318
month: '05'
oa: 1
oa_version: Published Version
page: 1055-1067
publication: Psychological Medicine
publication_identifier:
issn:
- 0033-2917
- 1469-8978
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: 'Embracing polygenicity: A review of methods and tools for psychiatric genetics
research'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2018'
...
---
_id: '7723'
abstract:
- lang: eng
text: Genome-wide association studies (GWAS) have identified thousands of loci that
are robustly associated with complex diseases. The use of linear mixed model (LMM)
methodology for GWAS is becoming more prevalent due to its ability to control
for population structure and cryptic relatedness and to increase power. The odds
ratio (OR) is a common measure of the association of a disease with an exposure
(e.g., a genetic variant) and is readably available from logistic regression.
However, when the LMM is applied to all-or-none traits it provides estimates of
genetic effects on the observed 0–1 scale, a different scale to that in logistic
regression. This limits the comparability of results across studies, for example
in a meta-analysis, and makes the interpretation of the magnitude of an effect
from an LMM GWAS difficult. In this study, we derived transformations from the
genetic effects estimated under the LMM to the OR that only rely on summary statistics.
To test the proposed transformations, we used real genotypes from two large, publicly
available data sets to simulate all-or-none phenotypes for a set of scenarios
that differ in underlying model, disease prevalence, and heritability. Furthermore,
we applied these transformations to GWAS summary statistics for type 2 diabetes
generated from 108,042 individuals in the UK Biobank. In both simulation and real-data
application, we observed very high concordance between the transformed OR from
the LMM and either the simulated truth or estimates from logistic regression.
The transformations derived and validated in this study improve the comparability
of results from prospective and already performed LMM GWAS on complex diseases
by providing a reliable transformation to a common comparative scale for the genetic
effects.
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: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary
statistics from linear mixed model association on all-or-none traits to odds ratio.
Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360
apa: Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018).
Transformation of summary statistics from linear mixed model association on all-or-none
traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360
chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M.
Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association
on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.117.300360.
ieee: L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation
of summary statistics from linear mixed model association on all-or-none traits
to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America,
pp. 1397–1408, 2018.
ista: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of
summary statistics from linear mixed model association on all-or-none traits to
odds ratio. Genetics. 208(4), 1397–1408.
mla: Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear
Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics,
vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360.
short: L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018)
1397–1408.
date_created: 2020-04-30T10:45:19Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2021-01-12T08:15:06Z
day: '01'
doi: 10.1534/genetics.117.300360
extern: '1'
intvolume: ' 208'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 1397-1408
publication: Genetics
publication_identifier:
issn:
- 0016-6731
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Transformation of summary statistics from linear mixed model association on
all-or-none traits to odds ratio
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 208
year: '2018'
...
---
_id: '7722'
abstract:
- lang: eng
text: We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide
polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero
effects), and the relationship between SNP effect size and minor allele frequency
for complex traits in conventionally unrelated individuals using genome-wide SNP
data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752)
and show that on average, 6% of SNPs have nonzero effects, which in total explain
22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of
natural selection in the genetic architecture of 23 traits, including reproductive,
cardiovascular, and anthropometric traits, as well as educational attainment.
The significant estimates of the relationship between effect size and minor allele
frequency in complex traits are consistent with a model of negative (or purifying)
selection, as confirmed by forward simulation. We conclude that negative selection
acts pervasively on the genetic variants associated with human complex traits.
article_processing_charge: No
article_type: original
author:
- first_name: Jian
full_name: Zeng, Jian
last_name: Zeng
- first_name: Ronald
full_name: de Vlaming, Ronald
last_name: de Vlaming
- first_name: Yang
full_name: Wu, Yang
last_name: Wu
- 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: Luke R.
full_name: Lloyd-Jones, Luke R.
last_name: Lloyd-Jones
- first_name: Loic
full_name: Yengo, Loic
last_name: Yengo
- first_name: Chloe X.
full_name: Yap, Chloe X.
last_name: Yap
- first_name: Angli
full_name: Xue, Angli
last_name: Xue
- first_name: Julia
full_name: Sidorenko, Julia
last_name: Sidorenko
- first_name: Allan F.
full_name: McRae, Allan F.
last_name: McRae
- first_name: Joseph E.
full_name: Powell, Joseph E.
last_name: Powell
- first_name: Grant W.
full_name: Montgomery, Grant W.
last_name: Montgomery
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Tonu
full_name: Esko, Tonu
last_name: Esko
- first_name: Greg
full_name: Gibson, Greg
last_name: Gibson
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
citation:
ama: Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the
genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753.
doi:10.1038/s41588-018-0101-4
apa: Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo,
L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture
of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4
chicago: Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke
R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection
in the Genetic Architecture of Human Complex Traits.” Nature Genetics.
Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4.
ieee: J. Zeng et al., “Signatures of negative selection in the genetic architecture
of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature,
pp. 746–753, 2018.
ista: Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX,
Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson
G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the
genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753.
mla: Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture
of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature,
2018, pp. 746–53, doi:10.1038/s41588-018-0101-4.
short: J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo,
C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu,
T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018)
746–753.
date_created: 2020-04-30T10:44:57Z
date_published: 2018-04-16T00:00:00Z
date_updated: 2021-01-12T08:15:06Z
day: '16'
doi: 10.1038/s41588-018-0101-4
extern: '1'
intvolume: ' 50'
issue: '5'
language:
- iso: eng
month: '04'
oa_version: None
page: 746-753
publication: Nature Genetics
publication_identifier:
issn:
- 1061-4036
- 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Signatures of negative selection in the genetic architecture of human complex
traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2018'
...
---
_id: '7724'
abstract:
- lang: eng
text: Modern molecular genetic datasets, primarily collected to study the biology
of human health and disease, can be used to directly measure the action of natural
selection and reveal important features of contemporary human evolution. Here
we leverage the UK Biobank data to test for the presence of linear and nonlinear
natural selection in a contemporary population of the United Kingdom. We obtain
phenotypic and genetic evidence consistent with the action of linear/directional
selection. Phenotypic evidence suggests that stabilizing selection, which acts
to reduce variance in the population without necessarily modifying the population
mean, is widespread and relatively weak in comparison with estimates from other
species.
article_processing_charge: No
article_type: original
author:
- first_name: Jaleal S.
full_name: Sanjak, Jaleal S.
last_name: Sanjak
- first_name: Julia
full_name: Sidorenko, Julia
last_name: Sidorenko
- 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: Kevin R.
full_name: Thornton, Kevin R.
last_name: Thornton
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of
directional and stabilizing selection in contemporary humans. Proceedings of
the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114
apa: Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher,
P. M. (2018). Evidence of directional and stabilizing selection in contemporary
humans. Proceedings of the National Academy of Sciences. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114
chicago: Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R.
Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection
in Contemporary Humans.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114.
ieee: J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher,
“Evidence of directional and stabilizing selection in contemporary humans,” Proceedings
of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National
Academy of Sciences, pp. 151–156, 2018.
ista: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence
of directional and stabilizing selection in contemporary humans. Proceedings of
the National Academy of Sciences. 115(1), 151–156.
mla: Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection
in Contemporary Humans.” Proceedings of the National Academy of Sciences,
vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56,
doi:10.1073/pnas.1707227114.
short: J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings
of the National Academy of Sciences 115 (2018) 151–156.
date_created: 2020-04-30T10:45:43Z
date_published: 2018-01-02T00:00:00Z
date_updated: 2021-01-12T08:15:07Z
day: '02'
doi: 10.1073/pnas.1707227114
extern: '1'
intvolume: ' 115'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 151-156
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: erratum
url: https://doi.org/10.1073/pnas.1806837115
status: public
title: Evidence of directional and stabilizing selection in contemporary humans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '7754'
abstract:
- lang: eng
text: Creating a selective gel that filters particles based on their interactions
is a major goal of nanotechnology, with far-reaching implications from drug delivery
to controlling assembly pathways. However, this is particularly difficult when
the particles are larger than the gel’s characteristic mesh size because such
particles cannot passively pass through the gel. Thus, filtering requires the
interacting particles to transiently reorganize the gel’s internal structure.
While significant advances, e.g., in DNA engineering, have enabled the design
of nano-materials with programmable interactions, it is not clear what physical
principles such a designer gel could exploit to achieve selective permeability.
We present an equilibrium mechanism where crosslink binding dynamics are affected
by interacting particles such that particle diffusion is enhanced. In addition
to revealing specific design rules for manufacturing selective gels, our results
have the potential to explain the origin of selective permeability in certain
biological materials, including the nuclear pore complex.
article_number: '4348'
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
- first_name: Katharina
full_name: Ribbeck, Katharina
last_name: Ribbeck
citation:
ama: Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks
of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5
apa: Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion
by binding to the crosslinks of a polymer gel. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-018-06851-5
chicago: Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced
Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5.
ieee: C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding
to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to
the crosslinks of a polymer gel. Nature Communications. 9, 4348.
mla: Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks
of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature,
2018, doi:10.1038/s41467-018-06851-5.
short: C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).
date_created: 2020-04-30T11:38:01Z
date_published: 2018-10-19T00:00:00Z
date_updated: 2021-01-12T08:15:18Z
day: '19'
doi: 10.1038/s41467-018-06851-5
extern: '1'
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-06851-5
month: '10'
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: Enhanced diffusion by binding to the crosslinks of a polymer gel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7783'
abstract:
- lang: eng
text: The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource
to better understand the genetic landscapes underlying quantitative traits. However,
such DGRP studies have so far only focused on nuclear genetic variants. To address
this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229
variants including 21 indels and 7 frameshifts. We used our mitochondrial variation
data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing
important population structure at the mitochondrial level. We further examined
whether this population structure was reflected on the nuclear genome by screening
for the presence of potential mito-nuclear genetic incompatibilities in the form
of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear
variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the
highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl).
Intriguingly, downstream phenotypic analyses did not uncover major fitness effects
associated with these GRDs, suggesting that a large number of mito-nuclear GRDs
may reflect population structure at the mitochondrial level rather than actual
genomic incompatibilities. This is further supported by the GRD landscape showing
particular large genomic regions associated with a single mitochondrial haplotype.
Next, we explored the functional relevance of the detected mitochondrial haplotypes
through an association analysis on a set of 259 assembled, non-correlating DGRP
phenotypes. We found multiple significant associations with stress- and metabolism-related
phenotypes, including food intake in males. We validated the latter observation
by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines
to low food intake ones. In conclusion, our study uncovered important mitochondrial
population structure and haplotype-specific metabolic variation in the DGRP, thus
demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype
relationship studies.
article_processing_charge: No
author:
- first_name: Roel P.J.
full_name: Bevers, Roel P.J.
last_name: Bevers
- first_name: Maria
full_name: Litovchenko, Maria
last_name: Litovchenko
- first_name: Adamandia
full_name: Kapopoulou, Adamandia
last_name: Kapopoulou
- first_name: Virginie S.
full_name: Braman, Virginie S.
last_name: Braman
- 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: Johan
full_name: Auwerx, Johan
last_name: Auwerx
- first_name: Brian
full_name: Hollis, Brian
last_name: Hollis
- first_name: Bart
full_name: Deplancke, Bart
last_name: Deplancke
citation:
ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population
structure and haplotype-specific phenotypic variation in the Drosophila Genetic
Reference Panel. bioRxiv. 2018.
apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson,
M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population
structure and haplotype-specific phenotypic variation in the Drosophila Genetic
Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.
chicago: Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S.
Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke.
“Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic
Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring
Harbor Laboratory, 2018.
ieee: R. P. J. Bevers et al., “Extensive mitochondrial population structure
and haplotype-specific phenotypic variation in the Drosophila Genetic Reference
Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.
ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J,
Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and
haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel.
bioRxiv, .
mla: Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and
Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.”
BioRxiv, Cold Spring Harbor Laboratory, 2018.
short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson,
J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018).
date_created: 2020-04-30T13:09:37Z
date_published: 2018-11-09T00:00:00Z
date_updated: 2021-01-12T08:15:30Z
day: '09'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/466771 '
month: '11'
oa: 1
oa_version: Preprint
page: '49'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Extensive mitochondrial population structure and haplotype-specific phenotypic
variation in the Drosophila Genetic Reference Panel
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6001'
abstract:
- lang: eng
text: "The concurrent memory reclamation problem is that of devising a way for a
deallocating thread to verify that no other concurrent threads hold references
to a memory block being deallocated. To date, in the absence of automatic garbage
collection, there is no satisfactory solution to this problem; existing tracking
methods like hazard pointers, reference counters, or epoch-based techniques like
RCU are either prohibitively expensive or require significant programming expertise
to the extent that implementing them efficiently can be worthy of a publication.
