---
_id: '11452'
abstract:
- lang: eng
text: We study efficient distributed algorithms for the fundamental problem of principal
component analysis and leading eigenvector computation on the sphere, when the
data are randomly distributed among a set of computational nodes. We propose a
new quantized variant of Riemannian gradient descent to solve this problem, and
prove that the algorithm converges with high probability under a set of necessary
spherical-convexity properties. We give bounds on the number of bits transmitted
by the algorithm under common initialization schemes, and investigate the dependency
on the problem dimension in each case.
acknowledgement: We would like to thank the anonymous reviewers for helpful comments
and suggestions. We also thank Aurelien Lucchi and Antonio Orvieto for fruitful
discussions at an early stage of this work. FA is partially supported by the SNSF
under research project No. 192363 and conducted part of this work while at IST Austria
under the European Union’s Horizon 2020 research and innovation programme (grant
agreement No. 805223 ScaleML). PD partly conducted this work while at IST Austria
and was supported by the European Union’s Horizon 2020 programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: No
arxiv: 1
author:
- first_name: Foivos
full_name: Alimisis, Foivos
last_name: Alimisis
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Bart
full_name: Vandereycken, Bart
last_name: Vandereycken
- 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: 'Alimisis F, Davies P, Vandereycken B, Alistarh D-A. Distributed principal
component analysis with limited communication. In: Advances in Neural Information
Processing Systems - 35th Conference on Neural Information Processing Systems.
Vol 4. Neural Information Processing Systems Foundation; 2021:2823-2834.'
apa: 'Alimisis, F., Davies, P., Vandereycken, B., & Alistarh, D.-A. (2021).
Distributed principal component analysis with limited communication. In Advances
in Neural Information Processing Systems - 35th Conference on Neural Information
Processing Systems (Vol. 4, pp. 2823–2834). Virtual, Online: Neural Information
Processing Systems Foundation.'
chicago: Alimisis, Foivos, Peter Davies, Bart Vandereycken, and Dan-Adrian Alistarh.
“Distributed Principal Component Analysis with Limited Communication.” In Advances
in Neural Information Processing Systems - 35th Conference on Neural Information
Processing Systems, 4:2823–34. Neural Information Processing Systems Foundation,
2021.
ieee: F. Alimisis, P. Davies, B. Vandereycken, and D.-A. Alistarh, “Distributed
principal component analysis with limited communication,” in Advances in Neural
Information Processing Systems - 35th Conference on Neural Information Processing
Systems, Virtual, Online, 2021, vol. 4, pp. 2823–2834.
ista: 'Alimisis F, Davies P, Vandereycken B, Alistarh D-A. 2021. Distributed principal
component analysis with limited communication. Advances in Neural Information
Processing Systems - 35th Conference on Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 4, 2823–2834.'
mla: Alimisis, Foivos, et al. “Distributed Principal Component Analysis with Limited
Communication.” Advances in Neural Information Processing Systems - 35th Conference
on Neural Information Processing Systems, vol. 4, Neural Information Processing
Systems Foundation, 2021, pp. 2823–34.
short: F. Alimisis, P. Davies, B. Vandereycken, D.-A. Alistarh, in:, Advances in
Neural Information Processing Systems - 35th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2021, pp.
2823–2834.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-06-19T22:01:58Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2022-06-20T08:31:52Z
day: '01'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2110.14391'
intvolume: ' 4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/1680e9fa7b4dd5d62ece800239bb53bd-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 2823-2834
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Advances in Neural Information Processing Systems - 35th Conference on
Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed principal component analysis with limited communication
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2021'
...
---
_id: '11453'
abstract:
- lang: eng
text: "Neuronal computations depend on synaptic connectivity and intrinsic electrophysiological
properties. Synaptic connectivity determines which inputs from presynaptic neurons
are integrated, while cellular properties determine how inputs are filtered over
time. Unlike their biological counterparts, most computational approaches to learning
in simulated neural networks are limited to changes in synaptic connectivity.
However, if intrinsic parameters change, neural computations are altered drastically.
Here, we include the parameters that determine the intrinsic properties,\r\ne.g.,
time constants and reset potential, into the learning paradigm. Using sparse feedback
signals that indicate target spike times, and gradient-based parameter updates,
we show that the intrinsic parameters can be learned along with the synaptic weights
to produce specific input-output functions. Specifically, we use a teacher-student
paradigm in which a randomly initialised leaky integrate-and-fire or resonate-and-fire
neuron must recover the parameters of a teacher neuron. We show that complex temporal
functions can be learned online and without backpropagation through time, relying
on event-based updates only. Our results are a step towards online learning of
neural computations from ungraded and unsigned sparse feedback signals with a
biologically inspired learning mechanism."
acknowledgement: We would like to thank Professor Dr. Henning Sprekeler for his valuable
suggestions and Dr. Andrew Saxe, Milan Klöwer and Anna Wallis for their constructive
feedback on the manuscript. Lukas Braun was supported by the Network of European
Neuroscience Schools through their NENS Exchange Grant program, by the European
Union through their European Community Action Scheme for the Mobility of University
Students, the Woodward Scholarship awarded by Wadham College, Oxford and the Medical
Research Council [MR/N013468/1]. Tim P. Vogels was supported by a Wellcome Trust
Senior Research Fellowship [214316/Z/18/Z].
article_processing_charge: No
author:
- first_name: Lukas
full_name: Braun, Lukas
last_name: Braun
- 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: 'Braun L, Vogels TP. Online learning of neural computations from sparse temporal
feedback. In: Advances in Neural Information Processing Systems - 35th Conference
on Neural Information Processing Systems. Vol 20. Neural Information Processing
Systems Foundation; 2021:16437-16450.'
apa: 'Braun, L., & Vogels, T. P. (2021). Online learning of neural computations
from sparse temporal feedback. In Advances in Neural Information Processing
Systems - 35th Conference on Neural Information Processing Systems (Vol. 20,
pp. 16437–16450). Virtual, Online: Neural Information Processing Systems Foundation.'
chicago: Braun, Lukas, and Tim P Vogels. “Online Learning of Neural Computations
from Sparse Temporal Feedback.” In Advances in Neural Information Processing
Systems - 35th Conference on Neural Information Processing Systems, 20:16437–50.
