---
_id: '9093'
abstract:
- lang: eng
text: We employ the Gross-Pitaevskii equation to study acoustic emission generated
in a uniform Bose gas by a static impurity. The impurity excites a sound-wave
packet, which propagates through the gas. We calculate the shape of this wave
packet in the limit of long wave lengths, and argue that it is possible to extract
properties of the impurity by observing this shape. We illustrate here this possibility
for a Bose gas with a trapped impurity atom -- an example of a relevant experimental
setup. Presented results are general for all one-dimensional systems described
by the nonlinear Schrödinger equation and can also be used in nonatomic systems,
e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate
the shape of the sound-wave packet for a three-dimensional Bose gas assuming a
spherically symmetric perturbation.
acknowledgement: "We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding
beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for
valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support
from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221,
and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through
grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17)
and from the German Aeronautics and Space Administration\r\n(DLR) through Grant
No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248
[VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)"
article_number: '025'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Oleksandr
full_name: Marchukov, Oleksandr
last_name: Marchukov
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose
gas. SciPost Physics. 2021;10(2). doi:10.21468/scipostphys.10.2.025
apa: Marchukov, O., & Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed
Bose gas. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.10.2.025
chicago: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a
Weakly-Perturbed Bose Gas.” SciPost Physics. SciPost Foundation, 2021.
https://doi.org/10.21468/scipostphys.10.2.025.
ieee: O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed
Bose gas,” SciPost Physics, vol. 10, no. 2. SciPost Foundation, 2021.
ista: Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed
Bose gas. SciPost Physics. 10(2), 025.
mla: Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed
Bose Gas.” SciPost Physics, vol. 10, no. 2, 025, SciPost Foundation, 2021,
doi:10.21468/scipostphys.10.2.025.
short: O. Marchukov, A. Volosniev, SciPost Physics 10 (2021).
date_created: 2021-02-04T12:39:24Z
date_published: 2021-02-03T00:00:00Z
date_updated: 2023-08-07T13:39:37Z
day: '03'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.10.2.025
ec_funded: 1
external_id:
arxiv:
- '2004.08075'
isi:
- '000646783100027'
file:
- access_level: open_access
checksum: 9fd614b7ab49999e7267874df2582f7e
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T07:06:22Z
date_updated: 2021-02-09T07:06:22Z
file_id: '9105'
file_name: 2021_SciPostPhysics_Marchukov.pdf
file_size: 666512
relation: main_file
success: 1
file_date_updated: 2021-02-09T07:06:22Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
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'
status: public
title: Shape of a sound wave in a weakly-perturbed Bose gas
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: 10
year: '2021'
...
---
_id: '9094'
abstract:
- lang: eng
text: Dendritic cells (DCs) are crucial for the priming of naive T cells and the
initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell
contact, the immunological synapse (IS). While it is established that F-actin
dynamics regulates signaling at the T cell side of the contact, little is known
about the cytoskeletal contribution on the DC side. Here, we show that the DC
actin cytoskeleton is decisive for the formation of a multifocal synaptic structure,
which correlates with T cell priming efficiency. DC actin at the IS appears in
transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence
of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase
in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of
activated and proliferating T cells, demonstrating an important role for DC actin
in the regulation of immune synapse functionality.
article_number: e202006081
article_processing_charge: No
article_type: original
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: LM
full_name: Altenburger, LM
last_name: Altenburger
- first_name: R
full_name: Hauschild, R
last_name: Hauschild
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- first_name: K
full_name: Rottner, K
last_name: Rottner
- first_name: Stradal
full_name: TEB, Stradal
last_name: TEB
- first_name: A
full_name: Diz-Muñoz, A
last_name: Diz-Muñoz
- first_name: JV
full_name: Stein, JV
last_name: Stein
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics
control contact duration and priming efficiency at the immunological synapse.
Journal of Cell Biology. 2021;220(4). doi:10.1083/jcb.202006081
apa: Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K.,
TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration
and priming efficiency at the immunological synapse. Journal of Cell Biology.
Rockefeller University Press. https://doi.org/10.1083/jcb.202006081
chicago: Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner,
Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin
Dynamics Control Contact Duration and Priming Efficiency at the Immunological
Synapse.” Journal of Cell Biology. Rockefeller University Press, 2021.
https://doi.org/10.1083/jcb.202006081.
ieee: A. F. Leithner et al., “Dendritic cell actin dynamics control contact
duration and priming efficiency at the immunological synapse,” Journal of Cell
Biology, vol. 220, no. 4. Rockefeller University Press, 2021.
ista: Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz
A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration
and priming efficiency at the immunological synapse. Journal of Cell Biology.
220(4), e202006081.
mla: Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact
Duration and Priming Efficiency at the Immunological Synapse.” Journal of Cell
Biology, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021,
doi:10.1083/jcb.202006081.
short: A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB,
A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).
date_created: 2021-02-05T10:08:04Z
date_published: 2021-04-05T00:00:00Z
date_updated: 2023-09-05T13:57:53Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.202006081
external_id:
isi:
- '000626365700001'
pmid:
- '33533935'
file:
- access_level: open_access
checksum: 843ebc153847c8626e13c9c5ce71d533
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T14:16:21Z
date_updated: 2022-05-12T14:16:21Z
file_id: '11367'
file_name: 2021_JournCellBiology_Leithner.pdf
file_size: 5102328
relation: main_file
success: 1
file_date_updated: 2022-05-12T14:16:21Z
has_accepted_license: '1'
intvolume: ' 220'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dendritic cell actin dynamics control contact duration and priming efficiency
at the immunological synapse
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 220
year: '2021'
...
---
_id: '9097'
abstract:
- lang: eng
text: Psoriasis is a chronic inflammatory skin disease clinically characterized
by the appearance of red colored, well-demarcated plaques with thickened skin
and with silvery scales. Recent studies have established the involvement of a
complex signalling network of interactions between cytokines, immune cells and
skin cells called keratinocytes. Keratinocytes form the cells of the outermost
layer of the skin (epidermis). Visible plaques in psoriasis are developed due
to the fast proliferation and unusual differentiation of keratinocyte cells. Despite
that, the exact mechanism of the appearance of these plaques in the cytokine-immune
cell network is not clear. A mathematical model embodying interactions between
key immune cells believed to be involved in psoriasis, keratinocytes and relevant
cytokines has been developed. The complex network formed of these interactions
poses several challenges. Here, we choose to study subnetworks of this complex
network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15.
These are chosen based on known evidence of their therapeutic efficacy. In addition,
we explore the role of IL-15 in the pathogenesis of psoriasis and its potential
as a future drug target for a novel treatment option. We perform steady state
analyses for these subnetworks and demonstrate that the interactions between cells,
driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation
of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The
model results explain and support the clinical potentiality of anti-cytokine treatments.
Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis
of psoriasis, depending upon the dominant cytokines of subnetworks. We observed
that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis
via a bistable route, whereas an increase in the level of TNFα would lead to a
monotonic and gradual disease progression. Further, we demonstrate how this insight,
bistability, could be exploited to improve the current therapies and develop novel
treatment strategies for psoriasis.
acknowledgement: RP acknowledges the Department of Science and Technology, India for
the support through the DST-INSPIRE Faculty Award (DST/INSPIRE/04/2015/001939).
This work was supported by the Engineering and Physical Sciences Research Council
(EPSRC), United Kingdom (Grant numbers EP/J018295/1, EP/J018392/1, EP/N014391/1).