None of the existing techniques are automatic or even semi-automated.\r\nIn this
article, we take a new approach to concurrent memory reclamation. Instead of manually
tracking access to memory locations as done in techniques like hazard pointers,
or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm,
called ThreadScan, leverages operating system signaling to automatically detect
which memory locations are being accessed by concurrent threads.\r\nInitial empirical
evidence shows that ThreadScan scales surprisingly well and requires negligible
programming effort beyond the standard use of Malloc and Free."
article_number: '18'
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. ThreadScan: Automatic and
scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4).
doi:10.1145/3201897'
apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan:
Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing.
Association for Computing Machinery. https://doi.org/10.1145/3201897'
chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit.
“ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on
Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.'
ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic
and scalable memory reclamation,” ACM Transactions on Parallel Computing,
vol. 4, no. 4. Association for Computing Machinery, 2018.'
ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic
and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4),
18.'
mla: 'Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.”
ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association
for Computing Machinery, 2018, doi:10.1145/3201897.'
short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on
Parallel Computing 4 (2018).
date_created: 2019-02-14T13:24:11Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-02-23T13:17:54Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3201897
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '09'
oa_version: None
publication: ACM Transactions on Parallel Computing
publication_identifier:
issn:
- 2329-4949
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '779'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'ThreadScan: Automatic and scalable memory reclamation'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '7812'
abstract:
- lang: eng
text: Deep neural networks (DNNs) continue to make significant advances, solving
tasks from image classification to translation or reinforcement learning. One
aspect of the field receiving considerable attention is efficiently executing
deep models in resource-constrained environments, such as mobile or embedded devices.
This paper focuses on this problem, and proposes two new compression methods,
which jointly leverage weight quantization and distillation of larger teacher
networks into smaller student networks. The first method we propose is called
quantized distillation and leverages distillation during the training process,
by incorporating distillation loss, expressed with respect to the teacher, into
the training of a student network whose weights are quantized to a limited set
of levels. The second method, differentiable quantization, optimizes the location
of quantization points through stochastic gradient descent, to better fit the
behavior of the teacher model. We validate both methods through experiments on
convolutional and recurrent architectures. We show that quantized shallow students
can reach similar accuracy levels to full-precision teacher models, while providing
order of magnitude compression, and inference speedup that is linear in the depth
reduction. In sum, our results enable DNNs for resource-constrained environments
to leverage architecture and accuracy advances developed on more powerful devices.
article_processing_charge: No
author:
- first_name: Antonio
full_name: Polino, Antonio
last_name: Polino
- first_name: Razvan
full_name: Pascanu, Razvan
last_name: Pascanu
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and
quantization. In: 6th International Conference on Learning Representations.
; 2018.'
apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via
distillation and quantization. In 6th International Conference on Learning
Representations. Vancouver, Canada.
chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression
via Distillation and Quantization.” In 6th International Conference on Learning
Representations, 2018.
ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation
and quantization,” in 6th International Conference on Learning Representations,
Vancouver, Canada, 2018.
ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation
and quantization. 6th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.”
6th International Conference on Learning Representations, 2018.
short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference
on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: 'ICLR: International Conference on Learning Representations'
start_date: 2018-04-30
date_created: 2020-05-10T22:00:51Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T13:18:41Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1802.05668'
file:
- access_level: open_access
checksum: a4336c167978e81891970e4e4517a8c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:02:00Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7894'
file_name: 2018_ICLR_Polino.pdf
file_size: 308339
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: 1
status: public
title: Model compression via distillation and quantization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7983'
abstract:
- lang: ger
text: 'Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten
an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien,
und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden
und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen
>3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung
detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2
+ O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und
wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir,
dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in
einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird.
Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit
von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu
verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie
basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität
von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.'
article_processing_charge: No
article_type: original
author:
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Sara E.
full_name: Renfrew, Sara E.
last_name: Renfrew
- first_name: Bryan D.
full_name: McCloskey, Bryan D.
last_name: McCloskey
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation
von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie.
2018;130(19):5627-5631. doi:10.1002/ange.201802277
apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018).
Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff.
Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277
chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander
Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.”
Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277.
ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische
Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie,
vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.
ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische
Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie.
130(19), 5627–5631.
mla: Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert
Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018,
pp. 5627–31, doi:10.1002/ange.201802277.
short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie
130 (2018) 5627–5631.
date_created: 2020-06-19T08:33:24Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2021-01-12T08:16:21Z
day: '04'
ddc:
- '540'
doi: 10.1002/ange.201802277
extern: '1'
file:
- access_level: open_access
checksum: 81506e0f7079e1e3591f3cd9f626bf67
content_type: application/pdf
creator: dernst
date_created: 2020-06-19T11:58:06Z
date_updated: 2020-07-14T12:48:06Z
file_id: '7988'
file_name: 2018_AngChemieDT_Mahne.pdf
file_size: 674789
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 130'
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 5627-5631
publication: Angewandte Chemie
publication_identifier:
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 130
year: '2018'
...
---
_id: '8015'
abstract:
- lang: eng
text: 'The neural code of cortical processing remains uncracked; however, it must
necessarily rely on faithful signal propagation between cortical areas. In this
issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation
balanced by local inhibition can enable reliable signal propagation in data-constrained
network models of macaque cortex. '
article_processing_charge: No
article_type: original
author:
- first_name: Jake P.
full_name: Stroud, Jake P.
last_name: Stroud
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit.
Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028'
apa: 'Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance,
amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028'
chicago: 'Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance,
Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.'
ieee: 'J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify,
transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.'
ista: 'Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify,
transmit. Neuron. 98(1), 8–9.'
mla: 'Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance,
Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.'
short: J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9.
date_created: 2020-06-25T12:53:39Z
date_published: 2018-04-04T00:00:00Z
date_updated: 2021-01-12T08:16:31Z
day: '04'
doi: 10.1016/j.neuron.2018.03.028
extern: '1'
external_id:
pmid:
- '29621492'
intvolume: ' 98'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2018.03.028
month: '04'
oa: 1
oa_version: Published Version
page: 8-9
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Cortical signal propagation: Balance, amplify, transmit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '8073'
abstract:
- lang: eng
text: Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support
the generation of complex movements. Although recent neuronal-network models capture
many qualitative aspects of M1 dynamics, they can generate only a few distinct
movements. Additionally, it is unclear how M1 efficiently controls movements over
a wide range of shapes and speeds. We demonstrate that modulation of neuronal
input–output gains in recurrent neuronal-network models with a fixed architecture
can dramatically reorganize neuronal activity and thus downstream muscle outputs.