Neural Information Processing Systems Foundation, 2021.
ieee: L. Braun and T. P. Vogels, “Online learning of neural computations from sparse
temporal feedback,” in Advances in Neural Information Processing Systems -
35th Conference on Neural Information Processing Systems, Virtual, Online,
2021, vol. 20, pp. 16437–16450.
ista: 'Braun L, Vogels TP. 2021. Online learning of neural computations from sparse
temporal feedback. Advances in Neural Information Processing Systems - 35th Conference
on Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems vol. 20, 16437–16450.'
mla: Braun, Lukas, and Tim P. Vogels. “Online Learning of Neural Computations from
Sparse Temporal Feedback.” Advances in Neural Information Processing Systems
- 35th Conference on Neural Information Processing Systems, vol. 20, Neural
Information Processing Systems Foundation, 2021, pp. 16437–50.
short: L. Braun, T.P. Vogels, in:, Advances in Neural Information Processing Systems
- 35th Conference on Neural Information Processing Systems, Neural Information
Processing Systems Foundation, 2021, pp. 16437–16450.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-06-19T22:01:59Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2022-06-20T07:12:58Z
day: '01'
department:
- _id: TiVo
intvolume: ' 20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/88e1ce84f9feef5a08d0df0334c53468-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 16437-16450
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Advances in Neural Information Processing Systems - 35th Conference on
Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online learning of neural computations from sparse temporal feedback
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2021'
...
---
_id: '11458'
abstract:
- lang: eng
text: 'The increasing computational requirements of deep neural networks (DNNs)
have led to significant interest in obtaining DNN models that are sparse, yet
accurate. Recent work has investigated the even harder case of sparse training,
where the DNN weights are, for as much as possible, already sparse to reduce computational
costs during training. Existing sparse training methods are often empirical and
can have lower accuracy relative to the dense baseline. In this paper, we present
a general approach called Alternating Compressed/DeCompressed (AC/DC) training
of DNNs, demonstrate convergence for a variant of the algorithm, and show that
AC/DC outperforms existing sparse training methods in accuracy at similar computational
budgets; at high sparsity levels, AC/DC even outperforms existing methods that
rely on accurate pre-trained dense models. An important property of AC/DC is that
it allows co-training of dense and sparse models, yielding accurate sparse–dense
model pairs at the end of the training process. This is useful in practice, where
compressed variants may be desirable for deployment in resource-constrained settings
without re-doing the entire training flow, and also provides us with insights
into the accuracy gap between dense and compressed models. The code is available
at: https://github.com/IST-DASLab/ACDC.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML), and a CNRS PEPS grant. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing (SciComp). We would also like to thank Christoph Lampert
for his feedback on an earlier version of this work, as well as for providing hardware
for the Transformer-XL experiments.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
- 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: 'Peste E-A, Iofinova EB, Vladu A, Alistarh D-A. AC/DC: Alternating Compressed/DeCompressed
training of deep neural networks. In: 35th Conference on Neural Information
Processing Systems. Vol 34. Curran Associates; 2021:8557-8570.'
apa: 'Peste, E.-A., Iofinova, E. B., Vladu, A., & Alistarh, D.-A. (2021). AC/DC:
Alternating Compressed/DeCompressed training of deep neural networks. In 35th
Conference on Neural Information Processing Systems (Vol. 34, pp. 8557–8570).
Virtual, Online: Curran Associates.'
chicago: 'Peste, Elena-Alexandra, Eugenia B Iofinova, Adrian Vladu, and Dan-Adrian
Alistarh. “AC/DC: Alternating Compressed/DeCompressed Training of Deep Neural
Networks.” In 35th Conference on Neural Information Processing Systems,
34:8557–70. Curran Associates, 2021.'
ieee: 'E.-A. Peste, E. B. Iofinova, A. Vladu, and D.-A. Alistarh, “AC/DC: Alternating
Compressed/DeCompressed training of deep neural networks,” in 35th Conference
on Neural Information Processing Systems, Virtual, Online, 2021, vol. 34,
pp. 8557–8570.'
ista: 'Peste E-A, Iofinova EB, Vladu A, Alistarh D-A. 2021. AC/DC: Alternating Compressed/DeCompressed
training of deep neural networks. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems vol. 34, 8557–8570.'
mla: 'Peste, Elena-Alexandra, et al. “AC/DC: Alternating Compressed/DeCompressed
Training of Deep Neural Networks.” 35th Conference on Neural Information Processing
Systems, vol. 34, Curran Associates, 2021, pp. 8557–70.'
short: E.-A. Peste, E.B. Iofinova, A. Vladu, D.-A. Alistarh, in:, 35th Conference
on Neural Information Processing Systems, Curran Associates, 2021, pp. 8557–8570.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-06-20T12:11:53Z
date_published: 2021-12-06T00:00:00Z
date_updated: 2023-06-01T12:54:45Z
day: '6'
department:
- _id: GradSch
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2106.12379'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/48000647b315f6f00f913caa757a70b3-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 8557-8570
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
related_material:
record:
- id: '13074'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'AC/DC: Alternating Compressed/DeCompressed training of deep neural networks'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '11463'
abstract:
- lang: eng
text: "Efficiently approximating local curvature information of the loss function
is a key tool for optimization and compression of deep neural networks. Yet, most
existing methods to approximate second-order information have high computational\r\nor
storage costs, which limits their practicality. In this work, we investigate matrix-free,
linear-time approaches for estimating Inverse-Hessian Vector Products (IHVPs)
for the case when the Hessian can be approximated as a sum of rank-one matrices,
as in the classic approximation of the Hessian by the empirical Fisher matrix.