The contribution of RP was also supported by the later Grant. This work was generously
supported by the Welcome Trust Institutional Strategic Support Award (204909/Z/16/Z)
too. The contribution of MG was supported by the EPSRC via EP/N014391/1 and a Wellcome
Trust Institutional Strategic Support Award (WT105618MA). The contribution of YA
was generously supported by the Wellcome Trust Institutional Strategic Support Award
(WT105618MA).
article_number: '2204'
article_processing_charge: No
article_type: original
author:
- first_name: Rakesh
full_name: Pandey, Rakesh
last_name: Pandey
- first_name: Yusur
full_name: Al-Nuaimi, Yusur
last_name: Al-Nuaimi
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
- first_name: Sarah K.
full_name: Spurgeon, Sarah K.
last_name: Spurgeon
- first_name: Marc
full_name: Goodfellow, Marc
last_name: Goodfellow
citation:
ama: Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. Role of subnetworks
mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis
of psoriasis. Scientific Reports. 2021;11. doi:10.1038/s41598-020-80507-7
apa: Pandey, R., Al-Nuaimi, Y., Mishra, R. K., Spurgeon, S. K., & Goodfellow,
M. (2021). Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network
involved in the pathogenesis of psoriasis. Scientific Reports. Springer
Nature. https://doi.org/10.1038/s41598-020-80507-7
chicago: Pandey, Rakesh, Yusur Al-Nuaimi, Rajiv Kumar Mishra, Sarah K. Spurgeon,
and Marc Goodfellow. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15
in a Network Involved in the Pathogenesis of Psoriasis.” Scientific Reports.
Springer Nature, 2021. https://doi.org/10.1038/s41598-020-80507-7.
ieee: R. Pandey, Y. Al-Nuaimi, R. K. Mishra, S. K. Spurgeon, and M. Goodfellow,
“Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved
in the pathogenesis of psoriasis,” Scientific Reports, vol. 11. Springer
Nature, 2021.
ista: Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. 2021. Role of
subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in
the pathogenesis of psoriasis. Scientific Reports. 11, 2204.
mla: Pandey, Rakesh, et al. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17
and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” Scientific
Reports, vol. 11, 2204, Springer Nature, 2021, doi:10.1038/s41598-020-80507-7.
short: R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific
Reports 11 (2021).
date_created: 2021-02-07T23:01:12Z
date_published: 2021-01-26T00:00:00Z
date_updated: 2022-08-19T07:22:23Z
day: '26'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41598-020-80507-7
file:
- access_level: open_access
checksum: e8a68df48750712671f5c47b0228e531
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T07:33:23Z
date_updated: 2021-02-09T07:33:23Z
file_id: '9106'
file_name: 2021_ScientificReports_Pandey.pdf
file_size: 2885056
relation: main_file
success: 1
file_date_updated: 2021-02-09T07:33:23Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved
in the pathogenesis of psoriasis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2021'
...
---
_id: '9098'
abstract:
- lang: eng
text: "We study properties of the volume of projections of the n-dimensional\r\ncross-polytope
$\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We
prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace
has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower
bound on the volume of such a projection onto a two-dimensional plane. Also, we
show that there exist local maxima which are not global ones for the volume of
a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2."
acknowledgement: Research was supported by the Russian Foundation for Basic Research,
project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and
Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926
(Theorems 1.2 and 7.3).
article_number: '112312'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
citation:
ama: Ivanov G. On the volume of projections of the cross-polytope. Discrete Mathematics.
2021;344(5). doi:10.1016/j.disc.2021.112312
apa: Ivanov, G. (2021). On the volume of projections of the cross-polytope. Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2021.112312
chicago: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.”
Discrete Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.disc.2021.112312.
ieee: G. Ivanov, “On the volume of projections of the cross-polytope,” Discrete
Mathematics, vol. 344, no. 5. Elsevier, 2021.
ista: Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete
Mathematics. 344(5), 112312.
mla: Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” Discrete
Mathematics, vol. 344, no. 5, 112312, Elsevier, 2021, doi:10.1016/j.disc.2021.112312.
short: G. Ivanov, Discrete Mathematics 344 (2021).
date_created: 2021-02-07T23:01:12Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:40:37Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.disc.2021.112312
external_id:
arxiv:
- '1808.09165'
isi:
- '000633365200001'
intvolume: ' 344'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.09165
month: '05'
oa: 1
oa_version: Preprint
publication: Discrete Mathematics
publication_identifier:
issn:
- 0012365X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the volume of projections of the cross-polytope
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 344
year: '2021'
...
---
_id: '9099'
abstract:
- lang: eng
text: We show that on an Abelian variety over an algebraically closed field of positive
characteristic, the obstruction to lifting an automorphism to a field of characteristic
zero as a morphism vanishes if and only if it vanishes for lifting it as a derived
autoequivalence. We also compare the deformation space of these two types of deformations.
acknowledgement: I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina
Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas
Hausel for hosting me in his research group at IST Austria, and the referees for
their valuable suggestions. This research has received funding from the European
Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie
Grant Agreement No. 754411.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences.
Archiv der Mathematik. 2021;116(5):515-527. doi:10.1007/s00013-020-01564-y
apa: Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived
autoequivalences. Archiv Der Mathematik. Springer Nature. https://doi.org/10.1007/s00013-020-01564-y
chicago: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived
Autoequivalences.” Archiv Der Mathematik. Springer Nature, 2021. https://doi.org/10.1007/s00013-020-01564-y.
ieee: T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,”
Archiv der Mathematik, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021.
ista: Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived
autoequivalences. Archiv der Mathematik. 116(5), 515–527.
mla: Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived
Autoequivalences.” Archiv Der Mathematik, vol. 116, no. 5, Springer Nature,
2021, pp. 515–27, doi:10.1007/s00013-020-01564-y.
short: T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:42:38Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00013-020-01564-y
ec_funded: 1
external_id:
arxiv:
- '2001.07762'
isi:
- '000612580200001'
intvolume: ' 116'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.07762
month: '05'
oa: 1
oa_version: Preprint
page: 515-527
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Archiv der Mathematik
publication_identifier:
eissn:
- '14208938'
issn:
- 0003889X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lifting automorphisms on Abelian varieties as derived autoequivalences
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 116
year: '2021'
...
---
_id: '9100'
abstract:
- lang: eng
text: 'Marine environments are inhabited by a broad representation of the tree of
life, yet our understanding of speciation in marine ecosystems is extremely limited
compared with terrestrial and freshwater environments. Developing a more comprehensive
picture of speciation in marine environments requires that we ''dive under the
surface'' by studying a wider range of taxa and ecosystems is necessary for a
more comprehensive picture of speciation. Although studying marine evolutionary
processes is often challenging, recent technological advances in different fields,
from maritime engineering to genomics, are making it increasingly possible to
study speciation of marine life forms across diverse ecosystems and taxa. Motivated
by recent research in the field, including the 14 contributions in this issue,
we highlight and discuss six axes of research that we think will deepen our understanding
of speciation in the marine realm: (a) study a broader range of marine environments
and organisms; (b) identify the reproductive barriers driving speciation between
marine taxa; (c) understand the role of different genomic architectures underlying
reproductive isolation; (d) infer the evolutionary history of divergence using
model‐based approaches; (e) study patterns of hybridization and introgression
between marine taxa; and (f) implement highly interdisciplinary, collaborative
research programmes. In outlining these goals, we hope to inspire researchers
to continue filling this critical knowledge gap surrounding the origins of marine
biodiversity.'
acknowledgement: "We would like to thank all the participants in the speciation symposium
of the Marine Evolution Conference in Sweden for the interesting discussions and
to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf
Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during
the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very
helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn
and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary
Biology, respectively, for the encouragement and support in putting together this
special issue, and to all reviewers involved. RF was financed by the European Union's
Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie
Grant Agreement Number 706376 and is currently financed by the FEDER Funds through
the Operational Competitiveness Factors Program COMPETE and by National Funds through
the Foundation for Science and Technology (FCT) within the scope of the project
‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by
the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded
to Roger K. Butlin."
article_processing_charge: No
article_type: original
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving
under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756'
apa: 'Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine
environments: Diving under the surface. Journal of Evolutionary Biology.
Wiley. https://doi.org/10.1111/jeb.13756'
chicago: 'Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine
Environments: Diving under the Surface.” Journal of Evolutionary Biology.