Consistent with the observation of diffuse neuromodulatory projections to M1,
a relatively small number of modulatory control units provide sufficient flexibility
to adjust high-dimensional network activity using a simple reward-based learning
rule. Furthermore, it is possible to assemble novel movements from previously
learned primitives, and one can separately change movement speed while preserving
movement shape. Our results provide a new perspective on the role of modulatory
systems in controlling recurrent cortical activity.
article_processing_charge: No
article_type: original
author:
- first_name: Jake P.
full_name: Stroud, Jake P.
last_name: Stroud
- first_name: Mason A.
full_name: Porter, Mason A.
last_name: Porter
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and
time via targeted gain modulation in cortical networks. Nature Neuroscience.
2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0
apa: Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor
primitives in space and time via targeted gain modulation in cortical networks.
Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0
chicago: Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels.
“Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.”
Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0.
ieee: J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives
in space and time via targeted gain modulation in cortical networks,” Nature
Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.
ista: Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space
and time via targeted gain modulation in cortical networks. Nature Neuroscience.
21(12), 1774–1783.
mla: Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain
Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12,
Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0.
short: J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience
21 (2018) 1774–1783.
date_created: 2020-06-30T13:18:02Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '01'
doi: 10.1038/s41593-018-0276-0
extern: '1'
external_id:
pmid:
- '30482949'
intvolume: ' 21'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1774-1783
pmid: 1
publication: Nature Neuroscience
publication_identifier:
issn:
- 1097-6256
- 1546-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41593-018-0307-x
status: public
title: Motor primitives in space and time via targeted gain modulation in cortical
networks
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 21
year: '2018'
...
---
_id: '8231'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Miroslawa
full_name: Matz, Miroslawa
last_name: Matz
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Edzard
full_name: Spillner, Edzard
last_name: Spillner
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine
anticancer IgE against the epidermal growth factor receptor. Journal of Allergy
and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021'
apa: 'Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E.,
… Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE
against the epidermal growth factor receptor. Journal of Allergy and Clinical
Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021'
chicago: 'Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann,
Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology:
Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.”
Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.'
ieee: 'J. Singer et al., “AllergoOncology: Generating a canine anticancer
IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical
Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.'
ista: 'Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis
SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE
against the epidermal growth factor receptor. Journal of Allergy and Clinical
Immunology. 142(3), 973–976.e11.'
mla: 'Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE
against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical
Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.'
short: J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N.
Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142
(2018) 973–976.e11.
date_created: 2020-08-10T11:51:36Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:37Z
day: '01'
doi: 10.1016/j.jaci.2018.04.021
extern: '1'
intvolume: ' 142'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jaci.2018.04.021
month: '09'
oa: 1
oa_version: Published Version
page: 973-976.e11
publication: Journal of Allergy and Clinical Immunology
publication_identifier:
issn:
- 0091-6749
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'AllergoOncology: Generating a canine anticancer IgE against the epidermal
growth factor receptor'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2018'
...
---
_id: '8234'
abstract:
- lang: eng
text: Molecular imaging probes such as PET-tracers have the potential to improve
the accuracy of tumor characterization by directly visualizing the biochemical
situation. Thus, molecular changes can be detected early before morphological
manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed
in colon cancer cell lines and human colorectal cancer (CRC), suggesting this
receptor as a tumor marker. The aim of this preclinical study was the evaluation
of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging.
First, affinity and selectivity of FE@SUPPY and its metabolites were determined,
proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell
line HT-29 was characterized regarding its hA3AR expression and was subsequently
chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as
a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher
accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy
colon tissue from the same patient. Nevertheless, first in vivo studies using
HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation
of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY
in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize
hA3ARs using FE@SUPPY.
article_number: '1269830'
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Balber, T.
last_name: Balber
- first_name: Judit
full_name: Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Singer
orcid: 0000-0002-8777-3502
- first_name: N.
full_name: Berroterán-Infante, N.
last_name: Berroterán-Infante
- first_name: M.
full_name: Dumanic, M.
last_name: Dumanic
- first_name: L.
full_name: Fetty, L.
last_name: Fetty
- first_name: J.
full_name: Fazekas-Singer, J.
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: C.
full_name: Vraka, C.
last_name: Vraka
- first_name: L.
full_name: Nics, L.
last_name: Nics
- first_name: M.
full_name: Bergmann, M.
last_name: Bergmann
- first_name: K.
full_name: Pallitsch, K.
last_name: Pallitsch
- first_name: H.
full_name: Spreitzer, H.
last_name: Spreitzer
- first_name: W.
full_name: Wadsak, W.
last_name: Wadsak
orcid: 0000-0003-4479-8053
- first_name: M.
full_name: Hacker, M.
last_name: Hacker
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
- first_name: H.
full_name: Viernstein, H.
last_name: Viernstein
- first_name: M.
full_name: Mitterhauser, M.
last_name: Mitterhauser
orcid: 0000-0003-3173-5272
citation:
ama: 'Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and
in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft
model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018.
doi:10.1155/2018/1269830'
apa: 'Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer,
J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of
[18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal
cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830'
chicago: 'Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty,
J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation
of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for
Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018.
https://doi.org/10.1155/2018/1269830.'
ieee: 'T. Balber et al., “Preclinical in vitro and in vivo evaluation of
[18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal
cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.'
ista: 'Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer
J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M,
Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and
in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft
model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.'
mla: 'Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY
for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.”
Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018,
doi:10.1155/2018/1269830.'
short: T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer,
C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker,
E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular
Imaging 2018 (2018).
date_created: 2020-08-10T11:53:07Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2021-01-12T08:17:38Z
day: '13'
doi: 10.1155/2018/1269830
extern: '1'
intvolume: ' 2018'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1155/2018/1269830
month: '02'
oa: 1
oa_version: Published Version
publication: Contrast Media & Molecular Imaging
publication_identifier:
issn:
- 1555-4309
- 1555-4317
publication_status: published
publisher: Hindawi
quality_controlled: '1'
status: public
title: 'Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET
imaging: Limitations of a xenograft model for colorectal cancer'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '8232'
abstract:
- lang: eng
text: 'Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in
EGFR expressing cancers including lung, colon, head and neck, and bladder cancers,
however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is
a highly selective tumor treatment that employs an antibody-photo-absorber conjugate
which is activated by NIR light. NIR-PIT is in clinical trials in patients with
recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However,
its use has otherwise been restricted to mouse models. This is an effort to explore
larger animal models with NIR-PIT. We describe the use of a recombinant canine
anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber,
IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell
lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate
showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing
cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation
of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing
mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700
i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light
exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared
with the other groups (p < 0.001), and significantly prolonged survival was achieved
(p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with
can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including
invasive transitional cell carcinoma in pet dogs, that could provide a pathway
to translation to humans.'
