---
_id: '8077'
abstract:
- lang: eng
text: The projection methods with vanilla inertial extrapolation step for variational
inequalities have been of interest to many authors recently due to the improved
convergence speed contributed by the presence of inertial extrapolation step.
However, it is discovered that these projection methods with inertial steps lose
the Fejér monotonicity of the iterates with respect to the solution, which is
being enjoyed by their corresponding non-inertial projection methods for variational
inequalities. This lack of Fejér monotonicity makes projection methods with vanilla
inertial extrapolation step for variational inequalities not to converge faster
than their corresponding non-inertial projection methods at times. Also, it has
recently been proved that the projection methods with vanilla inertial extrapolation
step may provide convergence rates that are worse than the classical projected
gradient methods for strongly convex functions. In this paper, we introduce projection
methods with alternated inertial extrapolation step for solving variational inequalities.
We show that the sequence of iterates generated by our methods converges weakly
to a solution of the variational inequality under some appropriate conditions.
The Fejér monotonicity of even subsequence is recovered in these methods and linear
rate of convergence is obtained. The numerical implementations of our methods
compared with some other inertial projection methods show that our method is more
efficient and outperforms some of these inertial projection methods.
acknowledgement: The authors are grateful to the two anonymous referees for their
insightful comments and suggestions which have improved the earlier version of the
manuscript greatly. The first author has received funding from the European Research
Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013)
(Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
citation:
ama: 'Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for
variational inequalities: Weak and linear convergence. Applied Numerical Mathematics.
2020;157:315-337. doi:10.1016/j.apnum.2020.06.009'
apa: 'Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating
inertial steps for variational inequalities: Weak and linear convergence. Applied
Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009'
chicago: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating
Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied
Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009.'
ieee: 'Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial
steps for variational inequalities: Weak and linear convergence,” Applied Numerical
Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.'
ista: 'Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps
for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics.
157, 315–337.'
mla: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating
Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied
Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009.'
short: Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.
date_created: 2020-07-02T09:02:33Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T07:50:43Z
day: '01'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1016/j.apnum.2020.06.009
ec_funded: 1
external_id:
isi:
- '000564648400018'
file:
- access_level: open_access
checksum: 87d81324a62c82baa925c009dfcb0200
content_type: application/pdf
creator: dernst
date_created: 2020-07-02T09:08:59Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8078'
file_name: 2020_AppliedNumericalMath_Shehu.pdf
file_size: 2874203
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 315-337
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Applied Numerical Mathematics
publication_identifier:
issn:
- 0168-9274
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Projection methods with alternating inertial steps for variational inequalities:
Weak and linear convergence'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 157
year: '2020'
...
---
_id: '8039'
abstract:
- lang: eng
text: In the present work, we report a solution-based strategy to produce crystallographically
textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric
performance in the direction normal to the substrate. Our strategy is based on
the formulation of a molecular precursor that can be continuously decomposed to
produce a SnSe powder or printed into predefined patterns. The precursor formulation
and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates.
The printed layer and the bulk material obtained after hot press displays a clear
preferential orientation of the crystallographic domains, resulting in an ultralow
thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate.
Such textured nanomaterials present highly anisotropic properties with the best
thermoelectric performance in plane, i.e., in the directions parallel to the substrate,
which coincide with the crystallographic bc plane of SnSe. This is an unfortunate
characteristic because thermoelectric devices are designed to create/harvest temperature
gradients in the direction normal to the substrate. We further demonstrate that
this limitation can be overcome with the introduction of small amounts of tellurium
in the precursor. The presence of tellurium allows one to reduce the band gap
and increase both the charge carrier concentration and the mobility, especially
the cross plane, with a minimal decrease of the Seebeck coefficient. These effects
translate into record out of plane ZT values at 800 K.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Ting
full_name: Zhang, Ting
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Mercè
full_name: Pacios, Mercè
last_name: Pacios
- first_name: Xiaoting
full_name: Yu, Xiaoting
last_name: Yu
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Zhang Y, Liu Y, Xing C, et al. Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices. ACS Applied Materials and
Interfaces. 2020;12(24):27104-27111. doi:10.1021/acsami.0c04331
apa: Zhang, Y., Liu, Y., Xing, C., Zhang, T., Li, M., Pacios, M., … Cabot, A. (2020).
Tin selenide molecular precursor for the solution processing of thermoelectric
materials and devices. ACS Applied Materials and Interfaces. American Chemical
Society. https://doi.org/10.1021/acsami.0c04331
chicago: Zhang, Yu, Yu Liu, Congcong Xing, Ting Zhang, Mengyao Li, Mercè Pacios,
Xiaoting Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing
of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces.
American Chemical Society, 2020. https://doi.org/10.1021/acsami.0c04331.
ieee: Y. Zhang et al., “Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices,” ACS Applied Materials
and Interfaces, vol. 12, no. 24. American Chemical Society, pp. 27104–27111,
2020.
ista: Zhang Y, Liu Y, Xing C, Zhang T, Li M, Pacios M, Yu X, Arbiol J, Llorca J,
Cadavid D, Ibáñez M, Cabot A. 2020. Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices. ACS Applied Materials and
Interfaces. 12(24), 27104–27111.
mla: Zhang, Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing
of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces,
vol. 12, no. 24, American Chemical Society, 2020, pp. 27104–11, doi:10.1021/acsami.0c04331.
short: Y. Zhang, Y. Liu, C. Xing, T. Zhang, M. Li, M. Pacios, X. Yu, J. Arbiol,
J. Llorca, D. Cadavid, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces
12 (2020) 27104–27111.
date_created: 2020-06-29T07:59:35Z
date_published: 2020-06-17T00:00:00Z
date_updated: 2023-08-22T07:50:08Z
day: '17'
department:
- _id: MaIb
doi: 10.1021/acsami.0c04331
ec_funded: 1
external_id:
isi:
- '000542925300032'
pmid:
- '32437128'
intvolume: ' 12'
isi: 1
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
page: 27104-27111
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tin selenide molecular precursor for the solution processing of thermoelectric
materials and devices
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2020'
...