We propose two new algorithms: the first is tailored towards network compression
and can compute the IHVP for dimension d, if the Hessian is given as a sum of
m rank-one matrices, using O(dm2) precomputation, O(dm) cost for computing the
IHVP, and query cost O(m) for any single element of the inverse Hessian. The second
algorithm targets an optimization setting, where we wish to compute the product
between the inverse Hessian, estimated over a sliding window of optimization steps,
and a given gradient direction, as required for preconditioned SGD. We give an
algorithm with cost O(dm + m2) for computing the IHVP and O(dm + m3) for adding
or removing any gradient from the sliding window. These\r\ntwo algorithms yield
state-of-the-art results for network pruning and optimization with lower computational
overhead relative to existing second-order methods. Implementations are available
at [9] and [17]."
acknowledgement: We gratefully acknowledge funding the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation programme (grant
agreement No 805223 ScaleML), as well as computational support from Amazon Web Services
(AWS) EC2.
article_processing_charge: No
arxiv: 1
author:
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- 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: 'Frantar E, Kurtic E, Alistarh D-A. M-FAC: Efficient matrix-free approximations
of second-order information. In: 35th Conference on Neural Information Processing
Systems. Vol 34. Curran Associates; 2021:14873-14886.'
apa: 'Frantar, E., Kurtic, E., & Alistarh, D.-A. (2021). M-FAC: Efficient matrix-free
approximations of second-order information. In 35th Conference on Neural Information
Processing Systems (Vol. 34, pp. 14873–14886). Virtual, Online: Curran Associates.'
chicago: 'Frantar, Elias, Eldar Kurtic, and Dan-Adrian Alistarh. “M-FAC: Efficient
Matrix-Free Approximations of Second-Order Information.” In 35th Conference
on Neural Information Processing Systems, 34:14873–86. Curran Associates,
2021.'
ieee: 'E. Frantar, E. Kurtic, and D.-A. Alistarh, “M-FAC: Efficient matrix-free
approximations of second-order information,” in 35th Conference on Neural Information
Processing Systems, Virtual, Online, 2021, vol. 34, pp. 14873–14886.'
ista: 'Frantar E, Kurtic E, Alistarh D-A. 2021. M-FAC: Efficient matrix-free approximations
of second-order information. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems vol. 34, 14873–14886.'
mla: 'Frantar, Elias, et al. “M-FAC: Efficient Matrix-Free Approximations of Second-Order
Information.” 35th Conference on Neural Information Processing Systems,
vol. 34, Curran Associates, 2021, pp. 14873–86.'
short: E. Frantar, E. Kurtic, D.-A. Alistarh, in:, 35th Conference on Neural Information
Processing Systems, Curran Associates, 2021, pp. 14873–14886.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-06-26T22:01:35Z
date_published: 2021-12-06T00:00:00Z
date_updated: 2022-06-27T07:05:12Z
day: '06'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2010.08222'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/7cfd5df443b4eb0d69886a583b33de4c-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 14873-14886
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'M-FAC: Efficient matrix-free approximations of second-order information'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '11464'
abstract:
- lang: eng
text: "We consider a standard distributed optimisation setting where N machines,
each holding a d-dimensional function\r\nfi, aim to jointly minimise the sum of
the functions ∑Ni=1fi(x). This problem arises naturally in large-scale distributed
optimisation, where a standard solution is to apply variants of (stochastic) gradient
descent. We focus on the communication complexity of this problem: our main result
provides the first fully unconditional bounds on total number of bits which need
to be sent and received by the N machines to solve this problem under point-to-point
communication, within a given error-tolerance. Specifically, we show that Ω(Ndlogd/Nε)
total bits need to be communicated between the machines to find an additive ϵ-approximation
to the minimum of ∑Ni=1fi(x). The result holds for both deterministic and randomised
algorithms, and, importantly, requires no assumptions on the algorithm structure.
The lower bound is tight under certain restrictions on parameter values, and is
matched within constant factors for quadratic objectives by a new variant of quantised
gradient descent, which we describe and analyse. Our results bring over tools
from communication complexity to distributed optimisation, which has potential
for further applications."
acknowledgement: We thank the NeurIPS reviewers for insightful comments that helped
us improve the positioning of our results, as well as for pointing out the subsampling
approach for complementing the randomised lower bound. We also thank Foivos Alimisis
and Peter Davies for useful discussions. This project has received funding from
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement No 805223 ScaleML).
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
citation:
ama: 'Alistarh D-A, Korhonen J. Towards tight communication lower bounds for distributed
optimisation. In: 35th Conference on Neural Information Processing Systems.
Vol 34. Curran Associates; 2021:7254-7266.'
apa: 'Alistarh, D.-A., & Korhonen, J. (2021). Towards tight communication lower
bounds for distributed optimisation. In 35th Conference on Neural Information
Processing Systems (Vol. 34, pp. 7254–7266). Virtual, Online: Curran Associates.'
chicago: Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication
Lower Bounds for Distributed Optimisation.” In 35th Conference on Neural Information
Processing Systems, 34:7254–66. Curran Associates, 2021.
ieee: D.-A. Alistarh and J. Korhonen, “Towards tight communication lower bounds
for distributed optimisation,” in 35th Conference on Neural Information Processing
Systems, Virtual, Online, 2021, vol. 34, pp. 7254–7266.
ista: 'Alistarh D-A, Korhonen J. 2021. Towards tight communication lower bounds
for distributed optimisation. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems vol. 34, 7254–7266.'
mla: Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication Lower
Bounds for Distributed Optimisation.” 35th Conference on Neural Information
Processing Systems, vol. 34, Curran Associates, 2021, pp. 7254–66.
short: D.-A. Alistarh, J. Korhonen, in:, 35th Conference on Neural Information Processing
Systems, Curran Associates, 2021, pp. 7254–7266.
conference:
end_date: 2021-12-14
location: Virtual, Online
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-06-26T22:01:35Z
date_published: 2021-12-06T00:00:00Z
date_updated: 2022-06-27T06:54:31Z
day: '06'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2010.08222'
intvolume: ' 34'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2021/file/3b92d18aa7a6176dd37d372bc2f1eb71-Paper.pdf
month: '12'
oa: 1
oa_version: Published Version
page: 7254-7266
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Curran Associates
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards tight communication lower bounds for distributed optimisation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '12076'
abstract:
- lang: eng
text: We find an asymptotic formula for the number of primitive vectors $(z_1,\ldots,z_4)\in
(\mathbb{Z}_{\neq 0})^4$ such that $z_1,\ldots, z_4$ are all squareful and bounded
by $B$, and $z_1+\cdots + z_4 = 0$. Our result agrees in the power of $B$ and
$\log B$ with the Campana-Manin conjecture of Pieropan, Smeets, Tanimoto and V\'{a}rilly-Alvarado.