article_processing_charge: No
article_type: original
author:
- first_name: Tadanobu
full_name: Nagaya, Tadanobu
last_name: Nagaya
- first_name: Shuhei
full_name: Okuyama, Shuhei
last_name: Okuyama
- first_name: Fusa
full_name: Ogata, Fusa
last_name: Ogata
- first_name: Yasuhiro
full_name: Maruoka, Yasuhiro
last_name: Maruoka
- first_name: Deborah W.
full_name: Knapp, Deborah W.
last_name: Knapp
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Peter L.
full_name: Choyke, Peter L.
last_name: Choyke
- first_name: Amy K.
full_name: LeBlanc, Amy K.
last_name: LeBlanc
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Hisataka
full_name: Kobayashi, Hisataka
last_name: Kobayashi
citation:
ama: Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting
bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody.
Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876
apa: Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis,
S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder
cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget.
Impact Journals. https://doi.org/10.18632/oncotarget.24876
chicago: Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah
W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy
Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR)
Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876.
ieee: T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder
cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget,
vol. 9. Impact Journals, pp. 19026–19038, 2018.
ista: Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer
J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy
targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR)
antibody. Oncotarget. 9, 19026–19038.
mla: Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder
Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget,
vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.
short: T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis,
J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget
9 (2018) 19026–19038.
date_created: 2020-08-10T11:52:54Z
date_published: 2018-04-10T00:00:00Z
date_updated: 2021-01-12T08:17:37Z
day: '10'
doi: 10.18632/oncotarget.24876
extern: '1'
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.24876
month: '04'
oa: 1
oa_version: Published Version
page: 19026-19038
publication: Oncotarget
publication_identifier:
eissn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal
growth factor receptor (EGFR) antibody
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8233'
abstract:
- lang: eng
text: The M2a subtype of macrophages plays an important role in human immunoglobulin
E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very
little is known about these cells in the dog. Here we describe an in vitro method
to activate canine histiocytic DH82 cells and primary canine monocyte-derived
macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side
comparison, we compared the canine cells to human MDMs, and the human monocytic
cell line U937 activated towards M1 and M2a cells on the cellular and molecular
level. In analogy to activated human M2a cells, canine M2a, differentiated from
both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared
to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the
high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes
(IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog
species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated
in canine and human M1 cells (cell lines and MDMs). We suggest that our novel
in vitro method will be suitable in comparative allergology studies focussing
on macrophages.
article_processing_charge: No
article_type: original
author:
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Jelena
full_name: Gotovina, Jelena
last_name: Gotovina
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Michael B.
full_name: Fischer, Michael B.
last_name: Fischer
- first_name: Karin
full_name: Hufnagl, Karin
last_name: Hufnagl
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human
macrophages be in vitro activated toward the M2a subtype relevant in allergy.
Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005
apa: Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini,
R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages
be in vitro activated toward the M2a subtype relevant in allergy. Developmental
& Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005
chicago: Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin
Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can
like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in
Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005.
ieee: I. Herrmann et al., “Canine macrophages can like human macrophages
be in vitro activated toward the M2a subtype relevant in allergy,” Developmental
& Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.
ista: Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim
E. 2018. Canine macrophages can like human macrophages be in vitro activated toward
the M2a subtype relevant in allergy. Developmental & Comparative Immunology.
82(5), 118–127.
mla: Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro
Activated toward the M2a Subtype Relevant in Allergy.” Developmental &
Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005.
short: I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini,
E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.
date_created: 2020-08-10T11:53:01Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:38Z
day: '01'
doi: 10.1016/j.dci.2018.01.005
extern: '1'
intvolume: ' 82'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.dci.2018.01.005
month: '05'
oa: 1
oa_version: Published Version
page: 118-127
publication: Developmental & Comparative Immunology
publication_identifier:
issn:
- 0145-305X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Canine macrophages can like human macrophages be in vitro activated toward
the M2a subtype relevant in allergy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2018'
...
---
_id: '8262'
abstract:
- lang: eng
text: "Background: The genus Burkholderia consists of species that occupy remarkably
diverse ecological niches. Its best known members are important pathogens, B.
mallei and B. pseudomallei, which cause glanders and melioidosis, respectively.
Burkholderia genomes are unusual due to their multichromosomal organization, generally
comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic
analysis of 127 Burkholderia strains. The pan-genome is open with the saturation
to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements
indicate a strong avoidance of intra-replichore inversions that is likely caused
by selection against the transfer of large groups of genes between the leading
and the lagging strands. Translocated genes also tend to retain their position
in the leading or the lagging strand, and this selection is stronger for large
syntenies. Integrated reconstruction of chromosome rearrangements in the context
of strains phylogeny reveals parallel rearrangements that may indicate inversion-based
phase variation and integration of new genomic islands. In particular, we detected
parallel inversions in the second chromosomes of B. pseudomallei with breakpoints
formed by genes encoding membrane components of multidrug resistance complex,
that may be linked to a phase variation mechanism. Two genomic islands, spreading
horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions:
This study demonstrates the power of integrated analysis of pan-genomes, chromosome
rearrangements, and selection regimes. Non-random inversion patterns indicate
selective pressure, inversions are particularly frequent in a recent pathogen
B. mallei, and, together with periods of positive selection at other branches,
may indicate adaptation to new niches. One such adaptation could be a possible
phase variation mechanism in B. pseudomallei."
article_number: '965'
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Elena V.
full_name: Moroz, Elena V.
last_name: Moroz
- first_name: Iakov I.
full_name: Davydov, Iakov I.
last_name: Davydov
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection
in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1
apa: Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018).
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1
chicago: Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand.
“Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia
Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1.
ieee: O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics,
vol. 19. Springer Nature, 2018.
ista: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19,
965.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome
Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature,
2018, doi:10.1186/s12864-018-5245-1.
short: O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).
date_created: 2020-08-15T11:02:08Z
date_published: 2018-12-27T00:00:00Z
date_updated: 2023-02-23T13:28:52Z
day: '27'
doi: 10.1186/s12864-018-5245-1
extern: '1'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12864-018-5245-1
month: '12'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp.