Wiley, 2021. https://doi.org/10.1111/jeb.13756.'
ieee: 'R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments:
Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no.
1. Wiley, pp. 4–15, 2021.'
ista: 'Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments:
Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.'
mla: 'Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.”
Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15,
doi:10.1111/jeb.13756.'
short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology
34 (2021) 4–15.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-01-18T00:00:00Z
date_updated: 2023-08-07T13:42:08Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.13756
external_id:
isi:
- '000608367500001'
file:
- access_level: open_access
checksum: 5755856a5368d4b4cdd6fad5ab27f4d1
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T09:04:02Z
date_updated: 2021-02-09T09:04:02Z
file_id: '9108'
file_name: 2021_JourEvolBiology_Faria.pdf
file_size: 561340
relation: main_file
success: 1
file_date_updated: 2021-02-09T09:04:02Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 4-15
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- '14209101'
issn:
- 1010061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Speciation in marine environments: Diving under the surface'
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: 34
year: '2021'
...
---
_id: '9101'
abstract:
- lang: eng
text: 'Behavioral predispositions are innate tendencies of animals to behave in
a given way without the input of learning. They increase survival chances and,
due to environmental and ecological challenges, may vary substantially even between
closely related taxa. These differences are likely to be especially pronounced
in long-lived species like crocodilians. This order is particularly relevant for
comparative cognition due to its phylogenetic proximity to birds. Here we compared
early life behavioral predispositions in two Alligatoridae species. We exposed
American alligator and spectacled caiman hatchlings to three different novel situations:
a novel object, a novel environment that was open and a novel environment with
a shelter. This was then repeated a week later. During exposure to the novel environments,
alligators moved around more and explored a larger range of the arena than the
caimans. When exposed to the novel object, the alligators reduced the mean distance
to the novel object in the second phase, while the caimans further increased it,
indicating diametrically opposite ontogenetic development in behavioral predispositions.
Although all crocodilian hatchlings face comparable challenges, e.g., high predation
pressure, the effectiveness of parental protection might explain the observed
pattern. American alligators are apex predators capable of protecting their offspring
against most dangers, whereas adult spectacled caimans are frequently predated
themselves. Their distancing behavior might be related to increased predator avoidance
and also explain the success of invasive spectacled caimans in the natural habitats
of other crocodilians.'
acknowledgement: We thank Jamie Gilks and Terry Miles for their support at Crocodiles
of the World. We are grateful to the Department of Cognitive Biology, University
of Vienna for provision of working space and hardware. Finally, we would like to
thank Cliodhna Quigley, Rachael Harrison and Urs A. Reber for discussion. Open Access
funding provided by Lund University. This project was funded by the Marietta Blau
grant (BMFWF) to S. A. R.
article_processing_charge: No
article_type: original
author:
- first_name: Stephan A.
full_name: Reber, Stephan A.
last_name: Reber
- first_name: Jinook
full_name: Oh, Jinook
id: 403169A4-080F-11EA-9993-BF3F3DDC885E
last_name: Oh
orcid: 0000-0001-7425-2372
- first_name: Judith
full_name: Janisch, Judith
last_name: Janisch
- first_name: Colin
full_name: Stevenson, Colin
last_name: Stevenson
- first_name: Shaun
full_name: Foggett, Shaun
last_name: Foggett
- first_name: Anna
full_name: Wilkinson, Anna
last_name: Wilkinson
citation:
ama: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. Early life
differences in behavioral predispositions in two Alligatoridae species. Animal
Cognition. 2021;24(4):753-764. doi:10.1007/s10071-020-01461-5
apa: Reber, S. A., Oh, J., Janisch, J., Stevenson, C., Foggett, S., & Wilkinson,
A. (2021). Early life differences in behavioral predispositions in two Alligatoridae
species. Animal Cognition. Springer Nature. https://doi.org/10.1007/s10071-020-01461-5
chicago: Reber, Stephan A., Jinook Oh, Judith Janisch, Colin Stevenson, Shaun Foggett,
and Anna Wilkinson. “Early Life Differences in Behavioral Predispositions in Two
Alligatoridae Species.” Animal Cognition. Springer Nature, 2021. https://doi.org/10.1007/s10071-020-01461-5.
ieee: S. A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, and A. Wilkinson,
“Early life differences in behavioral predispositions in two Alligatoridae species,”
Animal Cognition, vol. 24, no. 4. Springer Nature, pp. 753–764, 2021.
ista: Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. 2021. Early
life differences in behavioral predispositions in two Alligatoridae species. Animal
Cognition. 24(4), 753–764.
mla: Reber, Stephan A., et al. “Early Life Differences in Behavioral Predispositions
in Two Alligatoridae Species.” Animal Cognition, vol. 24, no. 4, Springer
Nature, 2021, pp. 753–64, doi:10.1007/s10071-020-01461-5.
short: S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal
Cognition 24 (2021) 753–764.
date_created: 2021-02-07T23:01:13Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-07T13:41:08Z
day: '01'
ddc:
- '590'
department:
- _id: SyCr
doi: 10.1007/s10071-020-01461-5
external_id:
isi:
- '000608382100001'
file:
- access_level: open_access
checksum: d9dfa0d1de6d684692b041d936dd858e
content_type: application/pdf
creator: dernst
date_created: 2021-02-09T07:40:14Z
date_updated: 2021-02-09T07:40:14Z
file_id: '9107'
file_name: 2021_AnimalCognition_Reber.pdf
file_size: 1117991
relation: main_file
success: 1
file_date_updated: 2021-02-09T07:40:14Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 753-764
publication: Animal Cognition
publication_identifier:
eissn:
- '14359456'
issn:
- '14359448'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Early life differences in behavioral predispositions in two Alligatoridae species
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: 24
year: '2021'
...
---
_id: '9111'
abstract:
- lang: eng
text: 'We study the probabilistic convergence between the mapper graph and the Reeb
graph of a topological space X equipped with a continuous function f:X→R. We first
give a categorification of the mapper graph and the Reeb graph by interpreting
them in terms of cosheaves and stratified covers of the real line R. We then introduce
a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium
on point-based graphics, 2007), referred to as the enhanced mapper graph, and
demonstrate that such a construction approximates the Reeb graph of (X,f) when
it is applied to points randomly sampled from a probability density function concentrated
on (X,f). Our techniques are based on the interleaving distance of constructible
cosheaves and topological estimation via kernel density estimates. Following Munch
and Wang (In: 32nd international symposium on computational geometry, volume 51
of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany,
pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible
R-space (with a fixed open cover), approximates the Reeb graph of the same space.
We then construct an isomorphism between the mapper of (X,f) to the mapper of
a super-level set of a probability density function concentrated on (X,f). Finally,
building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b),
we show that, with high probability, we can recover the mapper of the super-level
set given a sufficiently large sample. Our work is the first to consider the mapper
construction using the theory of cosheaves in a probabilistic setting. It is part
of an ongoing effort to combine sheaf theory, probability, and statistics, to
support topological data analysis with random data.'
acknowledgement: "AB was supported in part by the European Union’s Horizon 2020 research
and innovation\r\nprogramme under the Marie Sklodowska-Curie GrantAgreement No.
754411 and NSF IIS-1513616. OB was supported in part by the Israel Science Foundation,
Grant 1965/19. BW was supported in part by NSF IIS-1513616 and DBI-1661375. EM was
supported in part by NSF CMMI-1800466, DMS-1800446, and CCF-1907591.We would like
to thank the Institute for Mathematics and its Applications for hosting a workshop
titled Bridging Statistics and Sheaves in May 2018, where this work was conceived.\r\nOpen
Access funding provided by Institute of Science and Technology (IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Adam
full_name: Brown, Adam
id: 70B7FDF6-608D-11E9-9333-8535E6697425
last_name: Brown
- first_name: Omer
full_name: Bobrowski, Omer
last_name: Bobrowski
- first_name: Elizabeth
full_name: Munch, Elizabeth
last_name: Munch
- first_name: Bei
full_name: Wang, Bei
last_name: Wang
citation:
ama: Brown A, Bobrowski O, Munch E, Wang B. Probabilistic convergence and stability
of random mapper graphs. Journal of Applied and Computational Topology.