article_number: '2104.06966'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Shute AL. Sums of four squareful numbers. arXiv. doi:10.48550/arXiv.2104.06966
apa: Shute, A. L. (n.d.). Sums of four squareful numbers. arXiv. https://doi.org/10.48550/arXiv.2104.06966
chicago: Shute, Alec L. “Sums of Four Squareful Numbers.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2104.06966.
ieee: A. L. Shute, “Sums of four squareful numbers,” arXiv. .
ista: Shute AL. Sums of four squareful numbers. arXiv, 2104.06966.
mla: Shute, Alec L. “Sums of Four Squareful Numbers.” ArXiv, 2104.06966,
doi:10.48550/arXiv.2104.06966.
short: A.L. Shute, ArXiv (n.d.).
date_created: 2022-09-09T10:42:51Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2023-02-21T16:37:30Z
day: '15'
department:
- _id: TiBr
doi: 10.48550/arXiv.2104.06966
external_id:
arxiv:
- '2104.06966'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2104.06966
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '12072'
relation: dissertation_contains
status: public
status: public
title: Sums of four squareful numbers
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '12077'
abstract:
- lang: eng
text: "We compare the Manin-type conjecture for Campana points recently formulated\r\nby
Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction
of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$,
where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that
the two predicted leading constants do not agree, and we discuss whether thin
sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto
the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding
to squareful values of binary quadratic forms."
acknowledgement: The author would like to thank Damaris Schindler and Florian Wilsch
for their helpful comments on the heights and Tamagawa measures used in Section
3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable
feedback on an earlier version of this paper, and Tim Browning for many useful comments
and discussions during the development of this work. The author is also grateful
to the anonymous referee for providing many valuable comments and suggestions that
improved the quality of the paper.
article_number: '2104.14946'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Shute AL. On the leading constant in the Manin-type conjecture for Campana
points. arXiv. doi:10.48550/arXiv.2104.14946
apa: Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for
Campana points. arXiv. https://doi.org/10.48550/arXiv.2104.14946
chicago: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for
Campana Points.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2104.14946.
ieee: A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana
points,” arXiv. .
ista: Shute AL. On the leading constant in the Manin-type conjecture for Campana
points. arXiv, 2104.14946.
mla: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana
Points.” ArXiv, 2104.14946, doi:10.48550/arXiv.2104.14946.
short: A.L. Shute, ArXiv (n.d.).
date_created: 2022-09-09T10:43:17Z
date_published: 2021-04-30T00:00:00Z
date_updated: 2023-02-21T16:37:30Z
day: '30'
department:
- _id: TiBr
doi: 10.48550/arXiv.2104.14946
external_id:
arxiv:
- '2104.14946'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2104.14946
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '12072'
relation: dissertation_contains
status: public
status: public
title: On the leading constant in the Manin-type conjecture for Campana points
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '12186'
abstract:
- lang: eng
text: Activation of cell-surface and intracellular receptor-mediated immunity results
in rapid transcriptional reprogramming that underpins disease resistance. However,
the mechanisms by which co-activation of both immune systems lead to transcriptional
changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes
in gene expression and chromatin accessibility. Activation of cell-surface or
intracellular receptor-mediated immunity, or both, increases chromatin accessibility
at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with
publicly available information on transcription factor DNA-binding motifs enabled
comparison of individual gene regulatory networks activated by cell-surface or
intracellular receptor-mediated immunity, or by both. These results and analyses
reveal overlapping and conserved transcriptional regulatory mechanisms between
the two immune systems.
acknowledgement: "We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory.
PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation
Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future
Leader Fellowship from the Biotechnology and Biological Sciences Research Council
(BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by
the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported
by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and
RZ were supported by the Scottish Government Rural and Environment Science and Analytical
Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics
and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported
by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP)
funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by
a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research
Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by
Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). "
article_processing_charge: No
article_type: original
author:
- first_name: Pingtao
full_name: Ding, Pingtao
last_name: Ding
- first_name: Toshiyuki
full_name: Sakai, Toshiyuki
last_name: Sakai
- first_name: Ram
full_name: Krishna Shrestha, Ram
last_name: Krishna Shrestha
- first_name: Nicolas
full_name: Manosalva Perez, Nicolas
last_name: Manosalva Perez
- first_name: Wenbin
full_name: Guo, Wenbin
last_name: Guo
- first_name: Bruno Pok Man
full_name: Ngou, Bruno Pok Man
last_name: Ngou
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Chang
full_name: Liu, Chang
last_name: Liu
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Runxuan
full_name: Zhang, Runxuan
last_name: Zhang
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Dan
full_name: MacLean, Dan
last_name: MacLean
- first_name: Jonathan D G
full_name: Jones, Jonathan D G
last_name: Jones
citation:
ama: Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes
activated by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. 2021;72(22):7927-7941. doi:10.1093/jxb/erab373
apa: Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou,
B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated
by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. Oxford University Press. https://doi.org/10.1093/jxb/erab373
chicago: Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva
Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility
Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal
of Experimental Botany. Oxford University Press, 2021. https://doi.org/10.1093/jxb/erab373.
ieee: P. Ding et al., “Chromatin accessibility landscapes activated by cell-surface
and intracellular immune receptors,” Journal of Experimental Botany, vol.
72, no. 22. Oxford University Press, pp. 7927–7941, 2021.
ista: Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He
S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin
accessibility landscapes activated by cell-surface and intracellular immune receptors.
Journal of Experimental Botany. 72(22), 7927–7941.
mla: Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface
and Intracellular Immune Receptors.” Journal of Experimental Botany, vol.
72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:10.1093/jxb/erab373.
short: P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M.
Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones,
Journal of Experimental Botany 72 (2021) 7927–7941.
date_created: 2023-01-16T09:14:35Z
date_published: 2021-08-13T00:00:00Z
date_updated: 2023-05-08T11:01:18Z
day: '13'
department:
- _id: XiFe
doi: 10.1093/jxb/erab373
extern: '1'
external_id:
pmid:
- '34387350'
intvolume: ' 72'
issue: '22'
keyword:
- Plant Science
- Physiology
language:
- iso: eng
month: '08'
oa_version: None
page: 7927-7941
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
issn:
- 0022-0957
- 1460-2431
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin accessibility landscapes activated by cell-surface and intracellular
immune receptors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2021'
...