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
_id: '8265'
abstract:
- lang: eng
text: Genome rearrangements have played an important role in the evolution of Yersinia
pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic
trees for Y. pestis based on sequence comparison have short internal branches
and low bootstrap supports as only a small number of nucleotide substitutions
have occurred. On the other hand, even a small number of genome rearrangements
may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic
trees based on genome rearrangements using several popular approaches such as
Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements
by inversions. We also reconciled phylogenetic trees for each of the three CRISPR
loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis
of contradictions between the obtained evolutionary trees yielded numerous parallel
inversions and gain/loss events. Our data indicate that an integrated analysis
of sequence-based and inversion-based trees enhances the resolution of phylogenetic
reconstruction. In contrast, reconstructions of strain relationships based on
solely CRISPR loci may not be reliable, as the history is obscured by large deletions,
obliterating the order of spacer gains. Similarly, numerous parallel gene losses
preclude reconstruction of phylogeny based on gene content.
article_number: e4545
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Natalia O.
full_name: Dranenko, Natalia O.
last_name: Dranenko
- first_name: Elena S.
full_name: Ocheredko, Elena S.
last_name: Ocheredko
- first_name: German M.
full_name: Kanevsky, German M.
last_name: Kanevsky
- first_name: Yaroslav N.
full_name: Lozinsky, Yaroslav N.
last_name: Lozinsky
- first_name: Vera A.
full_name: Khalaycheva, Vera A.
last_name: Khalaycheva
- first_name: Irena I.
full_name: Artamonova, Irena I.
last_name: Artamonova
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny
reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545
apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky,
Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and
phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545
chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky,
Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S.
Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.”
PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.
ieee: O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction
in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.
ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva
VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction
in Yersinia pestis. PeerJ. 6, e4545.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction
in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545.
short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky,
V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).
date_created: 2020-08-15T11:08:23Z
date_published: 2018-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:57Z
day: '27'
doi: 10.7717/peerj.4545
extern: '1'
external_id:
pmid:
- '29607260'
intvolume: ' 6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7717/peerj.4545
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_identifier:
issn:
- 2167-8359
publication_status: published
publisher: PeerJ
quality_controlled: '1'
status: public
title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...
---
_id: '8274'
abstract:
- lang: eng
text: 'Background/Aim: Our aim was to investigate the crosstalk between tumor and
immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation
in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human
BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral
blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes
(dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated
by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2
overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages,
was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with
dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29
human colon cancer cells and reduced production of COX2 in BT474 human mammary
cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated
with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion:
Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape
a tolerogenic tumor microenvironment in CMT.'
article_processing_charge: No
article_type: original
author:
- first_name: Maria Isabel
full_name: Carvalho, Maria Isabel
last_name: Carvalho
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Irene
full_name: Flickinger, Irene
last_name: Flickinger
- first_name: Johann G.
full_name: Thalhammer, Johann G.
last_name: Thalhammer
- first_name: Isabel
full_name: Pires, Isabel
last_name: Pires
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Felisbina L.
full_name: Queiroga, Felisbina L.
last_name: Queiroga
citation:
ama: Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817.
doi:10.21873/anticanres.12525
apa: Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer,
J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression
between cancer cells and macrophages. Anticancer Research. International
Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525
chicago: Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann,
Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and
Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer
Cells and Macrophages.” Anticancer Research. International Institute of
Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525.
ieee: M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression
between cancer cells and macrophages,” Anticancer Research, vol. 38, no.
5. International Institute of Anticancer Research, pp. 2811–2817, 2018.
ista: Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG,
Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.
mla: Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression
between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no.
5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525.
short: M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G.
Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38
(2018) 2811–2817.
date_created: 2020-08-17T07:13:55Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:52Z
day: '01'
doi: 10.21873/anticanres.12525
extern: '1'
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 2811-2817
publication: Anticancer Research
publication_identifier:
eissn:
- 1791-7530
issn:
- 0250-7005
publication_status: published
publisher: International Institute of Anticancer Research
quality_controlled: '1'
status: public
title: Bidirectional regulation of COX-2 expression between cancer cells and macrophages
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2018'
...
---
_id: '8298'
abstract:
- lang: eng
text: Sharding, or partitioning the system’s state so that different subsets of
participants handle it, is a proven approach to building distributed systems whose
total capacity scales horizontally with the number of participants. Many distributed
ledgers have adopted this approach to increase their performance, however, they
focus on the permissionless setting that assumes the existence of a strong adversary.
In this paper, we deploy channels for permissioned blockchains. Our first contribution
is to adapt sharding on asset-management applications for the permissioned setting,
while preserving liveness and safety even on transactions spanning across-channels.
Our second contribution is to leverage channels as a confidentiality boundary,
enabling different organizations and consortia to preserve their privacy within
their channels and still be part of a bigger collaborative ecosystem. To make
our system concrete we map it on top of Hyperledger Fabric.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Elli
full_name: Androulaki, Elli
last_name: Androulaki
- first_name: Christian
full_name: Cachin, Christian
last_name: Cachin
- first_name: Angelo
full_name: De Caro, Angelo
last_name: De Caro
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. In: Computer Security.
Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6'
apa: 'Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018).
Channels: Horizontal scaling and confidentiality on permissioned blockchains.
In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer
Nature. https://doi.org/10.1007/978-3-319-99073-6_6'
chicago: 'Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris
Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.”
In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.'
ieee: 'E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal
scaling and confidentiality on permissioned blockchains,” in Computer Security,
Barcelona, Spain, 2018, vol. 11098, pp. 111–131.'
ista: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS:
European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.'
mla: 'Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality
on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature,
2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.'
short: E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security,
Springer Nature, 2018, pp. 111–131.
conference:
end_date: 2018-09-07
location: Barcelona, Spain
name: 'ESORICS: European Symposium on Research in Computer Security'
start_date: 2018-09-03
date_created: 2020-08-26T11:47:34Z
date_published: 2018-08-08T00:00:00Z
date_updated: 2021-01-12T08:17:57Z
day: '08'
doi: 10.1007/978-3-319-99073-6_6
extern: '1'
intvolume: ' 11098'
language:
- iso: eng
month: '08'
oa_version: None
page: 111-131
publication: Computer Security
publication_identifier:
eisbn:
- '9783319990736'
isbn:
- '9783319990729'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Channels: Horizontal scaling and confidentiality on permissioned blockchains'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11098
year: '2018'
...
---
_id: '8297'
abstract:
- lang: eng
text: "Designing a secure permissionless distributed ledger (blockchain) that performs
on par with centralized payment\r\nprocessors, such as Visa, is a challenging
task. Most existing distributed ledgers are unable to scale-out, i.e., to grow
their totalprocessing capacity with the number of validators; and those that do,
compromise security or decentralization. We present OmniLedger, a novel scale-out
distributed ledger that preserves longterm security under permissionless operation.
