---
_id: '7882'
abstract:
- lang: eng
text: A few-body cluster is a building block of a many-body system in a gas phase
provided the temperature at most is of the order of the binding energy of this
cluster. Here we illustrate this statement by considering a system of tubes filled
with dipolar distinguishable particles. We calculate the partition function, which
determines the probability to find a few-body cluster at a given temperature.
The input for our calculations—the energies of few-body clusters—is estimated
using the harmonic approximation. We first describe and demonstrate the validity
of our numerical procedure. Then we discuss the results featuring melting of the
zero-temperature many-body state into a gas of free particles and few-body clusters.
For temperature higher than its binding energy threshold, the dimers overwhelmingly
dominate the ensemble, where the remaining probability is in free particles. At
very high temperatures free (harmonic oscillator trap-bound) particle dominance
is eventually reached. This structure evolution appears both for one and two particles
in each layer providing crucial information about the behavior of ultracold dipolar
gases. The investigation addresses the transition region between few- and many-body
physics as a function of temperature using a system of ten dipoles in five tubes.
article_number: '484'
article_processing_charge: No
article_type: original
author:
- first_name: Jeremy R.
full_name: Armstrong, Jeremy R.
last_name: Armstrong
- first_name: Aksel S.
full_name: Jensen, Aksel S.
last_name: Jensen
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Nikolaj T.
full_name: Zinner, Nikolaj T.
last_name: Zinner
citation:
ama: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes
of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484
apa: Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020).
Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484
chicago: Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T.
Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI,
2020. https://doi.org/10.3390/math8040484.
ieee: J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in
separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020.
ista: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated
tubes of tilted dipoles. Mathematics. 8(4), 484.
mla: Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.”
Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484.
short: J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).
date_created: 2020-05-24T22:01:00Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2023-08-21T06:23:36Z
day: '01'
ddc:
- '510'
department:
- _id: MiLe
doi: 10.3390/math8040484
ec_funded: 1
external_id:
isi:
- '000531824100024'
file:
- access_level: open_access
checksum: a05a7df724522203d079673a0d4de4bc
content_type: application/pdf
creator: dernst
date_created: 2020-05-25T14:42:22Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7887'
file_name: 2020_Mathematics_Armstrong.pdf
file_size: 990540
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Mathematics
publication_identifier:
eissn:
- '22277390'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clusters in separated tubes of tilted dipoles
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: 8
year: '2020'
...
---
_id: '7804'
abstract:
- lang: eng
text: Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17)
modulates neural circuit function. We investigate IL-17 signaling in neurons,
and the extent it can alter organismal phenotypes. We combine immunoprecipitation
and mass spectrometry to biochemically characterize endogenous signaling complexes
that function downstream of IL-17 receptors in C. elegans neurons. We identify
the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling
from many immune receptors in mammals, but was not previously implicated in IL-17
signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs
of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1
is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1
signaling regulates multiple phenotypes, including escape behavior, associative
learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating
neural circuit function downstream of IL-17 to remodel physiology and behavior.
article_number: '2099'
article_processing_charge: No
article_type: original
author:
- first_name: Sean M.
full_name: Flynn, Sean M.
last_name: Flynn
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Stephen
full_name: Barratt, Stephen
last_name: Barratt
- first_name: Alastair
full_name: Crisp, Alastair
last_name: Crisp
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Sew Yeu
full_name: Peak-Chew, Sew Yeu
last_name: Peak-Chew
- first_name: Farida
full_name: Begum, Farida
last_name: Begum
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to
regulate C. elegans behavior, immunity and longevity. Nature Communications.
2020;11. doi:10.1038/s41467-020-15872-y
apa: Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., …
de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans
behavior, immunity and longevity. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-15872-y
chicago: Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair
Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario
de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior,
Immunity and Longevity.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-15872-y.
ieee: S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C.
elegans behavior, immunity and longevity,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum
F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C.
elegans behavior, immunity and longevity. Nature Communications. 11, 2099.
mla: Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C.
Elegans Behavior, Immunity and Longevity.” Nature Communications, vol.
11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y.
short: S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew,
F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).
date_created: 2020-05-10T22:00:47Z
date_published: 2020-04-29T00:00:00Z
date_updated: 2023-08-21T06:21:14Z
day: '29'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1038/s41467-020-15872-y
external_id:
isi:
- '000531855500029'
file:
- access_level: open_access
checksum: dce367abf2c1a1d15f58fe6f7de82893
content_type: application/pdf
creator: dernst
date_created: 2020-05-11T10:36:33Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7817'
file_name: 2020_NatureComm_Flynn.pdf
file_size: 4609120
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity
and longevity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '7875'
abstract:
- lang: eng
text: 'Cells navigating through complex tissues face a fundamental challenge: while
multiple protrusions explore different paths, the cell needs to avoid entanglement.
How a cell surveys and then corrects its own shape is poorly understood. Here,
we demonstrate that spatially distinct microtubule dynamics regulate amoeboid
cell migration by locally promoting the retraction of protrusions. In migrating
dendritic cells, local microtubule depolymerization within protrusions remote
from the microtubule organizing center triggers actomyosin contractility controlled
by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin
localization, thereby causing two effects that rate-limit locomotion: (1) impaired
cell edge coordination during path finding and (2) defective adhesion resolution.
Compromised shape control is particularly hindering in geometrically complex microenvironments,
where it leads to entanglement and ultimately fragmentation of the cell body.
We thus demonstrate that microtubules can act as a proprioceptive device: they
sense cell shape and control actomyosin retraction to sustain cellular coherence.'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
acknowledgement: "The authors thank the Scientific Service Units (Life Sciences, Bioimaging,
Preclinical) of the Institute of Science and Technology Austria for excellent support.
This work was funded by the European Research Council (ERC StG 281556 and CoG 724373),
two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20
to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O.
Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from
the People Program (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734)
and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014)
co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s
Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian
Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and
Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry
of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European
Funds for Social and Regional Development."
article_number: e201907154
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Irute
full_name: Girkontaite, Irute
last_name: Girkontaite
- first_name: Kerry
full_name: Tedford, Kerry
last_name: Tedford
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Oliver
full_name: Thorn-Seshold, Oliver
last_name: Thorn-Seshold
- first_name: Dirk
full_name: Trauner, Dirk
id: E8F27F48-3EBA-11E9-92A1-B709E6697425
last_name: Trauner
- first_name: Hans
full_name: Häcker, Hans
last_name: Häcker
- first_name: Klaus Dieter
full_name: Fischer, Klaus Dieter
last_name: Fischer
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- 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: Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape
and coherence in amoeboid migrating cells. The Journal of Cell Biology.
2020;219(6). doi:10.1083/jcb.201907154
apa: Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin,
J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in
amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.201907154
chicago: Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry
Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular
Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology.
Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.
ieee: A. Kopf et al., “Microtubules control cellular shape and coherence
in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no.
6. Rockefeller University Press, 2020.
ista: Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold
O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control
cellular shape and coherence in amoeboid migrating cells. The Journal of Cell
Biology. 219(6), e201907154.
mla: Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in
Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6,
e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154.
short: A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin,
O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt,
The Journal of Cell Biology 219 (2020).
date_created: 2020-05-24T22:00:56Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-21T06:28:17Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
- _id: NanoFab
doi: 10.1083/jcb.201907154
ec_funded: 1
external_id:
isi:
- '000538141100020'
pmid:
- '32379884'
file:
- access_level: open_access
checksum: cb0b9c77842ae1214caade7b77e4d82d
content_type: application/pdf
creator: dernst
date_created: 2020-11-24T13:25:13Z
date_updated: 2020-11-24T13:25:13Z
file_id: '8801'
file_name: 2020_JCellBiol_Kopf.pdf
file_size: 7536712
relation: main_file
success: 1
file_date_updated: 2020-11-24T13:25:13Z
has_accepted_license: '1'
intvolume: ' 219'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W 1250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: The Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microtubules control cellular shape and coherence in amoeboid migrating cells
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: 219
year: '2020'
...
---
_id: '7888'
abstract:
- lang: eng
text: Embryonic stem cell cultures are thought to self-organize into embryoid bodies,
able to undergo symmetry-breaking, germ layer specification and even morphogenesis.
Yet, it is unclear how to reconcile this remarkable self-organization capacity
with classical experiments demonstrating key roles for extrinsic biases by maternal
factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish
embryonic tissue explants, prepared prior to germ layer induction and lacking
extraembryonic tissues, can specify all germ layers and form a seemingly complete
mesendoderm anlage. Importantly, explant organization requires polarized inheritance
of maternal factors from dorsal-marginal regions of the blastoderm. Moreover,
induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels,
is highly variable in explants, reminiscent of embryos with reduced Nodal signals
from the extraembryonic tissues. Together, these data suggest that zebrafish explants
do not undergo bona fide self-organization, but rather display features of genetically
encoded self-assembly, where intrinsic genetic programs control the emergence
of order.
article_number: e55190
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic
explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190
apa: Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P.
J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190
chicago: Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp
J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.”
ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.
ieee: A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish
embryonic explants undergo genetically encoded self-assembly,” eLife, vol.
9. eLife Sciences Publications, 2020.
ista: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish
embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.
mla: Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically
Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications,
2020, doi:10.7554/elife.55190.
short: A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife
9 (2020).
date_created: 2020-05-25T15:01:40Z
date_published: 2020-04-06T00:00:00Z
date_updated: 2023-08-21T06:25:49Z
day: '06'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.7554/elife.55190
ec_funded: 1
external_id:
isi:
- '000531544400001'
pmid:
- '32250246'
file:
- access_level: open_access
checksum: f6aad884cf706846ae9357fcd728f8b5
content_type: application/pdf
creator: dernst
date_created: 2020-05-25T15:15:43Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7890'
file_name: 2020_eLife_Schauer.pdf
file_size: 7744848
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 266BC5CE-B435-11E9-9278-68D0E5697425
grant_number: LT000429
name: Coordination of mesendoderm fate specification and internalization during
zebrafish gastrulation
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '12891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Zebrafish embryonic explants undergo genetically encoded self-assembly
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7877'
abstract:
- lang: eng
text: The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount
for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS).
Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that
impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this
interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable
fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation.
Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication
inNIPBL, engineered in two different cell lines,alternative translation initiation
yields a form of NIPBL missing N-terminal residues. This form cannot interactwith
MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals
that cohesin loading can occur independently of functional NIPBL/MAU2 complexes
and highlights a novel mechanism protectiveagainst out-of-frame mutations that
is potentially relevant for other genetic conditions.
article_number: '107647'
article_processing_charge: No
article_type: original
author:
- first_name: Ilaria
full_name: Parenti, Ilaria
id: D93538B0-5B71-11E9-AC62-02EBE5697425
last_name: Parenti
- first_name: Farah
full_name: Diab, Farah
last_name: Diab
- first_name: Sara Ruiz
full_name: Gil, Sara Ruiz
last_name: Gil
- first_name: Eskeatnaf
full_name: Mulugeta, Eskeatnaf
last_name: Mulugeta
- first_name: Valentina
full_name: Casa, Valentina
last_name: Casa
- first_name: Riccardo
full_name: Berutti, Riccardo
last_name: Berutti
- first_name: Rutger W.W.
full_name: Brouwer, Rutger W.W.
last_name: Brouwer
- first_name: Valerie
full_name: Dupé, Valerie
last_name: Dupé
- first_name: Juliane
full_name: Eckhold, Juliane
last_name: Eckhold
- first_name: Elisabeth
full_name: Graf, Elisabeth
last_name: Graf
- first_name: Beatriz
full_name: Puisac, Beatriz
last_name: Puisac
- first_name: Feliciano
full_name: Ramos, Feliciano
last_name: Ramos
- first_name: Thomas
full_name: Schwarzmayr, Thomas
last_name: Schwarzmayr
- first_name: Macarena Moronta
full_name: Gines, Macarena Moronta
last_name: Gines
- first_name: Thomas
full_name: Van Staveren, Thomas
last_name: Van Staveren
- first_name: Wilfred F.J.
full_name: Van Ijcken, Wilfred F.J.
last_name: Van Ijcken
- first_name: Tim M.
full_name: Strom, Tim M.
last_name: Strom
- first_name: Juan
full_name: Pié, Juan
last_name: Pié
- first_name: Erwan
full_name: Watrin, Erwan
last_name: Watrin
- first_name: Frank J.
full_name: Kaiser, Frank J.
last_name: Kaiser
- first_name: Kerstin S.
full_name: Wendt, Kerstin S.
last_name: Wendt
citation:
ama: Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization
of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports.
2020;31(7). doi:10.1016/j.celrep.2020.107647
apa: Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt,
K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin
loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2020.107647
chicago: Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina
Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair
the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange
Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647.
ieee: I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization
of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell
Reports, vol. 31, no. 7. Elsevier, 2020.
ista: Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé
V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren
T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2
and NIPBL variants impair the heterodimerization of the cohesin loader subunits
and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.
mla: Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization
of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell
Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647.
short: I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer,
V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines,
T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser,
K.S. Wendt, Cell Reports 31 (2020).
date_created: 2020-05-24T22:00:57Z
date_published: 2020-05-19T00:00:00Z
date_updated: 2023-08-21T06:27:47Z
day: '19'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.celrep.2020.107647
external_id:
isi:
- '000535655200005'
file:
- access_level: open_access
checksum: 64d8f7467731ee5c166b10b939b8310b
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T11:05:01Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7892'
file_name: 2020_CellReports_Parenti.pdf
file_size: 4695682
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader
subunits and cause Cornelia de Lange syndrome
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: 31
year: '2020'
...