---
_id: '8133'
abstract:
- lang: eng
text: The molecular factors which control circulating levels of inflammatory proteins
are not well understood. Furthermore, association studies between molecular probes
and human traits are often performed by linear model-based methods which may fail
to account for complex structure and interrelationships within molecular datasets.In
this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS)
on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy
older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel).
We employ a Bayesian framework (BayesR+) which can account for issues pertaining
to data structure and unknown confounding variables (with sensitivity analyses
using ordinary least squares- (OLS) and mixed model-based approaches). We identified
13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and
Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG
each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged
genetic variants accounted for up to 45% of variance in protein levels (for MCP2,
36% of variance alone attributable to 1 polymorphism). Methylation data accounted
for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation
in protein levels (for VEGFA) was explained using genetic and epigenetic data
combined. We demonstrated putative causal relationships between CD6 and IL18R1
with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data
may aid understanding of the molecular regulation of the circulating inflammatory
proteome as well as causal relationships between inflammatory mediators and disease.
article_number: '60'
article_processing_charge: No
article_type: original
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Allan F.
full_name: Mcrae, Allan F.
last_name: Mcrae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- 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: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
2020;12(1). doi:10.1186/s13073-020-00754-1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
Springer Nature. https://doi.org/10.1186/s13073-020-00754-1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method
Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older
Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.
ieee: R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies
of inflammatory protein levels in healthy older adults,” Genome Medicine,
vol. 12, no. 1. Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Genome Medicine. 12(1), 60.
mla: Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies
of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine,
vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T07:55:37Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-020-00754-1
external_id:
isi:
- '000551778400001'
pmid:
- '32641083'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:27:38Z
date_updated: 2020-07-22T06:27:38Z
file_id: '8145'
file_name: 2020_GenomeMedicine_Hillary.pdf
file_size: 1136983
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:27:38Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Medicine
publication_identifier:
eissn:
- 1756994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9706'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-method genome- and epigenome-wide studies of inflammatory protein levels
in healthy older adults
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2020'
...
---
_id: '8127'
abstract:
- lang: eng
text: Mechanistic modeling in neuroscience aims to explain observed phenomena in
terms of underlying causes. However, determining which model parameters agree
with complex and stochastic neural data presents a significant challenge. We address
this challenge with a machine learning tool which uses deep neural density estimators—trained
using model simulations—to carry out Bayesian inference and retrieve the full
space of parameters compatible with raw data or selected data features. Our method
is scalable in parameters and data features and can rapidly analyze new data after
initial training. We demonstrate the power and flexibility of our approach on
receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize
the space of circuit configurations giving rise to rhythmic activity in the crustacean
stomatogastric ganglion, and use these results to derive hypotheses for underlying
compensation mechanisms. Our approach will help close the gap between data-driven
and theory-driven models of neural dynamics.
acknowledgement: We thank Mahmood S Hoseini and Michael Stryker for sharing their
data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham,
Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid
Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the
manuscript. This work was supported by the German Research Foundation (DFG) through
SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041
‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1
– Project number 390727645 and the German Federal Ministry of Education and Research
(BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome
Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant
(SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological
Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge
the Leibniz Supercomputing Centre for funding this project by providing computing
time on its Linux-Cluster.
article_number: e56261
article_processing_charge: No
article_type: original
author:
- first_name: Pedro J.
full_name: Gonçalves, Pedro J.
last_name: Gonçalves
orcid: 0000-0002-6987-4836
- first_name: Jan-Matthis
full_name: Lueckmann, Jan-Matthis
last_name: Lueckmann
orcid: 0000-0003-4320-4663
- first_name: Michael
full_name: Deistler, Michael
last_name: Deistler
orcid: 0000-0002-3573-0404
- first_name: Marcel
full_name: Nonnenmacher, Marcel
last_name: Nonnenmacher
orcid: 0000-0001-6044-6627
- first_name: Kaan
full_name: Öcal, Kaan
last_name: Öcal
orcid: 0000-0002-8528-6858
- first_name: Giacomo
full_name: Bassetto, Giacomo
last_name: Bassetto
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Sara A.
full_name: Haddad, Sara A.
last_name: Haddad
orcid: 0000-0003-0807-0823
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: David S.
full_name: Greenberg, David S.
last_name: Greenberg
- first_name: Jakob H.
full_name: Macke, Jakob H.
last_name: Macke
orcid: 0000-0001-5154-8912
citation:
ama: Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density
estimators to identify mechanistic models of neural dynamics. eLife. 2020;9.
doi:10.7554/eLife.56261
apa: Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K.,
Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to
identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.56261
chicago: Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher,
Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural
Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.
ieee: P. J. Gonçalves et al., “Training deep neural density estimators to
identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto
G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020.
Training deep neural density estimators to identify mechanistic models of neural
dynamics. eLife. 9, e56261.
mla: Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify
Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences
Publications, 2020, doi:10.7554/eLife.56261.
short: P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G.
Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg,
J.H. Macke, ELife 9 (2020).
date_created: 2020-07-16T12:26:04Z
date_published: 2020-09-17T00:00:00Z
date_updated: 2023-08-22T07:54:52Z
day: '17'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.7554/eLife.56261
ec_funded: 1
external_id:
isi:
- '000584989400001'
pmid:
- '32940606'
file:
- access_level: open_access
checksum: c4300ddcd93ed03fc9c6cdf1f77890be
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T11:37:32Z
date_updated: 2020-10-27T11:37:32Z
file_id: '8709'
file_name: 2020_eLife_Gonçalves.pdf
file_size: 17355867
relation: main_file
success: 1
file_date_updated: 2020-10-27T11:37:32Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Training deep neural density estimators to identify mechanistic models of neural
dynamics
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8126'
abstract:
- lang: eng
text: Cortical areas comprise multiple types of inhibitory interneurons with stereotypical
connectivity motifs, but their combined effect on postsynaptic dynamics has been
largely unexplored. Here, we analyse the response of a single postsynaptic model
neuron receiving tuned excitatory connections alongside inhibition from two plastic
populations. Depending on the inhibitory plasticity rule, synapses remain unspecific
(flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the
neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on
the modulatory state of inhibition. When both inhibitory populations are active,
inhibition balances excitation, resulting in uncorrelated postsynaptic responses
regardless of the inhibitory tuning profiles. Modulating the activity of a given
inhibitory population produces strong correlations to either preferred or non-preferred
inputs, in line with recent experimental findings showing dramatic context-dependent
changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive
field doesn’t follow directly from the weight profiles of its presynaptic afferents.
article_processing_charge: No
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Andrea I.
full_name: Luppi, Andrea I.
last_name: Luppi
- 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: Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge
from plasticity and allow attentional switching of receptive fields. The Journal
of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020
apa: Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory
weight profiles emerge from plasticity and allow attentional switching of receptive
fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020
chicago: Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory
Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive
Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.
ieee: E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight
profiles emerge from plasticity and allow attentional switching of receptive fields,”
The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience,
pp. 9634–9649, 2020.
ista: Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles
emerge from plasticity and allow attentional switching of receptive fields. The
Journal of Neuroscience. 40(50), 9634–9649.
mla: Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge
from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal
of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49,
doi:10.1523/JNEUROSCI.0276-20.2020.
short: E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020)
9634–9649.
date_created: 2020-07-16T12:25:04Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T07:54:26Z
day: '09'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0276-20.2020
external_id:
isi:
- '000606706400009'
pmid:
- '33168622'
file:
- access_level: open_access
checksum: 7977e4dd6b89357d1a5cc88babac56da
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:31:47Z
date_updated: 2020-12-28T08:31:47Z
file_id: '8977'
file_name: 2020_JourNeuroscience_Agnes.pdf
file_size: 2750920
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:31:47Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 9634-9649
pmid: 1
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complementary inhibitory weight profiles emerge from plasticity and allow attentional
switching of receptive fields
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2020'
...
---
_id: '8132'
abstract:
- lang: eng
text: The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral
branched actin network constituting one of the main drivers of eukaryotic cell
migration. Here, we uncover an essential role of the hematopoietic-specific WRC
component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies
an inborn error of immunity with systemic autoimmunity, at cellular level marked
by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia.
Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In
the absence of Hem1, B cells become deprived of extracellular stimuli necessary
to maintain the strength of B cell receptor signaling at a level permissive for
survival of non-autoreactive B cells. This shifts the balance of B cell fate choices
toward autoreactive B cells and thus autoimmunity.
article_number: eabc3979
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Samaneh
full_name: Zoghi, Samaneh
last_name: Zoghi
- first_name: Máté G.
full_name: Kiss, Máté G.
last_name: Kiss
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Christina
full_name: Rashkova, Christina
last_name: Rashkova
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Matthias
full_name: Haimel, Matthias
last_name: Haimel
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Rico Chandra
full_name: Ardy, Rico Chandra
last_name: Ardy
- first_name: Birgit
full_name: Hoeger, Birgit
last_name: Hoeger
- first_name: Jana
full_name: Block, Jana
last_name: Block
- first_name: David
full_name: Medgyesi, David
last_name: Medgyesi
- first_name: Celine
full_name: Sin, Celine
last_name: Sin
- first_name: Sepideh
full_name: Shahkarami, Sepideh
last_name: Shahkarami
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Vahid
full_name: Ziaee, Vahid
last_name: Ziaee
- first_name: Peter
full_name: Hammerl, Peter
last_name: Hammerl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Loïc
full_name: Dupré, Loïc
last_name: Dupré
- first_name: Johannes B.
full_name: Huppa, Johannes B.
last_name: Huppa
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alexis
full_name: Lomakin, Alexis
last_name: Lomakin
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Christoph J.
full_name: Binder, Christoph J.
last_name: Binder
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
- first_name: Nima
full_name: Rezaei, Nima
last_name: Rezaei
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs
B cell development and prevents autoimmunity. Science Immunology. 2020;5(49).
doi:10.1126/sciimmunol.abc3979
apa: Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., …
Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979
chicago: Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina
Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator
HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology.
AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.
ieee: E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.
ista: Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer
R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain
R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A,
Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal
regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology.
5(49), eabc3979.
mla: Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development
and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979,
AAAS, 2020, doi:10.1126/sciimmunol.abc3979.
short: E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel,
R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S.
Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B.
Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei,
K. Boztug, Science Immunology 5 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-10T00:00:00Z
date_updated: 2023-08-22T07:56:04Z
day: '10'
department:
- _id: MiSi
doi: 10.1126/sciimmunol.abc3979
external_id:
isi:
- '000546994600004'
pmid:
- '32646852'
intvolume: ' 5'
isi: 1
issue: '49'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Science Immunology
publication_identifier:
eissn:
- '24709468'
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '9706'
abstract:
- lang: eng
text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted
protein levels with biological and technical covariates. Protein levels were adjusted
for age, sex, array plate and four genetic principal components (population structure)
prior to analyses. Significant associations are emboldened. (Table S1). pQTLs
associated with inflammatory biomarker levels from Bayesian penalised regression
model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated
with inflammatory biomarker levels from ordinary least squares regression model
(P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary
least squares GWAS and EWAS performed on inflammatory protein levels (n = 70)
in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs
associated with inflammatory biomarker levels from ordinary least squares regression
model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary
least squares and Bayesian penalised regression models for concordantly identified
SNPs. (Table S6). Estimate of heritability for blood protein levels as well as
proportion of variance explained attributable to different prior mixtures. (Table
S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood)
and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant
SNPs identified by linear model and Bayesian penalised regression and whether
they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation
for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression
are putatively associated with circulating inflammatory proteins that harbour
pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified
by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table
S12). CpGs associated with inflammatory protein biomarkers as identified by linear
model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory
protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10.