2021;5(1):99-140. doi:10.1007/s41468-020-00063-x
apa: Brown, A., Bobrowski, O., Munch, E., & Wang, B. (2021). Probabilistic convergence
and stability of random mapper graphs. Journal of Applied and Computational
Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00063-x
chicago: Brown, Adam, Omer Bobrowski, Elizabeth Munch, and Bei Wang. “Probabilistic
Convergence and Stability of Random Mapper Graphs.” Journal of Applied and
Computational Topology. Springer Nature, 2021. https://doi.org/10.1007/s41468-020-00063-x.
ieee: A. Brown, O. Bobrowski, E. Munch, and B. Wang, “Probabilistic convergence
and stability of random mapper graphs,” Journal of Applied and Computational
Topology, vol. 5, no. 1. Springer Nature, pp. 99–140, 2021.
ista: Brown A, Bobrowski O, Munch E, Wang B. 2021. Probabilistic convergence and
stability of random mapper graphs. Journal of Applied and Computational Topology.
5(1), 99–140.
mla: Brown, Adam, et al. “Probabilistic Convergence and Stability of Random Mapper
Graphs.” Journal of Applied and Computational Topology, vol. 5, no. 1,
Springer Nature, 2021, pp. 99–140, doi:10.1007/s41468-020-00063-x.
short: A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational
Topology 5 (2021) 99–140.
date_created: 2021-02-11T14:41:02Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-09-05T15:37:56Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s41468-020-00063-x
ec_funded: 1
external_id:
arxiv:
- '1909.03488'
file:
- access_level: open_access
checksum: 3f02e9d47c428484733da0f588a3c069
content_type: application/pdf
creator: dernst
date_created: 2021-02-11T14:43:59Z
date_updated: 2021-02-11T14:43:59Z
file_id: '9112'
file_name: 2020_JourApplCompTopology_Brown.pdf
file_size: 2090265
relation: main_file
success: 1
file_date_updated: 2021-02-11T14:43:59Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 99-140
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probabilistic convergence and stability of random mapper graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2021'
...
---
_id: '9113'
abstract:
- lang: eng
text: “Hydrogen economy” could enable a carbon-neutral sustainable energy chain.
However, issues with safety, storage, and transport of molecular hydrogen impede
its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art
reforming is difficult, requiring high temperatures >200 °C and pressures >25
bar, and the resulting H2 is carbonized beyond tolerance levels for direct use
in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming
in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol
is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as
carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization
energy between the alkaline anode and the acidic cathode drives the process, particularly
the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature
coefficient of the resulting electromotive force allows us to harvest a large
fraction of the output energy from the surrounding, achieving a thermodynamic
efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming
even under open-air conditions, a challenge that state-of-the-art alcohol reforming
failed to overcome. We further show reforming of a wide range of alcohols. The
ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously
captured and pure H2 produced at mild conditions.
acknowledgement: M.O.T. acknowledges DST/TMD/HFC/2 K18/58, DST-SERB, MHRD fast track,
and DST Nanomission forfinancialassistance. Z.M.B. acknowledges CSIR-SRF fellowship
fromMHRD, India. S.A.F. acknowledges support from IST Austria.
article_processing_charge: No
article_type: original
author:
- first_name: Zahid Manzoor
full_name: Manzoor Bhat, Zahid Manzoor
last_name: Manzoor Bhat
- first_name: Ravikumar
full_name: Thimmappa, Ravikumar
last_name: Thimmappa
- first_name: 'Neethu Christudas '
full_name: 'Dargily, Neethu Christudas '
last_name: Dargily
- first_name: 'Abdul '
full_name: 'Raafik, Abdul '
last_name: Raafik
- first_name: 'Alagar Raja '
full_name: 'Kottaichamy, Alagar Raja '
last_name: Kottaichamy
- first_name: 'Mruthyunjayachari Chattanahalli '
full_name: 'Devendrachari, Mruthyunjayachari Chattanahalli '
last_name: Devendrachari
- first_name: Mahesh
full_name: Itagi, Mahesh
last_name: Itagi
- first_name: Harish
full_name: ' Makri Nimbegondi Kotresh, Harish'
last_name: ' Makri Nimbegondi Kotresh'
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: 'Musthafa '
full_name: 'Ottakam Thotiyl, Musthafa '
last_name: Ottakam Thotiyl
citation:
ama: Manzoor Bhat ZM, Thimmappa R, Dargily NC, et al. Ambient condition alcohol
reforming to hydrogen with electricity output. ACS Sustainable Chemistry and
Engineering. 2021;9(8):3104-3111. doi:10.1021/acssuschemeng.0c07547
apa: Manzoor Bhat, Z. M., Thimmappa, R., Dargily, N. C., Raafik, A., Kottaichamy,
A. R., Devendrachari, M. C., … Ottakam Thotiyl, M. (2021). Ambient condition alcohol
reforming to hydrogen with electricity output. ACS Sustainable Chemistry and
Engineering. American Chemical Society. https://doi.org/10.1021/acssuschemeng.0c07547
chicago: Manzoor Bhat, Zahid Manzoor, Ravikumar Thimmappa, Neethu Christudas Dargily,
Abdul Raafik, Alagar Raja Kottaichamy, Mruthyunjayachari Chattanahalli Devendrachari,
Mahesh Itagi, Harish Makri Nimbegondi Kotresh, Stefan Alexander Freunberger,
and Musthafa Ottakam Thotiyl. “Ambient Condition Alcohol Reforming to Hydrogen
with Electricity Output.” ACS Sustainable Chemistry and Engineering. American
Chemical Society, 2021. https://doi.org/10.1021/acssuschemeng.0c07547.
ieee: Z. M. Manzoor Bhat et al., “Ambient condition alcohol reforming to
hydrogen with electricity output,” ACS Sustainable Chemistry and Engineering,
vol. 9, no. 8. American Chemical Society, pp. 3104–3111, 2021.
ista: Manzoor Bhat ZM, Thimmappa R, Dargily NC, Raafik A, Kottaichamy AR, Devendrachari
MC, Itagi M, Makri Nimbegondi Kotresh H, Freunberger SA, Ottakam Thotiyl M. 2021.
Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable
Chemistry and Engineering. 9(8), 3104–3111.
mla: Manzoor Bhat, Zahid Manzoor, et al. “Ambient Condition Alcohol Reforming to
Hydrogen with Electricity Output.” ACS Sustainable Chemistry and Engineering,
vol. 9, no. 8, American Chemical Society, 2021, pp. 3104–11, doi:10.1021/acssuschemeng.0c07547.
short: Z.M. Manzoor Bhat, R. Thimmappa, N.C. Dargily, A. Raafik, A.R. Kottaichamy,
M.C. Devendrachari, M. Itagi, H. Makri Nimbegondi Kotresh, S.A. Freunberger,
M. Ottakam Thotiyl, ACS Sustainable Chemistry and Engineering 9 (2021) 3104–3111.
date_created: 2021-02-12T09:20:18Z
date_published: 2021-02-11T00:00:00Z
date_updated: 2023-08-07T13:43:19Z
day: '11'
department:
- _id: StFr
doi: 10.1021/acssuschemeng.0c07547
external_id:
isi:
- '000625460400010'
intvolume: ' 9'
isi: 1
issue: '8'
language:
- iso: eng
month: '02'
oa_version: None
page: 3104-3111
publication: ACS Sustainable Chemistry and Engineering
publication_identifier:
eissn:
- 2168-0485
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ambient condition alcohol reforming to hydrogen with electricity output
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2021'
...