---
_id: '7878'
abstract:
- lang: eng
text: Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal
signaling. While their function is well documented in slices, requirements for
their activation in vivo are poorly understood. We examine this question in adult
mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons
(MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes
beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s
and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases
Cai rises associated with locomotion. In vitro studies and freeze-fracture electron
microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by
close association of the two classes of receptors. Altogether our results suggest
that mGluR1s, acting in synergy with iGluRs, potently contribute to processing
cerebellar neuronal signaling under physiological conditions.
article_number: e56839
article_processing_charge: No
article_type: original
author:
- first_name: Jin
full_name: Bao, Jin
last_name: Bao
- first_name: Michael
full_name: Graupner, Michael
last_name: Graupner
- first_name: Guadalupe
full_name: Astorga, Guadalupe
last_name: Astorga
- first_name: Thibault
full_name: Collin, Thibault
last_name: Collin
- first_name: Abdelali
full_name: Jalil, Abdelali
last_name: Jalil
- first_name: Dwi Wahyu
full_name: Indriati, Dwi Wahyu
last_name: Indriati
- first_name: Jonathan
full_name: Bradley, Jonathan
last_name: Bradley
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Isabel
full_name: Llano, Isabel
last_name: Llano
citation:
ama: Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic
glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife.
2020;9. doi:10.7554/eLife.56839
apa: Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W.,
… Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate
receptors in cerebellar molecular layer interneurons in vivo. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.56839
chicago: Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali
Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano.
“Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar
Molecular Layer Interneurons in Vivo.” ELife. eLife Sciences Publications,
2020. https://doi.org/10.7554/eLife.56839.
ieee: J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate
receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol.
9. eLife Sciences Publications, 2020.
ista: Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto
R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors
in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.
mla: Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate
Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol.
9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839.
short: J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley,
R. Shigemoto, I. Llano, ELife 9 (2020).
date_created: 2020-05-24T22:00:58Z
date_published: 2020-05-13T00:00:00Z
date_updated: 2023-08-21T06:26:50Z
day: '13'
ddc:
- '570'
department:
- _id: RySh
doi: 10.7554/eLife.56839
external_id:
isi:
- '000535191600001'
pmid:
- '32401196'
file:
- access_level: open_access
checksum: 8ea99bb6660cc407dbdb00c173b01683
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T09:34:54Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7891'
file_name: 2020_eLife_Bao.pdf
file_size: 4832050
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar
molecular layer interneurons in vivo
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7880'
abstract:
- lang: eng
text: 'Following its evoked release, dopamine (DA) signaling is rapidly terminated
by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT).
DAT surface availability is dynamically regulated by endocytic trafficking, and
direct protein kinase C (PKC) activation acutely diminishes DAT surface expression
by accelerating DAT internalization. Previous cell line studies demonstrated that
PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases
a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT.
However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis
in DAergic terminals or whether there are region- and/or sex-dependent differences
in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls
PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important
questions. Ex vivo studies revealed that PKC activation acutely decreased DAT
surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated,
conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular
distribution in DAergic terminals from female ventral, but not dorsal, striatum.
Further, Rit2 was required for PKC-stimulated DAT internalization in both male
and female ventral striatum. FRET and surface pulldown studies in cell lines revealed
that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus
is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization.
Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate
PKC-stimulated DAT endocytosis. Together, our data provide greater insight into
mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected
region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic
terminals. '
article_processing_charge: No
article_type: original
author:
- first_name: Rita R.
full_name: Fagan, Rita R.
last_name: Fagan
- first_name: Patrick J.
full_name: Kearney, Patrick J.
last_name: Kearney
- first_name: Carolyn G.
full_name: Sweeney, Carolyn G.
last_name: Sweeney
- first_name: Dino
full_name: Luethi, Dino
last_name: Luethi
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Klaus
full_name: Schicker, Klaus
last_name: Schicker
- first_name: Brian S.
full_name: Alejandro, Brian S.
last_name: Alejandro
- first_name: Lauren C.
full_name: O'Connor, Lauren C.
last_name: O'Connor
- first_name: Harald H.
full_name: Sitte, Harald H.
last_name: Sitte
- first_name: Haley E.
full_name: Melikian, Haley E.
last_name: Melikian
citation:
ama: 'Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking
and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological
Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628'
apa: 'Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp,
F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking
and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological
Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628'
chicago: 'Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne
E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald
H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase:
Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry.
ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628.'
ieee: 'R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase:
Mechanism of action and in vivo impact,” Journal of Biological Chemistry,
vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.'
ista: 'Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker
K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter
trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of
Biological Chemistry. 295(16), 5229–5244.'
mla: 'Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase:
Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry,
vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628.'
short: R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp,
K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal
of Biological Chemistry 295 (2020) 5229–5244.
date_created: 2020-05-24T22:00:59Z
date_published: 2020-04-17T00:00:00Z
date_updated: 2023-08-21T06:26:22Z
day: '17'
department:
- _id: SaSi
doi: 10.1074/jbc.RA120.012628
external_id:
isi:
- '000530288000006'
pmid:
- '32132171'
intvolume: ' 295'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://escholarship.umassmed.edu/oapubs/4187
month: '04'
oa: 1
oa_version: Submitted Version
page: 5229-5244
pmid: 1
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083351X
issn:
- '00219258'
publication_status: published
publisher: ASBMB Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and
in vivo impact'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 295
year: '2020'
...
---
_id: '7876'
abstract:
- lang: eng
text: 'In contrast to lymph nodes, the lymphoid regions of the spleen—the white
pulp—are located deep within the organ, yielding the trafficking paths of T cells
in the white pulp largely invisible. In an intravital microscopy tour de force
reported in this issue of Immunity, Chauveau et al. show that T cells perform
unidirectional, perivascular migration through the enigmatic marginal zone bridging
channels. '
article_processing_charge: No
article_type: original
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
citation:
ama: 'Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp.
Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020'
apa: 'Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute
to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020'
chicago: 'Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute
to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.'
ieee: 'M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the
white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.'
ista: 'Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white
pulp. Immunity. 52(5), 721–723.'
mla: 'Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute
to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23,
doi:10.1016/j.immuni.2020.04.020.'
short: M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.
date_created: 2020-05-24T22:00:57Z
date_published: 2020-05-19T00:00:00Z
date_updated: 2023-08-21T06:27:18Z
day: '19'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2020.04.020
external_id:
isi:
- '000535371100002'
intvolume: ' 52'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf
month: '05'
oa: 1
oa_version: Published Version
page: 721-723
publication: Immunity
publication_identifier:
eissn:
- '10974180'
issn:
- '10747613'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'T cells: Bridge-and-channel commute to the white pulp'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...