(Table S14). Estimate of variance explained for blood protein levels by DNA methylation
as well as proportion of explained attributable to different prior mixtures -
BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide
DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression
model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker
levels explained by common genetic and methylation data (joint and conditional
estimates from BayesR+). Ordered by combined variance explained by genetic and
epigenetic data - smallest to largest. Significant results from t-tests comparing
distributions for variance explained by methylation or genetics alone versus combined
estimate are emboldened. (Table S17). Genetic and epigenetic factors identified
by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian
Randomisation analyses to assess whether proteins with concordantly identified
genetic signals are causally associated with Alzheimer’s disease risk. (Table
S19).'
article_processing_charge: No
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: McCartney, Daniel L.
last_name: McCartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: 'Allan F. '
full_name: 'McRae, Allan F. '
last_name: McRae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- 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: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. 2020. doi:10.6084/m9.figshare.12629697.v1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional
File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein
Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.
ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and
epigenome-wide studies of inflammatory protein levels in healthy older adults.”
Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional
file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein
levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.
mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and
Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.
Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, (2020).
date_created: 2021-07-23T08:59:15Z
date_published: 2020-07-09T00:00:00Z
date_updated: 2023-08-22T07:55:36Z
day: '09'
department:
- _id: MaRo
doi: 10.6084/m9.figshare.12629697.v1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.12629697.v1
month: '07'
oa: 1
oa_version: Published Version
other_data_license: CC0 + CC BY (4.0)
publisher: Springer Nature
related_material:
record:
- id: '8133'
relation: used_in_publication
status: public
status: public
title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory
protein levels in healthy older adults
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '8134'
abstract:
- lang: eng
text: We prove an upper bound on the free energy of a two-dimensional homogeneous
Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the
free energy per unit volume differs from the one of the non-interacting system
by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering
length of the two-body interaction potential, ρ is the density, β is the inverse
temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature
for superfluidity. In combination with the corresponding matching lower bound
proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality
in the asymptotic expansion.
article_number: '061901'
article_processing_charge: No
article_type: original
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas.
II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950
apa: Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional
dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP
Publishing. https://doi.org/10.1063/5.0005950
chicago: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP
Publishing, 2020. https://doi.org/10.1063/5.0005950.
ieee: S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute
Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no.
6. AIP Publishing, 2020.
ista: Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute
Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.
mla: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol.
61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.
short: S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).
date_created: 2020-07-19T22:00:59Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-08-22T08:12:40Z
day: '22'
department:
- _id: RoSe
doi: 10.1063/5.0005950
ec_funded: 1
external_id:
arxiv:
- '2002.08281'
isi:
- '000544595100001'
intvolume: ' 61'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.08281
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free energy of the two-dimensional dilute Bose gas. II. Upper bound
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8112'
article_number: '20190530'
article_processing_charge: No
article_type: letter_note
author:
- 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: 'Barton NH. On the completion of speciation. Philosophical Transactions
of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530'
apa: 'Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530'
chicago: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0530.'
ieee: 'N. H. Barton, “On the completion of speciation,” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The
Royal Society, 2020.'
ista: 'Barton NH. 2020. On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.'
mla: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530,
The Royal Society, 2020, doi:10.1098/rstb.2019.0530.'
short: 'N.H. Barton, Philosophical Transactions of the Royal Society. Series B:
Biological Sciences 375 (2020).'
date_created: 2020-07-13T03:41:39Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T07:53:52Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0530
external_id:
isi:
- '000552662100002'
pmid:
- '32654647'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the completion of speciation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8162'
abstract:
- lang: eng
text: In mammalian genomes, a subset of genes is regulated by genomic imprinting,
resulting in silencing of one parental allele. Imprinting is essential for cerebral
cortex development, but prevalence and functional impact in individual cells is
unclear. Here, we determined allelic expression in cortical cell types and established
a quantitative platform to interrogate imprinting in single cells. We created
cells with uniparental chromosome disomy (UPD) containing two copies of either
the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold
overexpressed or not expressed. By genetic labeling of UPD, we determined cellular
phenotypes and transcriptional responses to deregulated imprinted gene expression
at unprecedented single-cell resolution. We discovered an unexpected degree of
cell-type specificity and a novel function of imprinting in the regulation of
cortical astrocyte survival. More generally, our results suggest functional relevance
of imprinted gene expression in glial astrocyte lineage and thus for generating
cortical cell-type diversity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical
support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen
for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of
the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo
for comments on earlier versions of the manuscript. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical
Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian
Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031).
R.B. received support from the FWF Meitner-Programm (M 2416). This work was also
supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers
Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement 618444 to S.H.; and the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro)
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Thomas
full_name: Penz, Thomas
last_name: Penz
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
orcid: 0000-0001-6091-3088
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting
in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031
apa: Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher,
C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031
chicago: Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi
H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer.
“Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.
ieee: S. Laukoter et al., “Cell-type specificity of genomic imprinting in
cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.
ista: Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T,
Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. 107(6), 1160–1179.e9.
mla: Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral
Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.
short: S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher,
T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.
date_created: 2020-07-23T16:03:12Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:20:11Z
day: '23'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2020.06.031
ec_funded: 1
external_id:
isi:
- '000579698700006'
file:
- access_level: open_access
checksum: 7becdc16a6317304304631087ae7dd7f
content_type: application/pdf
creator: dernst
date_created: 2020-12-02T09:26:46Z
date_updated: 2020-12-02T09:26:46Z
file_id: '8828'
file_name: 2020_Neuron_Laukoter.pdf
file_size: 8911830
relation: main_file
success: 1
file_date_updated: 2020-12-02T09:26:46Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1160-1179.e9
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/
scopus_import: '1'
status: public
title: Cell-type specificity of genomic imprinting in cerebral cortex
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '8138'
abstract:
- lang: eng
text: Directional transport of the phytohormone auxin is a versatile, plant-specific
mechanism regulating many aspects of plant development. The recently identified
plant hormones, strigolactones (SLs), are implicated in many plant traits; among
others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters
for fine-tuning of growth and developmental responses. Here, we show in pea and
Arabidopsis that SLs target processes dependent on the canalization of auxin flow,
which involves auxin feedback on PIN subcellular distribution. D14 receptor- and
MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels
after wounding or from artificial auxin sources, during vasculature de novo formation
and regeneration. At the cellular level, SLs interfere with auxin effects on PIN
polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis.