---
_id: '9118'
abstract:
- lang: eng
text: Cesium lead halides have intrinsically unstable crystal lattices and easily
transform within perovskite and nonperovskite structures. In this work, we explore
the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS
at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6
nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into
the PbS lattice with a consequent increase in the concentration of free charge
carriers. This new doping strategy enables the adjustment of the density of charge
carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for
doping other nanocrystal-based semiconductors.
acknowledgement: "M.C. has received funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR
327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No.
SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme under grant agreement No 823717 − ESTEEM3. M.V.K. acknowledges
the support by the European Research Council under the Horizon 2020 Framework Program
(ERC Consolidator Grant SCALEHALO\r\nGrant Agreement No. 819740) and by FET-OPEN
project no. 862656 (DROP-IT)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
- first_name: Aziz
full_name: Genc, Aziz
last_name: Genc
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Dmitry N.
full_name: Dirin, Dmitry N.
last_name: Dirin
- first_name: Quinten A.
full_name: Akkerman, Quinten A.
last_name: Akkerman
- first_name: Maksym V.
full_name: Kovalenko, Maksym V.
last_name: Kovalenko
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Calcabrini M, Genc A, Liu Y, et al. Exploiting the lability of metal halide
perovskites for doping semiconductor nanocomposites. ACS Energy Letters.
2021;6(2):581-587. doi:10.1021/acsenergylett.0c02448
apa: Calcabrini, M., Genc, A., Liu, Y., Kleinhanns, T., Lee, S., Dirin, D. N., …
Ibáñez, M. (2021). Exploiting the lability of metal halide perovskites for doping
semiconductor nanocomposites. ACS Energy Letters. American Chemical Society.
https://doi.org/10.1021/acsenergylett.0c02448
chicago: Calcabrini, Mariano, Aziz Genc, Yu Liu, Tobias Kleinhanns, Seungho Lee,
Dmitry N. Dirin, Quinten A. Akkerman, Maksym V. Kovalenko, Jordi Arbiol, and Maria
Ibáñez. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor
Nanocomposites.” ACS Energy Letters. American Chemical Society, 2021. https://doi.org/10.1021/acsenergylett.0c02448.
ieee: M. Calcabrini et al., “Exploiting the lability of metal halide perovskites
for doping semiconductor nanocomposites,” ACS Energy Letters, vol. 6, no.
2. American Chemical Society, pp. 581–587, 2021.
ista: Calcabrini M, Genc A, Liu Y, Kleinhanns T, Lee S, Dirin DN, Akkerman QA, Kovalenko
MV, Arbiol J, Ibáñez M. 2021. Exploiting the lability of metal halide perovskites
for doping semiconductor nanocomposites. ACS Energy Letters. 6(2), 581–587.
mla: Calcabrini, Mariano, et al. “Exploiting the Lability of Metal Halide Perovskites
for Doping Semiconductor Nanocomposites.” ACS Energy Letters, vol. 6, no.
2, American Chemical Society, 2021, pp. 581–87, doi:10.1021/acsenergylett.0c02448.
short: M. Calcabrini, A. Genc, Y. Liu, T. Kleinhanns, S. Lee, D.N. Dirin, Q.A. Akkerman,
M.V. Kovalenko, J. Arbiol, M. Ibáñez, ACS Energy Letters 6 (2021) 581–587.
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-20T00:00:00Z
date_updated: 2023-08-07T13:46:00Z
day: '20'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsenergylett.0c02448
ec_funded: 1
external_id:
isi:
- '000619803400036'
file:
- access_level: open_access
checksum: 6fa7374bf8b95fdfe6e6c595322a6689
content_type: application/pdf
creator: dernst
date_created: 2021-02-17T07:36:52Z
date_updated: 2021-02-17T07:36:52Z
file_id: '9155'
file_name: 2021_ACSEnergyLetters_Calcabrini.pdf
file_size: 5071201
relation: main_file
success: 1
file_date_updated: 2021-02-17T07:36:52Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 581-587
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACS Energy Letters
publication_identifier:
eissn:
- 2380-8195
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '12885'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Exploiting the lability of metal halide perovskites for doping semiconductor
nanocomposites
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: 6
year: '2021'
...
---
_id: '9119'
abstract:
- lang: eng
text: 'We present DILS, a deployable statistical analysis platform for conducting
demographic inferences with linked selection from population genomic data using
an Approximate Bayesian Computation framework. DILS takes as input single‐population
or two‐population data sets (multilocus fasta sequences) and performs three types
of analyses in a hierarchical manner, identifying: (a) the best demographic model
to study the importance of gene flow and population size change on the genetic
patterns of polymorphism and divergence, (b) the best genomic model to determine
whether the effective size Ne and migration rate N, m are heterogeneously distributed
along the genome (implying linked selection) and (c) loci in genomic regions most
associated with barriers to gene flow. Also available via a Web interface, an
objective of DILS is to facilitate collaborative research in speciation genomics.
Here, we show the performance and limitations of DILS by using simulations and
finally apply the method to published data on a divergence continuum composed
by 28 pairs of Mytilus mussel populations/species.'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Iva
full_name: Popovic, Iva
last_name: Popovic
- first_name: Clément
full_name: Mazoyer, Clément
last_name: Mazoyer
- first_name: Bruno
full_name: Spataro, Bruno
last_name: Spataro
- first_name: Stéphane
full_name: Delmotte, Stéphane
last_name: Delmotte
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Étienne
full_name: Loire, Étienne
last_name: Loire
- first_name: Alexis
full_name: Simon, Alexis
last_name: Simon
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Laurent
full_name: Duret, Laurent
last_name: Duret
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
- first_name: Xavier
full_name: Vekemans, Xavier
last_name: Vekemans
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
citation:
ama: 'Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with
linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644.
doi:10.1111/1755-0998.13323'
apa: 'Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier,
J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using
ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323'
chicago: 'Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane
Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences
with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley,
2021. https://doi.org/10.1111/1755-0998.13323.'
ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection
by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644,
2021.'
ista: 'Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire
É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic
inferences with linked selection by using ABC. Molecular Ecology Resources. 21,
2629–2644.'
mla: 'Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection
by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44,
doi:10.1111/1755-0998.13323.'
short: C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier,
É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular
Ecology Resources 21 (2021) 2629–2644.
date_created: 2021-02-14T23:01:14Z
date_published: 2021-01-15T00:00:00Z
date_updated: 2023-08-07T13:45:18Z
day: '15'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13323
external_id:
isi:
- '000614183100001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2
month: '01'
oa: 1
oa_version: Preprint
page: 2629-2644
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- '17550998'
issn:
- 1755098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'DILS: Demographic inferences with linked selection by using ABC'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2021'
...
---
_id: '9158'
abstract:
- lang: eng
text: While several tools have been developed to study the ground state of many-body
quantum spin systems, the limitations of existing techniques call for the exploration
of new approaches. In this manuscript we develop an alternative analytical and
numerical framework for many-body quantum spin ground states, based on the disentanglement
formalism. In this approach, observables are exactly expressed as Gaussian-weighted
functional integrals over scalar fields. We identify the leading contribution
to these integrals, given by the saddle point of a suitable effective action.
Analytically, we develop a field-theoretical expansion of the functional integrals,
performed by means of appropriate Feynman rules. The expansion can be truncated
to a desired order to obtain analytical approximations to observables. Numerically,
we show that the disentanglement approach can be used to compute ground state
expectation values from classical stochastic processes. While the associated fluctuations
grow exponentially with imaginary time and the system size, this growth can be
mitigated by means of an importance sampling scheme based on knowledge of the
saddle point configuration. We illustrate the advantages and limitations of our
methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions.