---
_id: '12187'
abstract:
- lang: eng
text: Genomes of germ cells present an existential vulnerability to organisms because
germ cell mutations will propagate to future generations. Transposable elements
are one source of such mutations. In the small flowering plant Arabidopsis, Long
et al. found that genome methylation in the male germline is directed by small
interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective
by Mosher). These germline siRNAs silence germline transposons and establish inherited
methylation patterns in sperm, thus maintaining the integrity of the plant genome
across generations.
acknowledgement: 'We thank the John Innes Centre Bioimaging Facility (S. Lopez, E.
Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience
Institute Partnership Computing Infrastructure for Science Group for high-performance
computing resources. Funding: This work was funded by a European Research Council
Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable
Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research
Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John
Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship
(BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed
the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the
experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data.
Competing interests: The authors declare no competing interests. Data and material
availability: All sequencing data have been deposited in the Gene Expression Omnibus
(GEO) under accession no. GSE161625. Accession nos. of published datasets used in
this study are listed in table S6. Published software used in this study include
Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167),
Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452),
and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and
MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore
and https://github.com/broadinstitute/picard, respectively. All remaining data are
in the main paper or the supplementary materials.'
article_processing_charge: No
article_type: original
author:
- first_name: Jincheng
full_name: Long, Jincheng
last_name: Long
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Wenjing
full_name: She, Wenjing
last_name: She
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Samuel
full_name: Deans, Samuel
last_name: Deans
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Long J, Walker J, She W, et al. Nurse cell--derived small RNAs define paternal
epigenetic inheritance in Arabidopsis. Science. 2021;373(6550). doi:10.1126/science.abh0556
apa: Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X.
(2021). Nurse cell--derived small RNAs define paternal epigenetic inheritance
in Arabidopsis. Science. American Association for the Advancement of Science
(AAAS). https://doi.org/10.1126/science.abh0556
chicago: Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao,
Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell--Derived Small RNAs
Define Paternal Epigenetic Inheritance in Arabidopsis.” Science. American
Association for the Advancement of Science (AAAS), 2021. https://doi.org/10.1126/science.abh0556.
ieee: J. Long et al., “Nurse cell--derived small RNAs define paternal epigenetic
inheritance in Arabidopsis,” Science, vol. 373, no. 6550. American Association
for the Advancement of Science (AAAS), 2021.
ista: Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021.
Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis.
Science. 373(6550).
mla: Long, Jincheng, et al. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic
Inheritance in Arabidopsis.” Science, vol. 373, no. 6550, American Association
for the Advancement of Science (AAAS), 2021, doi:10.1126/science.abh0556.
short: J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X.
Feng, Science 373 (2021).
date_created: 2023-01-16T09:15:14Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2023-05-08T10:56:39Z
day: '02'
department:
- _id: XiFe
doi: 10.1126/science.abh0556
extern: '1'
external_id:
pmid:
- '34210850'
intvolume: ' 373'
issue: '6550'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science (AAAS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 373
year: '2021'
...
---
_id: '12767'
abstract:
- lang: eng
text: "Several problems in planning and reactive synthesis can be reduced to the
analysis of two-player quantitative graph games. Optimization is one form of analysis.
We argue that in many cases it may be better to replace the optimization problem
with the satisficing problem, where instead of searching for optimal solutions,
the goal is to search for solutions that adhere to a given threshold bound.\r\nThis
work defines and investigates the satisficing problem on a two-player graph game
with the discounted-sum cost model. We show that while the satisficing problem
can be solved using numerical methods just like the optimization problem, this
approach does not render compelling benefits over optimization. When the discount
factor is, however, an integer, we present another approach to satisficing, which
is purely based on automata methods. We show that this approach is algorithmically
more performant – both theoretically and empirically – and demonstrates the broader
applicability of satisficing over optimization."
acknowledgement: We thank anonymous reviewers for valuable inputs. This work is supported
in part by NSF grant 2030859 to the CRA for the CIFellows Project, NSF grants IIS-1527668,
CCF-1704883, IIS-1830549, the ERC CoG 863818 (ForM-SMArt), and an award from the
Maryland Procurement Office.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Suguman
full_name: Bansal, Suguman
last_name: Bansal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Moshe Y.
full_name: Vardi, Moshe Y.
last_name: Vardi
citation:
ama: 'Bansal S, Chatterjee K, Vardi MY. On satisficing in quantitative games. In:
27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems. Vol 12651. Springer Nature; 2021:20-37. doi:10.1007/978-3-030-72016-2'
apa: 'Bansal, S., Chatterjee, K., & Vardi, M. Y. (2021). On satisficing in quantitative
games. In 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems (Vol. 12651, pp. 20–37). Luxembourg City, Luxembourg:
Springer Nature. https://doi.org/10.1007/978-3-030-72016-2'
chicago: Bansal, Suguman, Krishnendu Chatterjee, and Moshe Y. Vardi. “On Satisficing
in Quantitative Games.” In 27th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems, 12651:20–37. Springer Nature,
2021. https://doi.org/10.1007/978-3-030-72016-2.
ieee: S. Bansal, K. Chatterjee, and M. Y. Vardi, “On satisficing in quantitative
games,” in 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems, Luxembourg City, Luxembourg, 2021, vol. 12651, pp.
20–37.
ista: 'Bansal S, Chatterjee K, Vardi MY. 2021. On satisficing in quantitative games.
27th International Conference on Tools and Algorithms for the Construction and
Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, LNCS, vol. 12651, 20–37.'
mla: Bansal, Suguman, et al. “On Satisficing in Quantitative Games.” 27th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems,
vol. 12651, Springer Nature, 2021, pp. 20–37, doi:10.1007/978-3-030-72016-2.
short: S. Bansal, K. Chatterjee, M.Y. Vardi, in:, 27th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems, Springer
Nature, 2021, pp. 20–37.
conference:
end_date: 2021-04-01
location: Luxembourg City, Luxembourg
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2021-03-27
date_created: 2023-03-26T22:01:09Z
date_published: 2021-03-21T00:00:00Z
date_updated: 2025-07-14T09:09:51Z
day: '21'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-72016-2
ec_funded: 1
external_id:
arxiv:
- '2101.02594'
file:
- access_level: open_access
checksum: b020b78b23587ce7610b1aafb4e63438
content_type: application/pdf
creator: dernst
date_created: 2023-03-28T11:00:33Z
date_updated: 2023-03-28T11:00:33Z
file_id: '12777'
file_name: 2021_LNCS_Bansal.pdf
file_size: 747418
relation: main_file
success: 1
file_date_updated: 2023-03-28T11:00:33Z
has_accepted_license: '1'
intvolume: ' 12651'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 20-37
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030720155'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On satisficing in quantitative games
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: 12651
year: '2021'
...