Our results identify a non-transcriptional mechanism of SL action, uncoupling
auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue
formation and regeneration.
acknowledgement: We are grateful to David Nelson for providing published materials
and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful
discussions. The research leading to these results has received funding from the
European Research Council (ERC) under the European Union's Horizon 2020 research
and innovation programme (742985). This work was also supported by the Beijing Municipal
Natural Science Foundation (5192011), Beijing Outstanding University Discipline
Program, the National Natural Science Foundation of China (31370309), CEITEC 2020
(LQ1601) project with financial contribution made by the Ministry of Education,
Youth and Sports of the Czech Republic within special support paid from the National
Program of Sustainability II funds, Australian Research Council (FT180100081), and
China Postdoctoral Science Foundation (2019M660864).
article_processing_charge: No
article_type: original
author:
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: J
full_name: Balla, J
last_name: Balla
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: P
full_name: Kalousek, P
last_name: Kalousek
- first_name: Z
full_name: Medveďová, Z
last_name: Medveďová
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: V
full_name: Reinöhl, V
last_name: Reinöhl
- first_name: S
full_name: Procházka, S
last_name: Procházka
- first_name: R
full_name: Halouzka, R
last_name: Halouzka
- first_name: P
full_name: Tarkowski, P
last_name: Tarkowski
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
- first_name: PB
full_name: Brewer, PB
last_name: Brewer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on
PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508.
doi:10.1038/s41467-020-17252-y
apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z.,
… Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin
transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y
chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová,
Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport
Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.
ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer
Nature, p. 3508, 2020.
ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang
Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig
C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization. Nature Communications. 11(1), 3508.
mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin
Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer
Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.
short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y.
Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P.
Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.
date_created: 2020-07-21T08:58:07Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2023-08-22T08:13:44Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17252-y
ec_funded: 1
external_id:
isi:
- '000550062200004'
pmid:
- '32665554'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T08:32:55Z
date_updated: 2020-07-22T08:32:55Z
file_id: '8148'
file_name: 2020_NatureComm_Zhang.pdf
file_size: 1759490
relation: main_file
success: 1
file_date_updated: 2020-07-22T08:32:55Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '3508'
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8168'
abstract:
- lang: eng
text: Speciation, that is, the evolution of reproductive barriers eventually leading
to complete isolation, is a crucial process generating biodiversity. Recent work
has contributed much to our understanding of how reproductive barriers begin to
evolve, and how they are maintained in the face of gene flow. However, little
is known about the transition from partial to strong reproductive isolation (RI)
and the completion of speciation. We argue that the evolution of strong RI is
likely to involve different processes, or new interactions among processes, compared
with the evolution of the first reproductive barriers. Transition to strong RI
may be brought about by changing external conditions, for example, following secondary
contact. However, the increasing levels of RI themselves create opportunities
for new barriers to evolve and, and interaction or coupling among barriers. These
changing processes may depend on genomic architecture and leave detectable signals
in the genome. We outline outstanding questions and suggest more theoretical and
empirical work, considering both patterns and processes associated with strong
RI, is needed to understand how speciation is completed.
article_number: '20190528'
article_processing_charge: No
article_type: original
author:
- first_name: Jonna
full_name: Kulmuni, Jonna
last_name: Kulmuni
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Kay
full_name: Lucek, Kay
last_name: Lucek
- first_name: Vincent
full_name: Savolainen, Vincent
last_name: Savolainen
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion
of speciation: The evolution of reproductive isolation beyond the first barriers.
Philosophical Transactions of the Royal Society Series B: Biological sciences.
2020;375(1806). doi:10.1098/rstb.2019.0528'
apa: 'Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M.
(2020). Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers. Philosophical Transactions of the Royal Society.
Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528'
chicago: 'Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja
M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive
Isolation beyond the First Barriers.” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.'
ieee: 'J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards
the completion of speciation: The evolution of reproductive isolation beyond the
first barriers,” Philosophical Transactions of the Royal Society. Series B:
Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.'
ista: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the
completion of speciation: The evolution of reproductive isolation beyond the first
barriers. Philosophical Transactions of the Royal Society. Series B: Biological
sciences. 375(1806), 20190528.'
mla: 'Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution
of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528,
The Royal Society, 2020, doi:10.1098/rstb.2019.0528.'
short: 'J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical
Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:21:31Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0528
ec_funded: 1
external_id:
isi:
- '000552662100001'
pmid:
- '32654637'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0528
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8167'
abstract:
- lang: eng
text: The evolution of strong reproductive isolation (RI) is fundamental to the
origins and maintenance of biological diversity, especially in situations where
geographical distributions of taxa broadly overlap. But what is the history behind
strong barriers currently acting in sympatry? Using whole-genome sequencing and
single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships,
(ii) the strength of RI, and (iii) the demographic history of divergence between
two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on
external morphology, Littorina arcana and Littorina saxatilis differ in their
mode of female reproduction (egg-laying versus brooding), which may generate a
strong post-zygotic barrier. We show that egg-laying and brooding snails are closely
related, but genetically distinct. Genotyping of 3092 snails from three locations
failed to recover any recent hybrid or backcrossed individuals, confirming that
RI is strong. There was, however, evidence for a very low level of asymmetrical
introgression, suggesting that isolation remains incomplete. The presence of strong,
asymmetrical RI was further supported by demographic analysis of these populations.