---
_id: '7909'
abstract:
- lang: eng
text: Cell migration entails networks and bundles of actin filaments termed lamellipodia
and microspikes or filopodia, respectively, as well as focal adhesions, all of
which recruit Ena/VASP family members hitherto thought to antagonize efficient
cell motility. However, we find these proteins to act as positive regulators of
migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP
proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture,
as evidenced by changed network geometry as well as reduction of filament length
and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping
protein accumulation. Loss of Ena/VASP function also abolished the formation of
microspikes normally embedded in lamellipodia, but not of filopodia capable of
emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated
adhesion accompanied by reduced traction forces exerted through these structures.
Our data thus uncover novel Ena/VASP functions of these actin polymerases that
are fully consistent with their promotion of cell migration.
article_number: e55351
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Damiano-Guercio, Julia
last_name: Damiano-Guercio
- first_name: Laëtitia
full_name: Kurzawa, Laëtitia
last_name: Kurzawa
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Matthias
full_name: Schaks, Matthias
last_name: Schaks
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Thomas
full_name: Pokrant, Thomas
last_name: Pokrant
- first_name: Stefan
full_name: Brühmann, Stefan
last_name: Brühmann
- first_name: Joern
full_name: Linkner, Joern
last_name: Linkner
- first_name: Laurent
full_name: Blanchoin, Laurent
last_name: Blanchoin
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
citation:
ama: Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes
with lamellipodium architecture, motility and integrin-dependent adhesion. eLife.
2020;9. doi:10.7554/eLife.55351
apa: Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova,
M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture,
motility and integrin-dependent adhesion. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.55351
chicago: Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev,
Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes
with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351.
ieee: J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium
architecture, motility and integrin-dependent adhesion,” eLife, vol. 9.
eLife Sciences Publications, 2020.
ista: Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M,
Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020.
Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent
adhesion. eLife. 9, e55351.
mla: Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium
Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9,
e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351.
short: J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova,
T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix,
ELife 9 (2020).
date_created: 2020-05-31T22:00:49Z
date_published: 2020-05-11T00:00:00Z
date_updated: 2023-08-21T06:32:25Z
day: '11'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.55351
ec_funded: 1
external_id:
isi:
- '000537208000001'
file:
- access_level: open_access
checksum: d33bd4441b9a0195718ce1ba5d2c48a6
content_type: application/pdf
creator: dernst
date_created: 2020-06-02T10:35:37Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7914'
file_name: 2020_eLife_Damiano_Guercio.pdf
file_size: 10535713
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent
adhesion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '7908'
abstract:
- lang: eng
text: Volatile anesthetics are widely used for surgery, but neuronal mechanisms
of anesthesia remain unidentified. At the calyx of Held in brainstem slices from
rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing
the release probability and the number of readily releasable vesicles. In presynaptic
recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated
exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization,
whereas it inhibited exocytosis evoked by a prolonged depolarization via directly
blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic
depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia
is likely mediated by distinct dual mechanisms, depending on input frequencies.
In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane
impaired the fidelity of repetitive spike transmission, more strongly at higher
frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited
monosynaptic corticocortical spike transmission, preferentially at a higher frequency.
We conclude that dual presynaptic mechanisms operate for the anesthetic action
of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass
filtering role in spike transmission at central excitatory synapses.
article_processing_charge: No
article_type: original
author:
- first_name: Han Ying
full_name: Wang, Han Ying
last_name: Wang
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Takayuki
full_name: Yamashita, Takayuki
last_name: Yamashita
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory
neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of
Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020
apa: Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent
block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020
chicago: Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi.
“Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual
Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience,
2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020.
ieee: H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent
block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,”
Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp.
4103–4115, 2020.
ista: Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block
of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms.
Journal of Neuroscience. 40(21), 4103–4115.
mla: Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission
by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience,
vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020.
short: H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience
40 (2020) 4103–4115.
date_created: 2020-05-31T22:00:48Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-21T06:31:25Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.2946-19.2020
external_id:
isi:
- '000535694700004'
file:
- access_level: open_access
checksum: 6571607ea9036154b67cc78e848a7f7d
content_type: application/pdf
creator: dernst
date_created: 2020-06-02T09:12:16Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7912'
file_name: 2020_JourNeuroscience_Wang.pdf
file_size: 3817360
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4103-4115
publication: Journal of Neuroscience
publication_identifier:
eissn:
- '15292401'
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequency-dependent block of excitatory neurotransmission by isoflurane via
dual presynaptic mechanisms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2020'
...
---
_id: '7931'
abstract:
- lang: eng
text: In the course of sample preparation for Next Generation Sequencing (NGS),
DNA is fragmented by various methods. Fragmentation shows a persistent bias with
regard to the cleavage rates of various dinucleotides. With the exception of CpG
dinucleotides the previously described biases were consistent with results of
the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides
including the methylated CpG and unmethylated CpG dinucleotides using data of
the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that
the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides.
Using this information, we developed a classifier for distinguishing cancer and
healthy tissues based on their CpG islands statuses of the fragmentation. A simple
Support Vector Machine classifier based on this algorithm shows an accuracy of
84%. The proposed method allows the detection of epigenetic markers purely based
on mechanochemical DNA fragmentation, which can be detected by a simple analysis
of the NGS sequencing data.
article_number: '8635'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A.
full_name: Uroshlev, Leonid A.
last_name: Uroshlev
- first_name: Eldar T.
full_name: Abdullaev, Eldar T.
last_name: Abdullaev
- first_name: Iren R.
full_name: Umarova, Iren R.
last_name: Umarova
- first_name: Irina A.
full_name: Il’Icheva, Irina A.
last_name: Il’Icheva
- first_name: Larisa A.
full_name: Panchenko, Larisa A.
last_name: Panchenko
- first_name: Robert V.
full_name: Polozov, Robert V.
last_name: Polozov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yury D.
full_name: Nechipurenko, Yury D.
last_name: Nechipurenko
- first_name: Sergei L.
full_name: Grokhovsky, Sergei L.
last_name: Grokhovsky
citation:
ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of
the methylation level of CpG islands from NGS data. Scientific Reports.
2020;10. doi:10.1038/s41598-020-65406-1
apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko,
L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports.
Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva,
Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko,
and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level
of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020.
https://doi.org/10.1038/s41598-020-65406-1.
ieee: L. A. Uroshlev et al., “A method for identification of the methylation
level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer
Nature, 2020.
ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov
RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports. 10,
8635.
mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation
Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635,
Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko,
R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports
10 (2020).
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2023-08-21T07:00:17Z
day: '25'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-020-65406-1
external_id:
isi:
- '000560774200007'
file:
- access_level: open_access
checksum: 099e51611a5b7ca04244d03b2faddf33
content_type: application/pdf
creator: dernst
date_created: 2020-06-08T06:27:32Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7947'
file_name: 2020_ScientificReports_Uroshlev.pdf
file_size: 1001724
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
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: A method for identification of the methylation level of CpG islands from NGS
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '7933'
abstract:
- lang: eng
text: We study a mobile quantum impurity, possessing internal rotational degrees
of freedom, confined to a ring in the presence of a many-particle bosonic bath.
By considering the recently introduced rotating polaron problem, we define the
Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied
by means of a variational ansatz in the truncated Fock space. The corresponding
spectrum indicates that there emerges a coupling between the internal and orbital
angular momenta of the impurity as a consequence of the phonon exchange. We interpret
the coupling as a phonon-mediated spin-orbit coupling and quantify it by using
a correlation function between the internal and the orbital angular momentum operators.
The strong-coupling regime is investigated within the Pekar approach, and it is
shown that the correlation function of the ground state shows a kink at a critical
coupling, that is explained by a sharp transition from the noninteracting state
to the states that exhibit strong interaction with the surroundings. The results
might find applications in such fields as spintronics or topological insulators
where spin-orbit coupling is of crucial importance.
article_number: '184104 '
article_processing_charge: No
article_type: original
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
citation:
ama: Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by
a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104
apa: Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit
coupling mediated by a bosonic environment. Physical Review B. American
Physical Society. https://doi.org/10.1103/PhysRevB.101.184104
chicago: Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit
Coupling Mediated by a Bosonic Environment.” Physical Review B. American
Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104.
ieee: M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated
by a bosonic environment,” Physical Review B, vol. 101, no. 18. American
Physical Society, 2020.
ista: Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated
by a bosonic environment. Physical Review B. 101(18), 184104.
mla: Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic
Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical
Society, 2020, doi:10.1103/PhysRevB.101.184104.
short: M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).
date_created: 2020-06-07T22:00:52Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2023-08-21T07:05:15Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.101.184104
ec_funded: 1
external_id:
arxiv:
- '1912.03092'
isi:
- '000530754700003'
intvolume: ' 101'
isi: 1
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.03092
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthetic spin-orbit coupling mediated by a bosonic environment
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 101
year: '2020'
...
---
_id: '7942'
abstract:
- lang: eng
text: An understanding of the missing antinodal electronic excitations in the pseudogap
state is essential for uncovering the physics of the underdoped cuprate high-temperature
superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed
thus far, however, have been unable to discern whether the antinodal states are
rendered unobservable due to their damping or whether they vanish due to their
gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two
scenarios by using quantum oscillations to examine whether the small Fermi surface
pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24,
exists in isolation against a majority of completely gapped density of states
spanning the antinodes, or whether it is thermodynamically coupled to a background
of ungapped antinodal states. We find that quantum oscillations associated with
the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic
of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This
finding reveals that the antinodal states are destroyed by a hard gap that extends
over the majority of the Brillouin zone, placing strong constraints on a drastic
underlying origin of quasiparticle disappearance over almost the entire Brillouin
zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18.
acknowledgement: M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society,
the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant
no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European
Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme
Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge
support from the National Key Research and Development Program of China (grant no.
2016YFA0401704). A portion of this work was performed at the National High Magnetic
Field Laboratory, which is supported by the National Science Foundation Cooperative
Agreement no. DMR-1644779, the state of Florida and the US Department of Energy.
Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science
of 100 T’ programme.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Máté
full_name: Hartstein, Máté
last_name: Hartstein
- first_name: Yu Te
full_name: Hsu, Yu Te
last_name: Hsu
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Juan
full_name: Porras, Juan
last_name: Porras
- first_name: Toshinao
full_name: Loew, Toshinao
last_name: Loew
- first_name: Matthieu Le
full_name: Tacon, Matthieu Le
last_name: Tacon
- first_name: Huakun
full_name: Zuo, Huakun
last_name: Zuo
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Zengwei
full_name: Zhu, Zengwei
last_name: Zhu
- first_name: Mun K.
full_name: Chan, Mun K.
last_name: Chan
- first_name: Ross D.
full_name: Mcdonald, Ross D.
last_name: Mcdonald
- first_name: Gilbert G.
full_name: Lonzarich, Gilbert G.
last_name: Lonzarich
- first_name: Bernhard
full_name: Keimer, Bernhard
last_name: Keimer
- first_name: Suchitra E.
full_name: Sebastian, Suchitra E.
last_name: Sebastian
- first_name: Neil
full_name: Harrison, Neil
last_name: Harrison
citation:
ama: Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum
oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature
Physics. 2020;16:841-847. doi:10.1038/s41567-020-0910-0
apa: Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L.,
… Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in
the pseudogap regime of underdoped high-Tc superconductors. Nature Physics.
Springer Nature. https://doi.org/10.1038/s41567-020-0910-0
chicago: Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew,
Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum
Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature
Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0910-0.
ieee: M. Hartstein et al., “Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors,” Nature Physics,
vol. 16. Springer Nature, pp. 841–847, 2020.
ista: Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J,
Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N.
2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime
of underdoped high-Tc superconductors. Nature Physics. 16, 841–847.
mla: Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations
in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics,
vol. 16, Springer Nature, 2020, pp. 841–47, doi:10.1038/s41567-020-0910-0.
short: M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo,
J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian,
N. Harrison, Nature Physics 16 (2020) 841–847.
date_created: 2020-06-07T22:00:56Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2023-08-21T07:06:49Z
day: '01'
department:
- _id: KiMo
doi: 10.1038/s41567-020-0910-0
external_id:
arxiv:
- '2005.14123'
isi:
- '000535464400005'
intvolume: ' 16'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.14123
month: '08'
oa: 1
oa_version: Preprint
page: 841-847
publication: Nature Physics
publication_identifier:
eissn:
- '17452481'
issn:
- '17452473'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9708'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Hard antinodal gap revealed by quantum oscillations in the pseudogap regime
of underdoped high-Tc superconductors
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2020'
...