It ensures security and correctness by using a bias-resistant public-randomness
protocol for choosing large, statistically representative shards that process
transactions, and by introducing an efficient crossshard commit protocol that
atomically handles transactions affecting multiple shards. OmniLedger also optimizes
performance via parallel intra-shard transaction processing, ledger pruning via
collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation
for low-value transactions. An evaluation ofour experimental prototype shows that
OmniLedger’s throughput\r\nscales linearly in the number of active validators,
supporting Visa-level workloads and beyond, while confirming typical transactions
in under two seconds."
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ewa
full_name: Syta, Ewa
last_name: Syta
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger:
A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium
on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5'
apa: 'Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &
Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding.
In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco,
CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5'
chicago: 'Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas
Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98.
IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.'
ieee: 'E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford,
“OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018
IEEE Symposium on Security and Privacy, San Francisco, CA, United States,
2018, pp. 583–598.'
ista: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018.
OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE
Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.'
mla: 'Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE,
2018, pp. 583–98, doi:10.1109/sp.2018.000-5.'
short: E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford,
in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.
conference:
end_date: 2018-05-24
location: San Francisco, CA, United States
name: 'SP: Symposium on Security and Privacy'
start_date: 2018-05-20
date_created: 2020-08-26T11:46:35Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '26'
doi: 10.1109/sp.2018.000-5
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/406
month: '07'
oa: 1
oa_version: Preprint
page: 583-598
publication: 2018 IEEE Symposium on Security and Privacy
publication_identifier:
isbn:
- '9781538643532'
issn:
- 2375-1207
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'OmniLedger: A secure, scale-out, decentralized ledger via sharding'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '8443'
abstract:
- lang: eng
text: Characterizing the structure of membrane proteins (MPs) generally requires
extraction from their native environment, most commonly with detergents. Yet,
the physicochemical properties of detergent micelles and lipid bilayers differ
markedly and could alter the structural organization of MPs, albeit without general
rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure
determination by NMR, but the physiological relevance of several prominent structures
has been questioned, though indirectly, by other biophysical techniques, e.g.,
functional/thermostability assay (TSA) and molecular dynamics (MD) simulations.
Here, we resolve unambiguously this controversy by probing the functional relevance
of three different mitochondrial carriers (MCs) in DPC at the atomic level, using
an exhaustive set of solution-NMR experiments, complemented by functional/TSA
and MD data. Our results provide atomic-level insight into the structure, substrate
interaction and dynamics of the detergent–membrane protein complexes and demonstrates
cogently that, while high-resolution NMR signals can be obtained for MCs in DPC,
they systematically correspond to nonfunctional states.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paola
full_name: Lunetti, Paola
last_name: Lunetti
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Rémy
full_name: Sounier, Rémy
last_name: Sounier
- first_name: Vincenza
full_name: Dolce, Vincenza
last_name: Dolce
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Loredana
full_name: Capobianco, Loredana
last_name: Capobianco
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins:
Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The
Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269'
apa: 'Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L.,
… Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical
Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269'
chicago: 'Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina
Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane
Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.”
The Journal of Physical Chemistry Letters. American Chemical Society, 2018.
https://doi.org/10.1021/acs.jpclett.8b00269.'
ieee: 'V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level
views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical
Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938,
2018.'
ista: 'Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher
B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch
B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry
Letters. 9(5), 933–938.'
mla: 'Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level
Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical
Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38,
doi:10.1021/acs.jpclett.8b00269.'
short: V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher,
M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez,
B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.
date_created: 2020-09-18T10:05:45Z
date_published: 2018-02-03T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '03'
doi: 10.1021/acs.jpclett.8b00269
extern: '1'
intvolume: ' 9'
issue: '5'
keyword:
- General Materials Science
language:
- iso: eng
month: '02'
oa_version: None
page: 933-938
publication: The Journal of Physical Chemistry Letters
publication_identifier:
issn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'How detergent impacts membrane proteins: Atomic-level views of mitochondrial
carriers in dodecylphosphocholine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8440'
abstract:
- lang: eng
text: Mycobacterium tuberculosis can remain dormant in the host, an ability that
explains the failure of many current tuberculosis treatments. Recently, the natural
products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill
Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of
the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein
substrates, such as proteins containing phosphorylated arginine residues, to the
ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit
ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using
NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding
to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these
dynamics are caused by conformational changes and do not result from unfolding
or oligomerization of this domain. Cyclomarin binding to this domain specifically
blocked these N-terminal dynamics. On the basis of these results, we propose a
mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics,
which modulates the chaperone enzymatic activity leading eventually to cell death.
article_processing_charge: No
article_type: original
author:
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Martha
full_name: Brennich, Martha
last_name: Brennich
- first_name: Uli
full_name: Kazmaier, Uli
last_name: Kazmaier
- first_name: Joel
full_name: Lelievre, Joel
last_name: Lelievre
- first_name: Lluis
full_name: Ballell, Lluis
last_name: Ballell
- first_name: Alfred
full_name: Goldberg, Alfred
last_name: Goldberg
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
citation:
ama: Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks
arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1
from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393.
doi:10.1074/jbc.ra118.002251
apa: Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg,
A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. American Society for Biochemistry &
Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251
chicago: Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis
Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin
Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain
of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251.
ieee: K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,”
Journal of Biological Chemistry, vol. 293, no. 22. American Society for
Biochemistry & Molecular Biology, pp. 8379–8393, 2018.
ista: Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda
P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. 293(22), 8379–8393.
mla: Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced
Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.”
Journal of Biological Chemistry, vol. 293, no. 22, American Society for
Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251.
short: K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg,
P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393.
date_created: 2020-09-18T10:05:18Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '01'
doi: 10.1074/jbc.ra118.002251
extern: '1'
intvolume: ' 293'
issue: '22'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '06'
oa_version: None
page: 8379-8393
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics
in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2018'
...