Our analytical and numerical approaches are applicable to a broad class of systems,
bridging concepts from quantum lattice models, continuum field theory, and classical
stochastic processes.
acknowledgement: "S D N would like to thank M J Bhaseen, J Chalker, B Doyon, V Gritsev,
A Lamacraft,\r\nA Michailidis and M Serbyn for helpful feedback and stimulating
conversations. S D N\r\nacknowledges funding from the Institute of Science and Technology
(IST) Austria, and\r\nfrom the European Union’s Horizon 2020 research and innovation
program under the\r\nMarie Sk\blodowska-Curie Grant Agreement No. 754411. S D N
also acknowledges funding\r\nfrom the EPSRC Center for Doctoral Training in Cross-Disciplinary
Approaches to Non-\r\nEquilibrium Systems (CANES) under Grant EP/L015854/1. S D
N is grateful to IST\r\nAustria for providing open access funding."
article_number: '013101'
article_processing_charge: No
article_type: original
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
citation:
ama: 'De Nicola S. Disentanglement approach to quantum spin ground states: Field
theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. 2021;2021(1). doi:10.1088/1742-5468/abc7c7'
apa: 'De Nicola, S. (2021). Disentanglement approach to quantum spin ground states:
Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/abc7c7'
chicago: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States:
Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics:
Theory and Experiment. IOP Publishing, 2021. https://doi.org/10.1088/1742-5468/abc7c7.'
ieee: 'S. De Nicola, “Disentanglement approach to quantum spin ground states: Field
theory and stochastic simulation,” Journal of Statistical Mechanics: Theory
and Experiment, vol. 2021, no. 1. IOP Publishing, 2021.'
ista: 'De Nicola S. 2021. Disentanglement approach to quantum spin ground states:
Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory
and Experiment. 2021(1), 013101.'
mla: 'De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States:
Field Theory and Stochastic Simulation.” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2021, no. 1, 013101, IOP Publishing, 2021, doi:10.1088/1742-5468/abc7c7.'
short: 'S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021
(2021).'
date_created: 2021-02-17T17:48:46Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2023-08-07T13:46:28Z
day: '05'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1088/1742-5468/abc7c7
ec_funded: 1
external_id:
isi:
- '000605080300001'
file:
- access_level: open_access
checksum: 64e2aae4837790db26e1dd1986c69c07
content_type: application/pdf
creator: dernst
date_created: 2021-02-19T14:04:40Z
date_updated: 2021-02-19T14:04:40Z
file_id: '9172'
file_name: 2021_JourStatMech_deNicola.pdf
file_size: 1693609
relation: main_file
success: 1
file_date_updated: 2021-02-19T14:04:40Z
has_accepted_license: '1'
intvolume: ' 2021'
isi: 1
issue: '1'
keyword:
- Statistics
- Probability and Uncertainty
- Statistics and Probability
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: 'Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- 1742-5468
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: 'Disentanglement approach to quantum spin ground states: Field theory and stochastic
simulation'
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: 2021
year: '2021'
...
---
_id: '9168'
abstract:
- lang: eng
text: Interspecific crossing experiments have shown that sex chromosomes play a
major role in reproductive isolation between many pairs of species. However, their
ability to act as reproductive barriers, which hamper interspecific genetic exchange,
has rarely been evaluated quantitatively compared to Autosomes. This genome-wide
limitation of gene flow is essential for understanding the complete separation
of species, and thus speciation. Here, we develop a mainland-island model of secondary
contact between hybridizing species of an XY (or ZW) sexual system. We obtain
theoretical predictions for the frequency of introgressed alleles, and the strength
of the barrier to neutral gene flow for the two types of chromosomes carrying
multiple interspecific barrier loci. Theoretical predictions are obtained for
scenarios where introgressed alleles are rare. We show that the same analytical
expressions apply for sex chromosomes and autosomes, but with different sex-averaged
effective parameters. The specific features of sex chromosomes (hemizygosity and
absence of recombination in the heterogametic sex) lead to reduced levels of introgression
on the X (or Z) compared to autosomes. This effect can be enhanced by certain
types of sex-biased forces, but it remains overall small (except when alleles
causing incompatibilities are recessive). We discuss these predictions in the
light of empirical data comprising model-based tests of introgression and cline
surveys in various biological systems.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The computations were performed with the IST Austria High-Performance
Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core
Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments
on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird,
and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian
Science Foundation FWF grant (Project M 2463-B29)."
article_number: iyaa025
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
2021;217(2). doi:10.1093/genetics/iyaa025'
apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers
to genetic exchange between hybridizing species: Sex chromosomes vs autosomes.
Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025'
chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression
and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes
vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.'
ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics,
vol. 217, no. 2. Genetics Society of America, 2021.'
ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic
exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics.
217(2), iyaa025.'
mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and
Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.”
Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021,
doi:10.1093/genetics/iyaa025.'
short: C. Fraisse, H. Sachdeva, Genetics 217 (2021).
date_created: 2021-02-18T14:41:30Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:47:01Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaa025
external_id:
isi:
- '000637218100005'
intvolume: ' 217'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/genetics/iyaa025
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: 'The rates of introgression and barriers to genetic exchange between hybridizing
species: Sex chromosomes vs autosomes'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 217
year: '2021'
...
---
_id: '9173'
abstract:
- lang: eng
text: We show that Hilbert schemes of points on supersingular Enriques surface in
characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties
but are not irreducible symplectic as the hodge number h2,0 > 1, even though a
supersingular Enriques surface is an irreducible symplectic variety. These are
the classes of varieties which appear only in characteristic 2 and they show that
the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic
2. It also gives examples of varieties with trivial canonical class which are
neither irreducible symplectic nor Calabi-Yau, thereby showing that there are
strictly more classes of simply connected varieties with trivial canonical class
in characteristic 2 than over C as given by Beauville-Bogolomov decomposition
theorem.
acknowledgement: I would like to thank M. Zdanwociz for various mathematical discussions
which lead to this article, Tamas Hausel for hosting me in his research group at
IST Austria and the anonymous referee for their helpful suggestions and comments.
This research has received funding from the European Union's Horizon 2020 Marie
Sklodowska-Curie Actions Grant No. 754411 and Institue of Science and Technology
Austria IST-PLUS Grant No. 754411.
article_number: '102957'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface. Bulletin des Sciences Mathematiques. 2021;167(03). doi:10.1016/j.bulsci.2021.102957
apa: Srivastava, T. K. (2021). Pathologies of the Hilbert scheme of points of a
supersingular Enriques surface. Bulletin Des Sciences Mathematiques. Elsevier.
https://doi.org/10.1016/j.bulsci.2021.102957
chicago: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a
Supersingular Enriques Surface.” Bulletin Des Sciences Mathematiques. Elsevier,
2021. https://doi.org/10.1016/j.bulsci.2021.102957.
ieee: T. K. Srivastava, “Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface,” Bulletin des Sciences Mathematiques, vol. 167, no. 03.
Elsevier, 2021.
ista: Srivastava TK. 2021. Pathologies of the Hilbert scheme of points of a supersingular
Enriques surface. Bulletin des Sciences Mathematiques. 167(03), 102957.
mla: Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular
Enriques Surface.” Bulletin Des Sciences Mathematiques, vol. 167, no. 03,
102957, Elsevier, 2021, doi:10.1016/j.bulsci.2021.102957.
short: T.K. Srivastava, Bulletin Des Sciences Mathematiques 167 (2021).
date_created: 2021-02-21T23:01:20Z
date_published: 2021-03-01T00:00:00Z
date_updated: 2023-08-07T13:47:48Z
day: '01'
department:
- _id: TaHa
doi: 10.1016/j.bulsci.2021.102957
ec_funded: 1
external_id:
arxiv:
- '2010.08976'
isi:
- '000623881600009'
intvolume: ' 167'
isi: 1
issue: '03'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2010.08976
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Bulletin des Sciences Mathematiques
publication_identifier:
issn:
- 0007-4497
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathologies of the Hilbert scheme of points of a supersingular Enriques surface
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 167
year: '2021'
...