Although the taxa are currently broadly sympatric, demographic modelling suggests
that they initially diverged during a short period of geographical separation
involving very low gene flow. Our study suggests that some geographical separation
may kick-start the evolution of strong RI, facilitating subsequent coexistence
of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent
effect of sympatry on RI remain open questions.
acknowledgement: Funding was provided by the Natural Environment Research Council
(NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin
Garlovsky and Hernan Morales for advice and/or useful discussion during the project.
Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton
participated in the collection and processing of samples. Mark Dunning helped with
the development of bioinformatic pipelines. The analysis of genomic data was conducted
on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and
an anonymous reviewer provided comments that improved the manuscript.
article_number: '20190545'
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- 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: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Isobel
full_name: Eyres, Isobel
last_name: Eyres
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545'
apa: 'Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T.,
Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545'
chicago: 'Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres,
Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong
Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0545.'
ieee: 'S. Stankowski et al., “The evolution of strong reproductive isolation
between sympatric intertidal snails,” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society,
2020.'
ista: 'Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K,
Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric
intertidal snails. Philosophical Transactions of the Royal Society. Series B:
Biological Sciences. 375(1806), 20190545.'
mla: 'Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between
Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society.
Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society,
2020, doi:10.1098/rstb.2019.0545.'
short: 'S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson,
R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological
Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:22:13Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0545
external_id:
isi:
- '000552662100014'
pmid:
- '32654639'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0545
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolution of strong reproductive isolation between sympatric intertidal
snails
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8170'
abstract:
- lang: eng
text: "Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is
measured as a function\r\nof time following rotational excitation by a nonresonant,
comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra,
obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal
distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy.
For\r\nCS2 and I2, they are the first experimental results reported. The alignment
dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using
the experimental in-droplet B and D values, agree in\r\ndetail with the measurement
for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium
droplets introduced here should apply to a range of molecules and complexes."
acknowledgement: "H. S. acknowledges support from the European Research Council-AdG
(Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a
Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian
Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC)
Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian
Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by
the European Union’s Horizon 2020 research and\r\ninnovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe
PIMC simulations were provided by the division for scientific computing at the Johannes
Kepler University."
article_number: '013001'
article_processing_charge: No
article_type: original
author:
- first_name: Adam S.
full_name: Chatterley, Adam S.
last_name: Chatterley
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Anders V.
full_name: Jørgensen, Anders V.
last_name: Jørgensen
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Robert E.
full_name: Zillich, Robert E.
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001'
apa: 'Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson,
B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001'
chicago: 'Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V.
Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich,
Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of
Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.”
Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.'
ieee: 'A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules
in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical
Review Letters, vol. 125, no. 1. American Physical Society, 2020.'
ista: 'Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov
I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence
spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the
frequency domains. Physical Review Letters. 125(1), 013001.'
mla: 'Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules
in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical
Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020,
doi:10.1103/PhysRevLett.125.013001.'
short: A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson,
I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical
Review Letters 125 (2020).
date_created: 2020-07-26T22:01:02Z
date_published: 2020-07-03T00:00:00Z
date_updated: 2023-08-22T08:22:43Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.125.013001
ec_funded: 1
external_id:
arxiv:
- '2006.02694'
isi:
- '000544526900006'
intvolume: ' 125'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.02694
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling
the time and the frequency domains'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 125
year: '2020'
...
---
_id: '8194'
abstract:
- lang: eng
text: 'Fixed-point arithmetic is a popular alternative to floating-point arithmetic
on embedded systems. Existing work on the verification of fixed-point programs
relies on custom formalizations of fixed-point arithmetic, which makes it hard
to compare the described techniques or reuse the implementations. In this paper,
we address this issue by proposing and formalizing an SMT theory of fixed-point
arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point
theory, and provide formal semantics for it based on rational arithmetic. We also
describe two decision procedures for this theory: one based on the theory of bit-vectors
and the other on the theory of reals. We implement the two decision procedures,
and evaluate our implementations using existing mature SMT solvers on a benchmark
suite we created. Finally, we perform a case study of using the theory we propose
to verify properties of quantized neural networks.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Baranowski, Marek
last_name: Baranowski
- first_name: Shaobo
full_name: He, Shaobo
last_name: He
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Thanh Son
full_name: Nguyen, Thanh Son
last_name: Nguyen
- first_name: Zvonimir
full_name: Rakamarić, Zvonimir
last_name: Rakamarić
citation:
ama: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point
arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31.
doi:10.1007/978-3-030-51074-9_2'
apa: 'Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020).
An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166,
pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2'
chicago: Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir
Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning,
12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.
ieee: M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT
theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France,
2020, vol. 12166, pp. 13–31.
ista: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory
of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference
on Automated Reasoning, LNCS, vol. 12166, 13–31.'
mla: Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated
Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.
short: M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated
Reasoning, Springer Nature, 2020, pp. 13–31.
conference:
end_date: 2020-07-04
location: Paris, France
name: 'IJCAR: International Joint Conference on Automated Reasoning'
start_date: 2020-07-01
date_created: 2020-08-02T22:00:59Z
date_published: 2020-06-24T00:00:00Z
date_updated: 2023-08-22T08:27:25Z
day: '24'
department:
- _id: ToHe
doi: 10.1007/978-3-030-51074-9_2
external_id:
isi:
- '000884318000002'
intvolume: ' 12166'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-030-51074-9_2
month: '06'
oa: 1
oa_version: Published Version
page: 13-31
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Automated Reasoning
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030510732'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An SMT theory of fixed-point arithmetic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12166
year: '2020'
...