---
_id: '12909'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Andrei
full_name: Hornoiu, Andrei
id: 77129392-B450-11EA-8745-D4653DDC885E
last_name: Hornoiu
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous
HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University
of Ljubljana; 2021:5. doi:10.3359/2021hpc'
apa: 'Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing
software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC
Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc'
chicago: Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer.
“Managing Software on a Heterogenous HPC Cluster.” In ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, 5. University of Ljubljana, 2021. https://doi.org/10.3359/2021hpc.
ieee: A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software
on a heterogenous HPC cluster,” in ASHPC21 – Austrian-Slovenian HPC Meeting
2021, Virtual, 2021, p. 5.
ista: Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on
a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC
- Austrian-Slovenian HPC Meeting, 5.
mla: Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” ASHPC21
– Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5,
doi:10.3359/2021hpc.
short: A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, University of Ljubljana, 2021, p. 5.
conference:
end_date: 2021-06-02
location: Virtual
name: ASHPC - Austrian-Slovenian HPC Meeting
start_date: 2021-05-31
date_created: 2023-05-05T13:17:36Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-05-16T07:43:54Z
day: '02'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3359/2021hpc
file:
- access_level: open_access
checksum: ba73f85858fb9d5737ebc7724646dd45
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:36:34Z
date_updated: 2023-05-16T07:36:34Z
file_id: '12971'
file_name: 2021_ASHPC_Schloegl.pdf
file_size: 422761
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:36:34Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication: ASHPC21 – Austrian-Slovenian HPC Meeting 2021
publication_identifier:
isbn:
- 978-961-6980-77-7
- 978-961-6133-48-7
publication_status: published
publisher: University of Ljubljana
status: public
title: Managing software on a heterogenous HPC cluster
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2023-08-08T13:34:07Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13057'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Geometric superinductance qubits: Controlling phase delocalization across a single
Josephson junction". Additional raw data are available from the corresponding
author on reasonable request.'
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Grisha
full_name: Szep, Grisha
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103'
chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction.” Zenodo, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.'
mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, (2021).
date_created: 2023-05-23T13:42:27Z
date_published: 2021-10-22T00:00:00Z
date_updated: 2023-08-11T10:44:21Z
day: '22'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.5592103
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5592104
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9928'
relation: used_in_publication
status: public
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13058'
abstract:
- lang: eng
text: The zip file includes source data used in the main text of the manuscript
"Theory of branching morphogenesis by local interactions and global guidance",
as well as a representative Jupyter notebook to reproduce the main figures. A
sample script for the simulations of branching and annihilating random walks is
also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary
branched networks under external guidance. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt.
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160
apa: Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.
ieee: M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance.’” Zenodo, 2021.
ista: Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.
mla: Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.
short: M.C. Ucar, (2021).
date_created: 2023-05-23T13:46:34Z
date_published: 2021-08-25T00:00:00Z
date_updated: 2023-08-14T13:18:46Z
day: '25'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.5257160
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5257161
month: '08'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10402'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "Theory of branching morphogenesis by local
interactions and global guidance"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13061'
abstract:
- lang: eng
text: Infections early in life can have enduring effects on an organism’s development
and immunity. In this study, we show that this equally applies to developing “superorganisms”
– incipient social insect colonies. When we exposed newly mated Lasius niger ant
queens to a low pathogen dose, their colonies grew more slowly than controls before
winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation
survival improved when the ratio of pupae to workers was small. Queens that reared
fewer pupae before worker emergence exhibited lower pathogen levels, indicating
that high brood rearing efforts interfere with the ability of the queen’s immune
system to suppress pathogen proliferation. Early-life queen pathogen-exposure
also improved the immunocompetence of her worker offspring, as demonstrated by
challenging the workers to the same pathogen a year later. Transgenerational transfer
of the queen’s pathogen experience to her workforce can hence durably reduce the
disease susceptibility of the whole superorganism.
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Filip
full_name: Naiser, Filip
last_name: Naiser
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
last_name: Naderlinger
- first_name: Jiri
full_name: Matas, Jiri
last_name: Matas
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early
queen infection shapes developmental dynamics and induces long-term disease protection
in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ
apa: Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &
Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces
long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ
chicago: Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger,
Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics
and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021.
https://doi.org/10.5061/DRYAD.7PVMCVDTJ.
ieee: B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S.
Cremer, “Early queen infection shapes developmental dynamics and induces long-term
disease protection in incipient ant colonies.” Dryad, 2021.
ista: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021.
Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.
mla: Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental
Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.
Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.
short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer,
(2021).
date_created: 2023-05-23T16:14:35Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2023-08-14T11:45:28Z
day: '29'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.5061/DRYAD.7PVMCVDTJ
ec_funded: 1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.7pvmcvdtj
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publisher: Dryad
related_material:
record:
- id: '10284'
relation: used_in_publication
status: public
status: public
title: Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13062'
abstract:
- lang: eng
text: 'This paper analyzes the conditions for local adaptation in a metapopulation
with infinitely many islands under a model of hard selection, where population
size depends on local fitness. Each island belongs to one of two distinct ecological
niches or habitats. Fitness is influenced by an additive trait which is under
habitat-dependent directional selection. Our analysis is based on the diffusion
approximation and accounts for both genetic drift and demographic stochasticity.