---
_id: '7948'
abstract:
- lang: eng
text: In agricultural systems, nitrate is the main source of nitrogen available
for plants. Besides its role as a nutrient, nitrate has been shown to act as a
signal molecule for plant growth, development and stress responses. In Arabidopsis,
the NRT1.1 nitrate transceptor represses lateral root (LR) development at low
nitrate availability by promoting auxin basipetal transport out of the LR primordia
(LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator
of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected
to repress local auxin biosynthesis and thus to reduce acropetal auxin supply
to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin
influx carrier, thus preventing cell wall remodeling required for overlying tissues
separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3
are suppressed at high nitrate availability, resulting in the nitrate induction
of TAR2 and LAX3 expression that is required for optimal stimulation of LR development
by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately
controls several crucial auxin-associated processes required for LRP development,
and as a consequence that NRT1.1 plays a much more integrated role than previously
anticipated in regulating the nitrate response of root system architecture.
article_processing_charge: No
article_type: original
author:
- first_name: A
full_name: Maghiaoui, A
last_name: Maghiaoui
- first_name: E
full_name: Bouguyon, E
last_name: Bouguyon
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: F
full_name: Perrine-Walker, F
last_name: Perrine-Walker
- first_name: C
full_name: Alcon, C
last_name: Alcon
- first_name: G
full_name: Krouk, G
last_name: Krouk
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: P
full_name: Nacry, P
last_name: Nacry
- first_name: A
full_name: Gojon, A
last_name: Gojon
- first_name: L
full_name: Bach, L
last_name: Bach
citation:
ama: Maghiaoui A, Bouguyon E, Cuesta C, et al. The Arabidopsis NRT1.1 transceptor
coordinately controls auxin biosynthesis and transport to regulate root branching
in response to nitrate. Journal of Experimental Botany. 2020;71(15):4480-4494.
doi:10.1093/jxb/eraa242
apa: Maghiaoui, A., Bouguyon, E., Cuesta, C., Perrine-Walker, F., Alcon, C., Krouk,
G., … Bach, L. (2020). The Arabidopsis NRT1.1 transceptor coordinately controls
auxin biosynthesis and transport to regulate root branching in response to nitrate.
Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa242
chicago: Maghiaoui, A, E Bouguyon, Candela Cuesta, F Perrine-Walker, C Alcon, G
Krouk, Eva Benková, P Nacry, A Gojon, and L Bach. “The Arabidopsis NRT1.1 Transceptor
Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching
in Response to Nitrate.” Journal of Experimental Botany. Oxford University
Press, 2020. https://doi.org/10.1093/jxb/eraa242.
ieee: A. Maghiaoui et al., “The Arabidopsis NRT1.1 transceptor coordinately
controls auxin biosynthesis and transport to regulate root branching in response
to nitrate,” Journal of Experimental Botany, vol. 71, no. 15. Oxford University
Press, pp. 4480–4494, 2020.
ista: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková
E, Nacry P, Gojon A, Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately
controls auxin biosynthesis and transport to regulate root branching in response
to nitrate. Journal of Experimental Botany. 71(15), 4480–4494.
mla: Maghiaoui, A., et al. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls
Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.”
Journal of Experimental Botany, vol. 71, no. 15, Oxford University Press,
2020, pp. 4480–94, doi:10.1093/jxb/eraa242.
short: A. Maghiaoui, E. Bouguyon, C. Cuesta, F. Perrine-Walker, C. Alcon, G. Krouk,
E. Benková, P. Nacry, A. Gojon, L. Bach, Journal of Experimental Botany 71 (2020)
4480–4494.
date_created: 2020-06-08T10:10:28Z
date_published: 2020-07-25T00:00:00Z
date_updated: 2023-08-21T07:07:30Z
day: '25'
department:
- _id: EvBe
doi: 10.1093/jxb/eraa242
external_id:
isi:
- '000553127600013'
pmid:
- '32428238'
intvolume: ' 71'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inrae.fr/hal-02619371
month: '07'
oa: 1
oa_version: Submitted Version
page: 4480-4494
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
eissn:
- 1460-2431
issn:
- 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis
and transport to regulate root branching in response to nitrate
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 71
year: '2020'
...
---
_id: '7940'
abstract:
- lang: eng
text: We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody
Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter
is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras.
As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this
class of affine Yangians. Another independent proof of the PBW theorem is given
recently by Guay, Regelskis, and Wendlandt [GRW18].
acknowledgement: Gufang Zhao is affiliated to IST Austria, Hausel group until July
of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli
spaces No. 320593 of the European Research Council.
article_processing_charge: No
article_type: original
author:
- first_name: Yaping
full_name: Yang, Yaping
id: 360D8648-F248-11E8-B48F-1D18A9856A87
last_name: Yang
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
citation:
ama: Yang Y, Zhao G. The PBW theorem for affine Yangians. Transformation Groups.
2020;25:1371-1385. doi:10.1007/s00031-020-09572-6
apa: Yang, Y., & Zhao, G. (2020). The PBW theorem for affine Yangians. Transformation
Groups. Springer Nature. https://doi.org/10.1007/s00031-020-09572-6
chicago: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation
Groups. Springer Nature, 2020. https://doi.org/10.1007/s00031-020-09572-6.
ieee: Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” Transformation
Groups, vol. 25. Springer Nature, pp. 1371–1385, 2020.
ista: Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation
Groups. 25, 1371–1385.
mla: Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation
Groups, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:10.1007/s00031-020-09572-6.
short: Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385.
date_created: 2020-06-07T22:00:55Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-08-21T07:06:21Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00031-020-09572-6
ec_funded: 1
external_id:
arxiv:
- '1804.04375'
isi:
- '000534874300003'
intvolume: ' 25'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04375
month: '12'
oa: 1
oa_version: Preprint
page: 1371-1385
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Transformation Groups
publication_identifier:
eissn:
- 1531586X
issn:
- '10834362'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The PBW theorem for affine Yangians
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2020'
...
---
_id: '9708'
abstract:
- lang: eng
text: This research data supports 'Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file
for plotting each figure is provided.
article_processing_charge: No
author:
- first_name: Mate
full_name: Hartstein, Mate
last_name: Hartstein
- first_name: Yu-Te
full_name: Hsu, Yu-Te
last_name: Hsu
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Juan
full_name: Porras, Juan
last_name: Porras
- first_name: Toshinao
full_name: Loew, Toshinao
last_name: Loew
- first_name: Matthieu
full_name: Le Tacon, Matthieu
last_name: Le Tacon
- first_name: Huakun
full_name: Zuo, Huakun
last_name: Zuo
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Zengwei
full_name: Zhu, Zengwei
last_name: Zhu
- first_name: Mun
full_name: Chan, Mun
last_name: Chan
- first_name: Ross
full_name: McDonald, Ross
last_name: McDonald
- first_name: Gilbert
full_name: Lonzarich, Gilbert
last_name: Lonzarich
- first_name: Bernhard
full_name: Keimer, Bernhard
last_name: Keimer
- first_name: Suchitra
full_name: Sebastian, Suchitra
last_name: Sebastian
- first_name: Neil
full_name: Harrison, Neil
last_name: Harrison
citation:
ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal
gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
superconductors.” 2020. doi:10.17863/cam.50169
apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M.,
… Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by
quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.”
Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169
chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew,
Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal
Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc
Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.
ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap
revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
superconductors.’” Apollo - University of Cambridge, 2020.
ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang
J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N.
2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University
of Cambridge, 10.17863/cam.50169.
mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed
by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”
Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169.
short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H.
Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian,
N. Harrison, (2020).
date_created: 2021-07-23T10:00:35Z
date_published: 2020-05-29T00:00:00Z
date_updated: 2023-08-21T07:06:48Z
day: '29'
department:
- _id: KiMo
doi: 10.17863/cam.50169
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.17863/CAM.50169
month: '05'
oa: 1
oa_version: Published Version
publisher: Apollo - University of Cambridge
related_material:
record:
- id: '7942'
relation: used_in_publication
status: public
status: public
title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '7955'
abstract:
- lang: eng
text: Simple stochastic games are turn-based 2½-player games with a reachability
objective. The basic question asks whether one player can ensure reaching a given
target with at least a given probability. A natural extension is games with a
conjunction of such conditions as objective. Despite a plethora of recent results
on the analysis of systems with multiple objectives, the decidability of this
basic problem remains open. In this paper, we present an algorithm approximating
the Pareto frontier of the achievable values to a given precision. Moreover, it
is an anytime algorithm, meaning it can be stopped at any time returning the current
approximation and its error bound.
acknowledgement: "Pranav Ashok, Jan Křetínský and Maximilian Weininger were funded
in part by TUM IGSSE Grant 10.06 (PARSEC) and the German Research Foundation (DFG)
project KR 4890/2-1\r\n“Statistical Unbounded Verification”. Krishnendu Chatterjee
was supported by the ERC CoG 863818 (ForM-SMArt) and Vienna Science and Technology
Fund (WWTF) Project ICT15-\r\n003. Tobias Winkler was supported by the RTG 2236
UnRAVe."
article_processing_charge: No
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jan
full_name: Kretinsky, Jan
last_name: Kretinsky
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
- first_name: Tobias
full_name: Winkler, Tobias
last_name: Winkler
citation:
ama: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. Approximating
values of generalized-reachability stochastic games. In: Proceedings of the
35th Annual ACM/IEEE Symposium on Logic in Computer Science . Association
for Computing Machinery; 2020:102-115. doi:10.1145/3373718.3394761'
apa: 'Ashok, P., Chatterjee, K., Kretinsky, J., Weininger, M., & Winkler, T.
(2020). Approximating values of generalized-reachability stochastic games. In
Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science
(pp. 102–115). Saarbrücken, Germany: Association for Computing Machinery.
https://doi.org/10.1145/3373718.3394761'
chicago: Ashok, Pranav, Krishnendu Chatterjee, Jan Kretinsky, Maximilian Weininger,
and Tobias Winkler. “Approximating Values of Generalized-Reachability Stochastic
Games.” In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer
Science , 102–15. Association for Computing Machinery, 2020. https://doi.org/10.1145/3373718.3394761.
ieee: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, and T. Winkler, “Approximating
values of generalized-reachability stochastic games,” in Proceedings of the
35th Annual ACM/IEEE Symposium on Logic in Computer Science , Saarbrücken,
Germany, 2020, pp. 102–115.
ista: 'Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. 2020. Approximating
values of generalized-reachability stochastic games. Proceedings of the 35th Annual
ACM/IEEE Symposium on Logic in Computer Science . LICS: Symposium on Logic in
Computer Science, 102–115.'
mla: Ashok, Pranav, et al. “Approximating Values of Generalized-Reachability Stochastic
Games.” Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer
Science , Association for Computing Machinery, 2020, pp. 102–15, doi:10.1145/3373718.3394761.
short: P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, T. Winkler, in:, Proceedings
of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association
for Computing Machinery, 2020, pp. 102–115.
conference:
end_date: 2020-07-11
location: Saarbrücken, Germany
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2020-07-08
date_created: 2020-06-14T22:00:48Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-21T08:24:36Z
day: '08'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3373718.3394761
ec_funded: 1
external_id:
arxiv:
- '1908.05106'
isi:
- '000665014900010'
file:
- access_level: open_access
checksum: d0d0288fe991dd16cf5f02598b794240
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T09:38:14Z
date_updated: 2020-11-25T09:38:14Z
file_id: '8804'
file_name: 2020_LICS_Ashok.pdf
file_size: 1001395
relation: main_file
success: 1
file_date_updated: 2020-11-25T09:38:14Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 102-115
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: 'Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer
Science '
publication_identifier:
isbn:
- '9781450371049'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Approximating values of generalized-reachability stochastic games
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '7957'
abstract:
- lang: eng
text: "Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain
development and function and are characterized by wide genetic and clinical variability.
In this review, we discuss the multiple factors that influence the clinical presentation
of NDDs, with particular attention to gene vulnerability, mutational load, and
the two-hit model. Despite the complex architecture of\r\nmutational events associated
with NDDs, the various proteins involved appear to converge on common pathways,
such as synaptic plasticity/function, chromatin remodelers and the mammalian target
of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind
these pathways will hopefully lead to the identification of candidates that could
be targeted for treatment approaches."
acknowledgement: We wish to thank Jasmin Morandell for generously sharing Figure 2.
This work was supported by the European Research Council Starting Grant (grant 715508
) to G.N.
article_processing_charge: No
article_type: original
author:
- first_name: Ilaria
full_name: Parenti, Ilaria
id: D93538B0-5B71-11E9-AC62-02EBE5697425
last_name: Parenti
- first_name: Luis E
full_name: Garcia Rabaneda, Luis E
id: 33D1B084-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Rabaneda
- first_name: Hanna
full_name: Schön, Hanna
id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425
last_name: Schön
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders:
From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621.
doi:10.1016/j.tins.2020.05.004'
apa: 'Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020).
Neurodevelopmental disorders: From genetics to functional pathways. Trends
in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004'
chicago: 'Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino.
“Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends
in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.'
ieee: 'I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental
disorders: From genetics to functional pathways,” Trends in Neurosciences,
vol. 43, no. 8. Elsevier, pp. 608–621, 2020.'
ista: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental
disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8),
608–621.'
mla: 'Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional
Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp.