---
_id: '8442'
abstract:
- lang: eng
text: Membrane proteins perform a host of vital cellular functions. Deciphering
the molecular mechanisms whereby they fulfill these functions requires detailed
biophysical and structural investigations. Detergents have proven pivotal to extract
the protein from its native surroundings. Yet, they provide a milieu that departs
significantly from that of the biological membrane, to the extent that the structure,
the dynamics, and the interactions of membrane proteins in detergents may considerably
vary, as compared to the native environment. Understanding the impact of detergents
on membrane proteins is, therefore, crucial to assess the biological relevance
of results obtained in detergents. Here, we review the strengths and weaknesses
of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR
studies of membrane proteins. While this class of detergents is often successful
for membrane protein solubilization, a growing list of examples points to destabilizing
and denaturing properties, in particular for α-helical membrane proteins. Our
comprehensive analysis stresses the importance of stringent controls when working
with this class of detergents and when analyzing the structure and dynamics of
membrane proteins in alkyl phosphocholine detergents.
article_processing_charge: No
article_type: original
author:
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Jason R.
full_name: Schnell, Jason R.
last_name: Schnell
- first_name: Nicole
full_name: Zitzmann, Nicole
last_name: Zitzmann
- first_name: Eva
full_name: Pebay-Peyroula, Eva
last_name: Pebay-Peyroula
- first_name: Laurent J.
full_name: Catoire, Laurent J.
last_name: Catoire
- first_name: Bruno
full_name: Miroux, Bruno
last_name: Miroux
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Gianluigi
full_name: Veglia, Gianluigi
last_name: Veglia
- first_name: Timothy A.
full_name: Cross, Timothy A.
last_name: Cross
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein
structure in alkyl phosphocholine detergents: A critical assessment of NMR and
biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570'
apa: 'Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire,
L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570'
chicago: 'Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann,
Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of
Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical
Assessment of NMR and Biophysical Studies.” Chemical Reviews. American
Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.'
ieee: 'C. Chipot et al., “Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society,
pp. 3559–3607, 2018.'
ista: 'Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ,
Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native
membrane protein structure in alkyl phosphocholine detergents: A critical assessment
of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.'
mla: 'Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure
in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical
Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society,
2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.'
short: C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire,
B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118
(2018) 3559–3607.
date_created: 2020-09-18T10:05:35Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '28'
doi: 10.1021/acs.chemrev.7b00570
extern: '1'
intvolume: ' 118'
issue: '7'
keyword:
- General Chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 3559-3607
publication: Chemical Reviews
publication_identifier:
issn:
- 0009-2665
- 1520-6890
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Perturbations of native membrane protein structure in alkyl phosphocholine
detergents: A critical assessment of NMR and biophysical studies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2018'
...
---
_id: '8441'
abstract:
- lang: eng
text: Solid-state near-rotary-resonance measurements of the spin–lattice relaxation
rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular
dynamics in the microsecond time scale. The small difference between the spin-lock
(SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions,
at the same time it brings up some methodological challenges. In this work, several
issues affecting correct measurements and analysis of 15N R1ρ data are considered
in detail. Among them are signal amplitude as a function of the difference between
SL and MAS frequencies, “dead time” in the initial part of the relaxation decay
caused by transient spin-dynamic oscillations, measurements under HORROR condition
and proper treatment of the multi-exponential relaxation decays. The multiple
15N R1ρ measurements at different SL fields and temperatures have been conducted
in 1D mode (i.e. without site-specific resolution) for a set of four different
microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin)
to study the overall protein rocking in a crystal. While the amplitude of this
motion varies very significantly, its correlation time for all four sample is
practically the same, 30–50 μs. The amplitude of the rocking motion correlates
with the packing density of a protein crystal. It has been suggested that the
rocking motion is not diffusive but likely a jump-like dynamic process.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Krushelnitsky, Alexey
last_name: Krushelnitsky
- first_name: Diego
full_name: Gauto, Diego
last_name: Gauto
- first_name: Diana C.
full_name: Rodriguez Camargo, Diana C.
last_name: Rodriguez Camargo
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Kay
full_name: Saalwächter, Kay
last_name: Saalwächter
citation:
ama: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4'
apa: 'Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., &
Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ
15N MAS NMR experiments: The model case of protein overall-rocking in crystals.
Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4'
chicago: 'Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda,
and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ
15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.'
ieee: 'A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter,
“Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals,” Journal of Biomolecular
NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.'
ista: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 71(1), 53–67.'
mla: 'Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance
R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp.
53–67, doi:10.1007/s10858-018-0191-4.'
short: A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter,
Journal of Biomolecular NMR 71 (2018) 53–67.
date_created: 2020-09-18T10:05:28Z
date_published: 2018-05-30T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '30'
doi: 10.1007/s10858-018-0191-4
extern: '1'
intvolume: ' 71'
issue: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: 53-67
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2018'
...
---
_id: '8439'
abstract:
- lang: eng
text: Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer
of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly
hampers their structural study in an environment similar to the bacterial surface.
We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long
O-antigen polysaccharides assembled in solution as vesicles or elongated micelles.
Solid-state NMR with magic-angle spinning permitted the identification of NMR
signals arising from regions with different flexibilities in the LPS, from the
lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS
enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa
LPS, for which we could confirm that a specific oligosaccharide is involved in
the antibiotic binding. The possibility to study LPS alone and bound to a ligand
when it is assembled in membrane-like structures opens great prospects for the
investigation of proteins and antibiotics that specifically target such an important
molecule at the surface of Gram-negative bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Cedric
full_name: Laguri, Cedric
last_name: Laguri
- first_name: Alba
full_name: Silipo, Alba
last_name: Silipo
- first_name: Alessandra M.
full_name: Martorana, Alessandra M.
last_name: Martorana
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Roberta
full_name: Marchetti, Roberta
last_name: Marchetti
- first_name: Alessandra
full_name: Polissi, Alessandra
last_name: Polissi
- first_name: Antonio
full_name: Molinaro, Antonio
last_name: Molinaro
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact
lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113.
doi:10.1021/acschembio.8b00271
apa: Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi,
A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide
endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271
chicago: Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta
Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid
State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology.
American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271.
ieee: C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide
endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society,
pp. 2106–2113, 2018.
ista: Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro
A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin.
ACS Chemical Biology. 13(8), 2106–2113.
mla: Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide
Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society,
2018, pp. 2106–13, doi:10.1021/acschembio.8b00271.
short: C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi,
A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.
date_created: 2020-09-18T10:05:09Z
date_published: 2018-07-02T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '02'
doi: 10.1021/acschembio.8b00271
extern: '1'
intvolume: ' 13'
issue: '8'
keyword:
- Molecular Medicine
- Biochemistry
- General Medicine
language:
- iso: eng
month: '07'
oa_version: None
page: 2106-2113
publication: ACS Chemical Biology
publication_identifier:
issn:
- 1554-8929
- 1554-8937
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Solid state NMR studies of intact lipopolysaccharide endotoxin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2018'
...