By neglecting linkage disequilibria, it yields the joint distribution of allele
frequencies and population size on each island. We find that under hard selection,
the conditions for local adaptation in a rare habitat are more restrictive for
more polygenic traits: even moderate migration load per locus at very many loci
is sufficient for population sizes to decline. This further reduces the efficacy
of selection at individual loci due to increased drift and because smaller populations
are more prone to swamping due to migration, causing a positive feedback between
increasing maladaptation and declining population sizes. Our analysis also highlights
the importance of demographic stochasticity, which exacerbates the decline in
numbers of maladapted populations, leading to population collapse in the rare
habitat at significantly lower migration than predicted by deterministic arguments.'
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation
in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1'
apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for:
Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.
Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1'
chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code
for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary
Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.'
ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic
local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad,
2021.'
ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local
adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.'
mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation
in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.'
short: E. Szep, H. Sachdeva, N.H. Barton, (2021).
date_created: 2023-05-23T16:17:02Z
date_published: 2021-03-02T00:00:00Z
date_updated: 2023-09-05T15:44:05Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.8GTHT76P1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.8gtht76p1
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9252'
relation: used_in_publication
status: public
status: public
title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic
eco-evolutionary model'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13063'
abstract:
- lang: eng
text: We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability
estimation, an alternative to marker discovery, and accurate genomic prediction,
taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability
parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation
captured for height, body mass index, cardiovascular disease, and type 2 diabetes
is attributable to proximal regulatory regions within 10kb upstream of genes,
while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to
distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each
chromosome are associated with each trait, with over 3,100 independent exonic
and intronic regions and over 5,400 independent regulatory regions having >95%
probability of contributing >0.001% to the genetic variance of these four traits.
Our open-source software (GMRM) provides a scalable alternative to current approaches
for biobank data.
article_processing_charge: No
author:
- 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: Robinson MR. Probabilistic inference of the genetic architecture of functional
enrichment of complex traits. 2021. doi:10.5061/dryad.sqv9s4n51
apa: Robinson, M. R. (2021). Probabilistic inference of the genetic architecture
of functional enrichment of complex traits. Dryad. https://doi.org/10.5061/dryad.sqv9s4n51
chicago: Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture
of Functional Enrichment of Complex Traits.” Dryad, 2021. https://doi.org/10.5061/dryad.sqv9s4n51.
ieee: M. R. Robinson, “Probabilistic inference of the genetic architecture of functional
enrichment of complex traits.” Dryad, 2021.
ista: Robinson MR. 2021. Probabilistic inference of the genetic architecture of
functional enrichment of complex traits, Dryad, 10.5061/dryad.sqv9s4n51.
mla: Robinson, Matthew Richard. Probabilistic Inference of the Genetic Architecture
of Functional Enrichment of Complex Traits. Dryad, 2021, doi:10.5061/dryad.sqv9s4n51.
short: M.R. Robinson, (2021).
date_created: 2023-05-23T16:20:16Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-09-26T10:36:15Z
day: '04'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.5061/dryad.sqv9s4n51
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.sqv9s4n51
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
link:
- relation: software
url: https://github.com/medical-genomics-group/gmrm
record:
- id: '8429'
relation: used_in_publication
status: public
status: public
title: Probabilistic inference of the genetic architecture of functional enrichment
of complex traits
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13068'
abstract:
- lang: eng
text: Source data and source code for the graphs in "Spatiotemporal dynamics of
self-organized branching pancreatic cancer-derived organoids".
article_processing_charge: No
author:
- first_name: Samuel
full_name: Randriamanantsoa, Samuel
last_name: Randriamanantsoa
- first_name: Aristeidis
full_name: Papargyriou, Aristeidis
last_name: Papargyriou
- first_name: Carlo
full_name: Maurer, Carlo
last_name: Maurer
- first_name: Katja
full_name: Peschke, Katja
last_name: Peschke
- first_name: Maximilian
full_name: Schuster, Maximilian
last_name: Schuster
- first_name: Giulia
full_name: Zecchin, Giulia
last_name: Zecchin
- first_name: Katja
full_name: Steiger, Katja
last_name: Steiger
- first_name: Rupert
full_name: Öllinger, Rupert
last_name: Öllinger
- first_name: Dieter
full_name: Saur, Dieter
last_name: Saur
- first_name: Christina
full_name: Scheel, Christina
last_name: Scheel
- first_name: Roland
full_name: Rad, Roland
last_name: Rad
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Maximilian
full_name: Reichert, Maximilian
last_name: Reichert
- first_name: Andreas R.
full_name: Bausch, Andreas R.
last_name: Bausch
citation:
ama: Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics
of self-organized branching in pancreas-derived organoids. 2021. doi:10.5281/ZENODO.5148117
apa: Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M.,
Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids. Zenodo. https://doi.org/10.5281/ZENODO.5148117
chicago: Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke,
Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics
of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5148117.
ieee: S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids.” Zenodo, 2021.
ista: Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin
G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch
AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived
organoids, Zenodo, 10.5281/ZENODO.5148117.
mla: Randriamanantsoa, Samuel, et al. Spatiotemporal Dynamics of Self-Organized
Branching in Pancreas-Derived Organoids. Zenodo, 2021, doi:10.5281/ZENODO.5148117.
short: S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster,
G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo,
M. Reichert, A.R. Bausch, (2021).
date_created: 2023-05-23T16:39:24Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2023-08-04T09:25:23Z
day: '30'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.5148117
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.6577226
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '12217'
relation: used_in_publication
status: public
status: public
title: Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13069'
abstract:
- lang: eng
text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes
by fine-tuning lipid desaturation levels in a process previously described to
be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal
Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock
response (HSR)- causes extensive fat remodelling in peripheral tissues. These
changes include a decrease in fat desaturase and acid lipase expression in the
intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids.
The observed remodelling of plasma membrane is in line with ectothermic adaptive
responses and gives worms a cumulative advantage to warm temperatures. We have
determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory
neurons and TGF-β/BMP are required for signalling across tissues to modulate fat
desaturation. We also find neuronal hsf-1 is not only sufficient but also partially
necessary to control the fat remodelling response and for survival at warm temperatures.