---
_id: '9188'
abstract:
- lang: eng
text: Genomic imprinting is an epigenetic mechanism that results in parental allele-specific
expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental
regulators and play pivotal roles in many biological processes such as nutrient
transfer from the mother to offspring and neuronal development. Imprinted genes
are also involved in human disease, including neurodevelopmental disorders, and
often occur in clusters that are regulated by a common imprint control region
(ICR). In extra-embryonic tissues ICRs can act over large distances, with the
largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical
imprinted expression that shows near exclusive maternal or paternal expression,
widespread biased imprinted expression has been identified mainly in brain. In
this review we discuss recent developments mapping cell type specific imprinted
expression in extra-embryonic tissues and neocortex in the mouse. We highlight
the advantages of using an inducible uniparental chromosome disomy (UPD) system
to generate cells carrying either two maternal or two paternal copies of a specific
chromosome to analyze the functional consequences of genomic imprinting. Mosaic
Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant
induction of UPD sparsely in specific cell types, and thus to over-express or
suppress all imprinted genes on that chromosome. To illustrate the utility of
this technique, we explain how MADM-induced UPD revealed new insights about the
function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs
led to identification of highly cell type specific phenotypes related to perturbed
imprinted expression in the mouse neocortex. Finally, we give an outlook on how
MADM could be used to probe cell type specific imprinted expression in other tissues
in mouse, particularly in extra-embryonic tissues.
acknowledgement: We thank Melissa Stouffer for critically reading the manuscript.
This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung
n[f + b] life science call grant (C13-002) 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_number: '104986'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome
disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry
International. 2021;145(5). doi:10.1016/j.neuint.2021.104986
apa: Pauler, F., Hudson, Q., Laukoter, S., & Hippenmeyer, S. (2021). Inducible
uniparental chromosome disomy to probe genomic imprinting at single-cell level
in brain and beyond. Neurochemistry International. Elsevier. https://doi.org/10.1016/j.neuint.2021.104986
chicago: Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer.
“Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell
Level in Brain and Beyond.” Neurochemistry International. Elsevier, 2021.
https://doi.org/10.1016/j.neuint.2021.104986.
ieee: F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental
chromosome disomy to probe genomic imprinting at single-cell level in brain and
beyond,” Neurochemistry International, vol. 145, no. 5. Elsevier, 2021.
ista: Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental
chromosome disomy to probe genomic imprinting at single-cell level in brain and
beyond. Neurochemistry International. 145(5), 104986.
mla: Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic
Imprinting at Single-Cell Level in Brain and Beyond.” Neurochemistry International,
vol. 145, no. 5, 104986, Elsevier, 2021, doi:10.1016/j.neuint.2021.104986.
short: F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International
145 (2021).
date_created: 2021-02-23T12:31:43Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:48:26Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuint.2021.104986
ec_funded: 1
external_id:
isi:
- '000635575000005'
pmid:
- '33600873'
file:
- access_level: open_access
checksum: c6d7a40089cd29e289f9b22e75768304
content_type: application/pdf
creator: kschuh
date_created: 2021-08-11T12:30:38Z
date_updated: 2021-08-11T12:30:38Z
file_id: '9883'
file_name: 2021_NCI_Pauler.pdf
file_size: 7083499
relation: main_file
success: 1
file_date_updated: 2021-08-11T12:30:38Z
has_accepted_license: '1'
intvolume: ' 145'
isi: 1
issue: '5'
keyword:
- Cell Biology
- Cellular and Molecular Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
publication: Neurochemistry International
publication_identifier:
issn:
- 0197-0186
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell
level in brain and beyond
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: 145
year: '2021'
...
---
_id: '9189'
abstract:
- lang: eng
text: Transposable elements exist widely throughout plant genomes and play important
roles in plant evolution. Auxin is an important regulator that is traditionally
associated with root development and drought stress adaptation. The DEEPER ROOTING
1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified
a transposon that acts as an autonomous auxin‐responsive promoter and its presence
at specific genome positions conveys physiological adaptations related to drought
avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in
the root tip show deeper and longer root phenotypes and are thus better adapted
to drought. The INDITTO2 transposon contains an auxin response element and displays
auxin‐responsive promoter activity; it is thus able to convey auxin regulation
of transcription to genes in its proximity. In the rice Acuce, which displays
DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted
at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the
INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare
was sufficient to promote its drought avoidance. Our data identify an example
of how transposons can act as promoters and convey hormonal regulation to nearby
loci, improving plant fitness in response to different abiotic stresses.
article_processing_charge: No
article_type: original
author:
- first_name: Y
full_name: Zhao, Y
last_name: Zhao
- first_name: L
full_name: Wu, L
last_name: Wu
- first_name: Q
full_name: Fu, Q
last_name: Fu
- first_name: D
full_name: Wang, D
last_name: Wang
- first_name: J
full_name: Li, J
last_name: Li
- first_name: B
full_name: Yao, B
last_name: Yao
- first_name: S
full_name: Yu, S
last_name: Yu
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: J
full_name: Qian, J
last_name: Qian
- first_name: X
full_name: Zhou, X
last_name: Zhou
- first_name: L
full_name: Han, L
last_name: Han
- first_name: S
full_name: Zhao, S
last_name: Zhao
- first_name: C
full_name: Ma, C
last_name: Ma
- first_name: Y
full_name: Zhang, Y
last_name: Zhang
- first_name: C
full_name: Luo, C
last_name: Luo
- first_name: Q
full_name: Dong, Q
last_name: Dong
- first_name: S
full_name: Li, S
last_name: Li
- first_name: L
full_name: Zhang, L
last_name: Zhang
- first_name: X
full_name: Jiang, X
last_name: Jiang
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: H
full_name: Luo, H
last_name: Luo
- first_name: K
full_name: Li, K
last_name: Li
- first_name: J
full_name: Yang, J
last_name: Yang
- first_name: Q
full_name: Luo, Q
last_name: Luo
- first_name: L
full_name: Li, L
last_name: Li
- first_name: S
full_name: Peng, S
last_name: Peng
- first_name: H
full_name: Huang, H
last_name: Huang
- first_name: Z
full_name: Zuo, Z
last_name: Zuo
- first_name: C
full_name: Liu, C
last_name: Liu
- first_name: L
full_name: Wang, L
last_name: Wang
- first_name: C
full_name: Li, C
last_name: Li
- first_name: X
full_name: He, X
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Du, Y
last_name: Du
citation:
ama: Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1
transcription for rice drought avoidance. Plant, Cell & Environment.
2021;44(6):1846-1857. doi:10.1111/pce.14029
apa: Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2
transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance.
Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029
chicago: Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon
Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant,
Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.
ieee: Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no.
6. Wiley, pp. 1846–1857, 2021.
ista: Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han
L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H,
Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X,
Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.
mla: Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription
for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no.
6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.
short: Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian,
X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X.
Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo,
C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment
44 (2021) 1846–1857.
date_created: 2021-02-24T10:07:21Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-11-07T08:18:36Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/pce.14029
external_id:
isi:
- '000625398600001'
pmid:
- '33576018'
file:
- access_level: open_access
checksum: a812418fede076741c9c4dc07f317068
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:02:11Z
date_updated: 2023-11-02T17:02:11Z
file_id: '14481'
file_name: Zhao PlantCellEnv 2021_accepted.pdf
file_size: 8437528
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:02:11Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1846-1857
pmid: 1
publication: Plant, Cell & Environment
publication_identifier:
eissn:
- 1365-3040
issn:
- 0140-7791
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought
avoidance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2021'
...
---
_id: '9192'
abstract:
- lang: eng
text: Here are the research data underlying the publication " Effects of fine-scale
population structure on inbreeding in a long-term study of snapdragons (Antirrhinum
majus)." Further information are summed up in the README document.