---
_id: '8169'
abstract:
- lang: eng
text: Many recent studies have addressed the mechanisms operating during the early
stages of speciation, but surprisingly few studies have tested theoretical predictions
on the evolution of strong reproductive isolation (RI). To help address this gap,
we first undertook a quantitative review of the hybrid zone literature for flowering
plants in relation to reproductive barriers. Then, using Populus as an exemplary
model group, we analysed genome-wide variation for phylogenetic tree topologies
in both early- and late-stage speciation taxa to determine how these patterns
may be related to the genomic architecture of RI. Our plant literature survey
revealed variation in barrier complexity and an association between barrier number
and introgressive gene flow. Focusing on Populus, our genome-wide analysis of
tree topologies in speciating poplar taxa points to unusually complex genomic
architectures of RI, consistent with earlier genome-wide association studies.
These architectures appear to facilitate the ‘escape’ of introgressed genome segments
from polygenic barriers even with strong RI, thus affecting their relationships
with recombination rates. Placed within the context of the broader literature,
our data illustrate how phylogenomic approaches hold great promise for addressing
the evolution and temporary breakdown of RI during late stages of speciation.
acknowledgement: This work was supported by a fellowship from the China Scholarship
Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306
to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and
the University of Vienna. We thank members of J.L.’s lab for collecting samples,
Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation
Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific
Cluster (VSC) for access to computational resources, and Claus Vogel and members
of the PopGen Vienna graduate school for helpful discussions.
article_number: '20190544'
article_processing_charge: No
article_type: original
author:
- first_name: Huiying
full_name: Shang, Huiying
last_name: Shang
- first_name: Jaqueline
full_name: Hess, Jaqueline
last_name: Hess
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Pär K.
full_name: Ingvarsson, Pär K.
last_name: Ingvarsson
- first_name: Jianquan
full_name: Liu, Jianquan
last_name: Liu
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
citation:
ama: 'Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation
in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical
Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806).
doi:10.1098/rstb.2019.0544'
apa: 'Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &
Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale
patterns and lessons from a perennial model group. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544'
chicago: 'Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson,
Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation
in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0544.'
ieee: 'H. Shang et al., “Evolution of strong reproductive isolation in plants:
Broad-scale patterns and lessons from a perennial model group,” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences, vol. 375,
no. 1806. The Royal Society, 2020.'
ista: 'Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020.
Evolution of strong reproductive isolation in plants: Broad-scale patterns and
lessons from a perennial model group. Philosophical Transactions of the Royal
Society. Series B: Biological Sciences. 375(1806), 20190544.'
mla: 'Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants:
Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences, vol. 375,
no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.'
short: 'H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer,
Philosophical Transactions of the Royal Society. Series B: Biological Sciences
375 (2020).'
date_created: 2020-07-26T22:01:02Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:23:24Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0544
external_id:
isi:
- '000552662100013'
pmid:
- '32654641'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
month: '07'
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- '14712970'
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Evolution of strong reproductive isolation in plants: Broad-scale patterns
and lessons from a perennial model group'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8189'
abstract:
- lang: eng
text: Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric
vehicles and portable electronics, but their deployment is currently limited by
the unavailability of proper electrocatalysis for the ethanol oxidation reaction
(EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous
into a palladium-tin alloy and demonstrate a significant performance improvement
toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals
that incorporate 35% of phosphorus. These nanoparticles are supported on carbon
black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up
to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts.
Furthermore, a twofold lower Tafel slope and a much longer durability are revealed
for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is
rationalized with the aid of density functional theory (DFT) calculations considering
different phosphorous chemical environments. Depending on its oxidation state,
surface phosphorus introduces sites with low energy OH− adsorption and/or strongly
influences the electronic structure of palladium and tin to facilitate the oxidation
of the acetyl to acetic acid, which is considered the EOR rate limiting step.
DFT calculations also points out that the durability improvement of Pd2Sn:P/C
catalyst is associated to the promotion of OH adsorption that accelerates the
oxidation of intermediate poisoning COads, reactivating the catalyst surface.
acknowledgement: This work was supported by the European Regional Development Funds
and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP,
ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship
Council for the scholarship support. J. Liu acknowledges support from the Jiangsu
University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange
Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the
project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors
acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246,
and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme
(MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat
de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER
RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.
article_number: '105116'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoting
full_name: Yu, Xiaoting
last_name: Yu
- first_name: Junfeng
full_name: Liu, Junfeng
last_name: Liu
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Yong
full_name: Zuo, Yong
last_name: Zuo
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Déspina
full_name: Nasiou, Déspina
last_name: Nasiou
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Kai
full_name: Pan, Kai
last_name: Pan
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Ying
full_name: Xie, Ying
last_name: Xie
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic
ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116
apa: Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous
incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano
Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116
chicago: Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong
Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic
Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116.
ieee: X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic
ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020.
ista: Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan
K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys
for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.
mla: Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic
Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020,
doi:10.1016/j.nanoen.2020.105116.
short: X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol,
K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).
date_created: 2020-08-02T22:00:57Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T08:24:05Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.nanoen.2020.105116
external_id:
isi:
- '000581738300030'
intvolume: ' 77'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
publication: Nano Energy
publication_identifier:
issn:
- 2211-2855
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 77
year: '2020'
...
---
_id: '8220'
abstract:
- lang: eng
text: Understanding to what extent stem cell potential is a cell-intrinsic property
or an emergent behavior coming from global tissue dynamics and geometry is a key
outstanding question of systems and stem cell biology. Here, we propose a theory
of stem cell dynamics as a stochastic competition for access to a spatially localized
niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce
a steady cellular stream which advects cells away from the niche, while random
rearrangements enable cells away from the niche to be favorably repositioned.