This is the first study to show that a thermostat-based mechanism can cell non-autonomously
coordinate membrane saturation and composition across tissues in a multicellular
animal.
article_processing_charge: No
author:
- first_name: Laetitia
full_name: Chauve, Laetitia
last_name: Chauve
- first_name: Francesca
full_name: Hodge, Francesca
last_name: Hodge
- first_name: Sharlene
full_name: Murdoch, Sharlene
last_name: Murdoch
- first_name: Fatemah
full_name: Masoudzadeh, Fatemah
last_name: Masoudzadeh
- first_name: Harry-Jack
full_name: Mann, Harry-Jack
last_name: Mann
- first_name: Andrea
full_name: Lopez-Clavijo, Andrea
last_name: Lopez-Clavijo
- first_name: Hanneke
full_name: Okkenhaug, Hanneke
last_name: Okkenhaug
- first_name: Greg
full_name: West, Greg
last_name: West
- first_name: Bebiana C.
full_name: Sousa, Bebiana C.
last_name: Sousa
- first_name: Anne
full_name: Segonds-Pichon, Anne
last_name: Segonds-Pichon
- first_name: Cheryl
full_name: Li, Cheryl
last_name: Li
- first_name: Steven
full_name: Wingett, Steven
last_name: Wingett
- first_name: Hermine
full_name: Kienberger, Hermine
last_name: Kienberger
- first_name: Karin
full_name: Kleigrewe, Karin
last_name: Kleigrewe
- 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: Michael
full_name: Wakelam, Michael
last_name: Wakelam
- first_name: Olivia
full_name: Casanueva, Olivia
last_name: Casanueva
citation:
ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans. 2021. doi:10.5281/ZENODO.5519410
apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo,
A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.
Zenodo. https://doi.org/10.5281/ZENODO.5519410
chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh,
Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1
Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation
to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.
ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.”
Zenodo, 2021.
ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug
H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe
K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans, Zenodo, 10.5281/ZENODO.5519410.
mla: Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat
Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.
Zenodo, 2021, doi:10.5281/ZENODO.5519410.
short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo,
H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger,
K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).
date_created: 2023-05-23T16:40:56Z
date_published: 2021-12-25T00:00:00Z
date_updated: 2023-08-14T11:53:26Z
day: '25'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.5281/ZENODO.5519410
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5547464
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10322'
relation: used_in_publication
status: public
status: public
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues
to enable adaptation to high temperatures in C. elegans
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13072'
abstract:
- lang: eng
text: CpGs and corresponding mean weights for DNAm-based prediction of cognitive
abilities (6 traits)
article_processing_charge: No
author:
- first_name: Daniel L
full_name: McCartney, Daniel L
last_name: McCartney
- first_name: Robert F
full_name: Hillary, Robert F
last_name: Hillary
- first_name: Eleanor LS
full_name: Conole, Eleanor LS
last_name: Conole
- first_name: Daniel
full_name: Trejo Banos, Daniel
last_name: Trejo Banos
- first_name: Danni A
full_name: Gadd, Danni A
last_name: Gadd
- first_name: Rosie M
full_name: Walker, Rosie M
last_name: Walker
- first_name: Cliff
full_name: Nangle, Cliff
last_name: Nangle
- first_name: Robin
full_name: Flaig, Robin
last_name: Flaig
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Alison D
full_name: Murray, Alison D
last_name: Murray
- first_name: Susana
full_name: Munoz Maniega, Susana
last_name: Munoz Maniega
- first_name: Maria
full_name: del C Valdes-Hernandez, Maria
last_name: del C Valdes-Hernandez
- first_name: Mathew A
full_name: Harris, Mathew A
last_name: Harris
- first_name: Mark E
full_name: Bastin, Mark E
last_name: Bastin
- first_name: Joanna M
full_name: Wardlaw, Joanna M
last_name: Wardlaw
- first_name: Sarah E
full_name: Harris, Sarah E
last_name: Harris
- first_name: David J
full_name: Porteous, David J
last_name: Porteous
- first_name: Elliot M
full_name: Tucker-Drob, Elliot M
last_name: Tucker-Drob
- first_name: Andrew M
full_name: McIntosh, Andrew M
last_name: McIntosh
- first_name: Kathryn L
full_name: Evans, Kathryn L
last_name: Evans
- first_name: Ian J
full_name: Deary, Ian J
last_name: Deary
- first_name: Simon R
full_name: Cox, Simon R
last_name: Cox
- 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: Riccardo E
full_name: Marioni, Riccardo E
last_name: Marioni
citation:
ama: McCartney DL, Hillary RF, Conole EL, et al. Blood-based epigenome-wide analyses
of cognitive abilities. 2021. doi:10.5281/ZENODO.5794028
apa: McCartney, D. L., Hillary, R. F., Conole, E. L., Trejo Banos, D., Gadd, D.
A., Walker, R. M., … Marioni, R. E. (2021). Blood-based epigenome-wide analyses
of cognitive abilities. Zenodo. https://doi.org/10.5281/ZENODO.5794028
chicago: McCartney, Daniel L, Robert F Hillary, Eleanor LS Conole, Daniel Trejo
Banos, Danni A Gadd, Rosie M Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide
Analyses of Cognitive Abilities.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5794028.
ieee: D. L. McCartney et al., “Blood-based epigenome-wide analyses of cognitive
abilities.” Zenodo, 2021.
ista: McCartney DL, Hillary RF, Conole EL, Trejo Banos D, Gadd DA, Walker RM, Nangle
C, Flaig R, Campbell A, Murray AD, Munoz Maniega S, del C Valdes-Hernandez M,
Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh
AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2021. Blood-based epigenome-wide
analyses of cognitive abilities, Zenodo, 10.5281/ZENODO.5794028.
mla: McCartney, Daniel L., et al. Blood-Based Epigenome-Wide Analyses of Cognitive
Abilities. Zenodo, 2021, doi:10.5281/ZENODO.5794028.
short: D.L. McCartney, R.F. Hillary, E.L. Conole, D. Trejo Banos, D.A. Gadd, R.M.
Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S. Munoz Maniega, M. del
C Valdes-Hernandez, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J.
Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R.
Robinson, R.E. Marioni, (2021).
date_created: 2023-05-23T16:46:20Z
date_published: 2021-12-20T00:00:00Z
date_updated: 2023-08-02T14:05:12Z
day: '20'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.5281/ZENODO.5794028
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5794029
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10702'
relation: used_in_publication
status: public
status: public
title: Blood-based epigenome-wide analyses of cognitive abilities
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...