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- 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: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2021). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2021.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9192.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2021).
contributor:
- contributor_type: project_member
first_name: Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_leader
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2021-02-24T17:49:21Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '26'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:9192
file:
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checksum: f85537815809a8a4b7da9d01163f88c0
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creator: larathoo
date_created: 2021-02-24T17:45:13Z
date_updated: 2021-02-24T17:45:13Z
file_id: '9193'
file_name: Data_Code.zip
file_size: 5934452
relation: main_file
success: 1
file_date_updated: 2021-02-24T17:45:13Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: used_in_publication
status: public
- id: '11321'
relation: later_version
status: public
- id: '8254'
relation: earlier_version
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9200'
abstract:
- lang: eng
text: Formal design of embedded and cyber-physical systems relies on mathematical
modeling. In this paper, we consider the model class of hybrid automata whose
dynamics are defined by affine differential equations. Given a set of time-series
data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting
behavior that is close to the data, up to a specified precision, and changes in
synchrony with the data. A fundamental problem in our synthesis algorithm is to
check membership of a time series in a hybrid automaton. Our solution integrates
reachability and optimization techniques for affine dynamical systems to obtain
both a sufficient and a necessary condition for membership, combined in a refinement
framework. The algorithm processes one time series at a time and hence can be
interrupted, provide an intermediate result, and be resumed. We report experimental
results demonstrating the applicability of our synthesis approach.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 754411.
article_processing_charge: No
arxiv: 1
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000-0003-2936-5719
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with
affine dynamics from time-series data. In: HSCC ’21: Proceedings of the 24th
International Conference on Hybrid Systems: Computation and Control. Association
for Computing Machinery; 2021:2102.12734. doi:10.1145/3447928.3456704'
apa: 'Garcia Soto, M., Henzinger, T. A., & Schilling, C. (2021). Synthesis of
hybrid automata with affine dynamics from time-series data. In HSCC ’21: Proceedings
of the 24th International Conference on Hybrid Systems: Computation and Control
(p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery.
https://doi.org/10.1145/3447928.3456704'
chicago: 'Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis
of Hybrid Automata with Affine Dynamics from Time-Series Data.” In HSCC ’21:
Proceedings of the 24th International Conference on Hybrid Systems: Computation
and Control, 2102.12734. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447928.3456704.'
ieee: 'M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata
with affine dynamics from time-series data,” in HSCC ’21: Proceedings of the
24th International Conference on Hybrid Systems: Computation and Control,
Nashville, TN, United States, 2021, p. 2102.12734.'
ista: 'Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata
with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th
International Conference on Hybrid Systems: Computation and Control. HSCC: International
Conference on Hybrid Systems Computation and Control, 2102.12734.'
mla: 'Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics
from Time-Series Data.” HSCC ’21: Proceedings of the 24th International Conference
on Hybrid Systems: Computation and Control, Association for Computing Machinery,
2021, p. 2102.12734, doi:10.1145/3447928.3456704.'
short: 'M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings
of the 24th International Conference on Hybrid Systems: Computation and Control,
Association for Computing Machinery, 2021, p. 2102.12734.'
conference:
end_date: 2021-05-21
location: Nashville, TN, United States
name: 'HSCC: International Conference on Hybrid Systems Computation and Control'
start_date: 2021-05-19
date_created: 2021-02-26T16:30:39Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-07T13:49:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3447928.3456704
ec_funded: 1
external_id:
arxiv:
- '2102.12734'
isi:
- '000932821700028'
file:
- access_level: open_access
checksum: 4c1202c1abf71384c3ee6fea88c2f80e
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T13:53:22Z
date_updated: 2021-05-25T13:53:22Z
file_id: '9424'
file_name: 2021_HSCC_Soto.pdf
file_size: 1474786
relation: main_file
success: 1
file_date_updated: 2021-05-25T13:53:22Z
has_accepted_license: '1'
isi: 1
keyword:
- hybrid automaton
- membership
- system identification
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '2102.12734'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'HSCC ''21: Proceedings of the 24th International Conference on Hybrid
Systems: Computation and Control'
publication_identifier:
isbn:
- '9781450383394'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis of hybrid automata with affine dynamics from time-series data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9205'
abstract:
- lang: eng
text: Cryo-EM grid preparation is an important bottleneck in protein structure determination,
especially for membrane proteins, typically requiring screening of a large number
of conditions. We systematically investigated the effects of buffer components,
blotting conditions and grid types on the outcome of grid preparation of five
different membrane protein samples. Aggregation was the most common type of problem
which was addressed by changing detergents, salt concentration or reconstitution
of proteins into nanodiscs or amphipols. We show that the optimal concentration
of detergent is between 0.05 and 0.4% and that the presence of a low concentration
of detergent with a high critical micellar concentration protects the proteins
from denaturation at the air-water interface. Furthermore, we discuss the strategies
for achieving an adequate ice thickness, particle coverage and orientation distribution
on free ice and on support films. Our findings provide a clear roadmap for comprehensive
screening of conditions for cryo-EM grid preparation of membrane proteins.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank the Electron Microscopy Facilities at the Institute of Science
and Technology Austria and at the Vienna Biocenter for providing access and training
for the electron microscopes. This project has received funding from the European
Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement no. 665385 .
article_number: '102139'
article_processing_charge: No
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins.
iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139
apa: Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization
for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139
chicago: Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization
for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139.
ieee: D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for
membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021.
ista: Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane
proteins. iScience. 24(3), 102139.
mla: Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience,
vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139.
short: D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).
date_created: 2021-02-28T23:01:24Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T13:54:06Z
day: '19'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.isci.2021.102139
ec_funded: 1
external_id:
isi:
- '000631646000012'
pmid:
- '33665558'
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creator: dernst
date_created: 2021-03-03T07:38:14Z
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language:
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month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: iScience
publication_identifier:
eissn:
- '25890042'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM grid optimization for membrane proteins
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: 24
year: '2021'
...
---
_id: '9206'
abstract:
- lang: eng
text: 'The precise engineering of thermoelectric materials using nanocrystals as
their building blocks has proven to be an excellent strategy to increase energy
conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS
colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline
PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb
significantly influences the size, geometry, crystal lattice and especially the
carrier concentration of PbS. The increase of charge carrier concentration achieved
with the introduction of Sb translates into an increase of the electrical and
thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb
nanomaterial were characterized by two-fold higher thermoelectric figures of merit
than undoped PbS. '
acknowledgement: "This work was supported by European Regional Development Funds and
the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges
support from the US National Science Foundation under grant No. DMR-1748188. DC
acknowledges support from COLCIENCIAS under project 120480863414. "
article_number: '853'
article_processing_charge: No
article_type: original
author:
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Kaya
full_name: Wei, Kaya
last_name: Wei
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Taisiia
full_name: Berestok, Taisiia
last_name: Berestok
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: George S.
full_name: Nolas, George S.
last_name: Nolas
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric
properties of Sb-doped PbS nanocrystal building blocks. Materials. 2021;14(4).
doi:10.3390/ma14040853
apa: Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021).
Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal
building blocks. Materials. MDPI. https://doi.org/10.3390/ma14040853
chicago: Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia
Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties
of Sb-Doped PbS Nanocrystal Building Blocks.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14040853.
ieee: D. Cadavid et al., “Synthesis, bottom up assembly and thermoelectric
properties of Sb-doped PbS nanocrystal building blocks,” Materials, vol.
14, no. 4. MDPI, 2021.
ista: Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel
A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties
of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853.
mla: Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties
of Sb-Doped PbS Nanocrystal Building Blocks.” Materials, vol. 14, no. 4,
853, MDPI, 2021, doi:10.3390/ma14040853.
short: D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez,
A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021).
date_created: 2021-02-28T23:01:24Z
date_published: 2021-02-10T00:00:00Z
date_updated: 2023-08-07T13:50:03Z
day: '10'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.3390/ma14040853
external_id:
isi:
- '000624094100001'
file:
- access_level: open_access
checksum: 76d6c7f97b810ce504ab151c9bf3524e
content_type: application/pdf
creator: dernst
date_created: 2021-03-03T07:32:01Z
date_updated: 2021-03-03T07:32:01Z
file_id: '9218'
file_name: 2021_Materials_Cadavid.pdf
file_size: 2722517
relation: main_file
success: 1
file_date_updated: 2021-03-03T07:32:01Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Materials
publication_identifier:
eissn:
- 1996-1944
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS
nanocrystal building blocks
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: 14
year: '2021'
...