Importantly, even when assuming that all cells in a tissue are molecularly equivalent,
we predict a common (“universal”) functional dependence of the long-term clonal
survival probability on distance from the niche, as well as the emergence of a
well-defined number of functional stem cells, dependent only on the rate of random
movements vs. mitosis-driven advection. We test the predictions of this theory
on datasets of pubertal mammary gland tips and embryonic kidney tips, as well
as homeostatic intestinal crypts. Importantly, we find good agreement for the
predicted functional dependency of the competition as a function of position,
and thus functional stem cell number in each organ. This argues for a key role
of positional fluctuations in dictating stem cell number and dynamics, and we
discuss the applicability of this theory to other settings.
acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for
stimulating discussions. This project was supported by\r\nthe European Research
Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from
the CancerGenomics.nl (Netherlands Organization for Scientific Research) program
(J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by
Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust
Grant 098357/Z/12/Z."
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Saskia I.J.
full_name: Ellenbroek, Saskia I.J.
last_name: Ellenbroek
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival
as a noisy competition for niche access. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117
apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J.,
Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage
survival as a noisy competition for niche access. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1921205117
chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia
I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo.
“Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.
ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy
competition for niche access,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 117, no. 29. National Academy of Sciences,
pp. 16969–16975, 2020.
ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van
Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition
for niche access. Proceedings of the National Academy of Sciences of the United
States of America. 117(29), 16969–16975.
mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition
for Niche Access.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp.
16969–75, doi:10.1073/pnas.1921205117.
short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D.
Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences
of the United States of America 117 (2020) 16969–16975.
date_created: 2020-08-09T22:00:52Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2023-08-22T08:29:30Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1921205117
ec_funded: 1
external_id:
isi:
- '000553292900014'
pmid:
- '32611816'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T06:50:28Z
date_updated: 2020-08-10T06:50:28Z
file_id: '8223'
file_name: 2020_PNAS_Corominas.pdf
file_size: 1111604
relation: main_file
success: 1
file_date_updated: 2020-08-10T06:50:28Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16969-16975
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/order-from-noise/
scopus_import: '1'
status: public
title: Stem cell lineage survival as a noisy competition for niche access
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8199'
abstract:
- lang: eng
text: We investigate a mechanism to transiently stabilize topological phenomena
in long-lived quasi-steady states of isolated quantum many-body systems driven
at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady
states which is exponentially large in the inverse driving frequency. Within this
lifetime, the quasi-steady state is characterized by maximum entropy subject to
the constraint of fixed number of particles in the system's Floquet-Bloch bands.
In such a state, all the non-universal properties of these bands are washed out,
hence only the topological properties persist.
acknowledgement: "N.L., T.G. and E.B. acknowledge support from the European Research
Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme
(Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship
at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and
Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research
and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No.
754411. N.L. acknowledges support from the People Programme (Marie Curie Actions)
of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA
Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence
(I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12).
M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC)
under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement
No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B.
acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft"
article_number: '015'
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Mark Spencer
full_name: Rudner, Mark Spencer
last_name: Rudner
- first_name: Netanel
full_name: Lindner, Netanel
last_name: Lindner
citation:
ama: Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal
quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9.
doi:10.21468/scipostphys.9.1.015
apa: Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially
long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015
chicago: Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially
Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.”
SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.
ieee: T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps,” SciPost Physics,
vol. 9. SciPost Foundation, 2020.
ista: Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps. SciPost Physics.
9, 015.
mla: Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady
States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost
Foundation, 2020, doi:10.21468/scipostphys.9.1.015.
short: T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).
date_created: 2020-08-04T13:04:15Z
date_published: 2020-07-29T00:00:00Z
date_updated: 2023-08-22T08:28:24Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.9.1.015
ec_funded: 1
external_id:
isi:
- '000557362300008'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-06T08:56:06Z
date_updated: 2020-08-06T08:56:06Z
file_id: '8202'
file_name: 2020_SciPostPhys_Gulden.pdf
file_size: 531137
relation: main_file
success: 1
file_date_updated: 2020-08-06T08:56:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exponentially long lifetime of universal quasi-steady states in topological
Floquet pumps
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8261'
abstract:
- lang: eng
text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal
CA3 region, but how they process spatial information remains enigmatic. To examine
the role of GCs in spatial coding, we measured excitatory postsynaptic potentials
(EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt.
Intracellular recording from morphologically identified GCs revealed that most
cells were active, but activity level varied over a wide range. Whereas only ∼5%
of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus,
the GC population broadly encodes spatial information, but only a subset relays
this information to the CA3 network. Fourier analysis indicated that GCs received
conjunctive place-grid-like synaptic input, suggesting code conversion in single
neurons. GC firing was correlated with dendritic complexity and intrinsic excitability,
but not extrinsic excitatory input or dendritic cable properties. Thus, functional
maturation may control input-output transformation and spatial code conversion.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari,
Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of
this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery
Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp
recording. We are grateful to Florian Marr for cell labeling, cell reconstruction,
and technical assistance; Ben Suter for helpful discussions; Christina Altmutter
for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor
Asenov (Machine Shop) for device construction. We also thank the Scientific Service
Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical
Facility) for efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow
from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225.
doi:10.1016/j.neuron.2020.07.006
apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial
information flow from input to output in hippocampal granule cells. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006
chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of
Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.
ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information
flow from input to output in hippocampal granule cells,” Neuron, vol. 107,
no. 6. Elsevier, pp. 1212–1225, 2020.
ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information
flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.
mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from
Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6,
Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.
short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.
date_created: 2020-08-14T09:36:05Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:30:55Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.neuron.2020.07.006
ec_funded: 1
external_id:
isi:
- '000579698700009'
pmid:
- '32763145'
file:
- access_level: open_access
checksum: 44a5960fc083a4cb3488d22224859fdc
content_type: application/pdf
creator: dernst
date_created: 2020-12-04T09:29:21Z
date_updated: 2020-12-04T09:29:21Z
file_id: '8920'
file_name: 2020_Neuron_Zhang.pdf
file_size: 3011120
relation: main_file
success: 1
file_date_updated: 2020-12-04T09:29:21Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1212-1225
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/
status: public
title: Selective routing of spatial information flow from input to output in hippocampal
granule cells
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...