608–21, doi:10.1016/j.tins.2020.05.004.'
short: I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences
43 (2020) 608–621.
date_created: 2020-06-14T22:00:49Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2023-08-21T08:25:31Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.tins.2020.05.004
ec_funded: 1
external_id:
isi:
- '000553090600008'
pmid:
- '32507511'
file:
- access_level: open_access
checksum: 67db0251b1d415ae59005f876fcf9e34
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T09:43:40Z
date_updated: 2020-11-25T09:43:40Z
file_id: '8805'
file_name: 2020_TrendsNeuroscience_Parenti.pdf
file_size: 1439550
relation: main_file
success: 1
file_date_updated: 2020-11-25T09:43:40Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 608-621
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
publication: Trends in Neurosciences
publication_identifier:
eissn:
- 1878108X
issn:
- '01662236'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Neurodevelopmental disorders: From genetics to functional pathways'
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: 43
year: '2020'
...
---
_id: '7960'
abstract:
- lang: eng
text: Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection
of sets from A has at most b path-connected components, which all are open, then
fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k.
These results also extend to two-dimensional compact surfaces.
acknowledgement: "We are very grateful to Pavel Paták for many helpful discussions
and remarks. We also thank the referees for helpful comments, which greatly improved
the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK
was also partially supported by NSF grant DMS1300120. The research stay of ZP at
IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement
of internationalization in the field of research and development at Charles University,
through the support of quality projects MSCA-IF."
article_processing_charge: No
article_type: original
author:
- first_name: Gil
full_name: Kalai, Gil
last_name: Kalai
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
citation:
ama: Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and
Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z
apa: Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets.
Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z
chicago: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.”
Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z.
ieee: G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete
and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020.
ista: Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete
and Computational Geometry. 64, 304–323.
mla: Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete
and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z.
short: G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323.
date_created: 2020-06-14T22:00:50Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-21T08:26:34Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-020-00205-z
external_id:
arxiv:
- '1907.00885'
isi:
- '000537329400001'
intvolume: ' 64'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.00885
month: '09'
oa: 1
oa_version: Preprint
page: 304-323
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intersection patterns of planar sets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2020'
...
---
_id: '7962'
abstract:
- lang: eng
text: 'A string graph is the intersection graph of a family of continuous arcs in
the plane. The intersection graph of a family of plane convex sets is a string
graph, but not all string graphs can be obtained in this way. We prove the following
structure theorem conjectured by Janson and Uzzell: The vertex set of almost all
string graphs on n vertices can be partitioned into five cliques such that some
pair of them is not connected by any edge (n→∞). We also show that every graph
with the above property is an intersection graph of plane convex sets. As a corollary,
we obtain that almost all string graphs on n vertices are intersection graphs
of plane convex sets.'
article_processing_charge: No
article_type: original
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: Bruce
full_name: Reed, Bruce
last_name: Reed
- first_name: Yelena
full_name: Yuditsky, Yelena
last_name: Yuditsky
citation:
ama: Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs
of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917.
doi:10.1007/s00454-020-00213-z
apa: Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are
intersection graphs of plane convex sets. Discrete and Computational Geometry.
Springer Nature. https://doi.org/10.1007/s00454-020-00213-z
chicago: Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs
Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry.
Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z.
ieee: J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection
graphs of plane convex sets,” Discrete and Computational Geometry, vol.
63, no. 4. Springer Nature, pp. 888–917, 2020.
ista: Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection
graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917.
mla: Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane
Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer
Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z.
short: J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020)
888–917.
date_created: 2020-06-14T22:00:51Z
date_published: 2020-06-05T00:00:00Z
date_updated: 2023-08-21T08:49:18Z
day: '05'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00213-z
external_id:
arxiv:
- '1803.06710'
isi:
- '000538229000001'
intvolume: ' 63'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.06710
month: '06'
oa: 1
oa_version: Preprint
page: 888-917
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Almost all string graphs are intersection graphs of plane convex sets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 63
year: '2020'
...
---
_id: '13460'
abstract:
- lang: eng
text: Binary interaction can cause stellar envelopes to be stripped, which significantly
reduces the radius of the star. The orbit of a binary composed of a stripped star
and a compact object can therefore be so tight that the gravitational radiation
the system produces reaches frequencies accessible to the Laser Interferometer
Space Antenna (LISA). Two such stripped stars in tight orbits with white dwarfs
are known so far (ZTF J2130+4420 and CD−30°11223), but many more are expected
to exist. These binaries provide important constraints for binary evolution models
and may be used as LISA verification sources. We develop a Monte Carlo code that
uses detailed evolutionary models to simulate the Galactic population of stripped
stars in tight orbits with either neutron star or white dwarf companions. We predict
0–100 stripped star + white dwarf binaries and 0–4 stripped star + neutron star
binaries with a signal-to-noise ratio >5 after 10 yr of observations with LISA.
More than 90% of these binaries are expected to show large radial velocity shifts
of ≳200 $\,\mathrm{km}\,{{\rm{s}}}^{-1}$, which are spectroscopically detectable.
Photometric variability due to tidal deformation of the stripped star is also
expected and has been observed in ZTF J2130+4420 and CD−30°11223. In addition,
the stripped star + neutron star binaries are expected to be X-ray bright with
LX ≳ 1033–1036 $\,\mathrm{erg}\,{{\rm{s}}}^{-1}$. Our results show that stripped
star binaries are promising multimessenger sources for the upcoming electromagnetic
and gravitational wave facilities.
article_number: '56'
article_processing_charge: No
article_type: original
author:
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: V.
full_name: Korol, V.
last_name: Korol
- first_name: A.
full_name: Lamberts, A.
last_name: Lamberts
- first_name: T.
full_name: Kupfer, T.
last_name: Kupfer
- first_name: K.
full_name: Breivik, K.
last_name: Breivik
- first_name: B.
full_name: Ludwig, B.
last_name: Ludwig
- first_name: M. R.
full_name: Drout, M. R.
last_name: Drout
citation:
ama: 'Götberg YLL, Korol V, Lamberts A, et al. Stars stripped in binaries: The living
gravitational-wave sources. The Astrophysical Journal. 2020;904(1). doi:10.3847/1538-4357/abbda5'
apa: 'Götberg, Y. L. L., Korol, V., Lamberts, A., Kupfer, T., Breivik, K., Ludwig,
B., & Drout, M. R. (2020). Stars stripped in binaries: The living gravitational-wave
sources. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/abbda5'
chicago: 'Götberg, Ylva Louise Linsdotter, V. Korol, A. Lamberts, T. Kupfer, K.
Breivik, B. Ludwig, and M. R. Drout. “Stars Stripped in Binaries: The Living Gravitational-Wave
Sources.” The Astrophysical Journal. American Astronomical Society, 2020.
https://doi.org/10.3847/1538-4357/abbda5.'
ieee: 'Y. L. L. Götberg et al., “Stars stripped in binaries: The living gravitational-wave
sources,” The Astrophysical Journal, vol. 904, no. 1. American Astronomical
Society, 2020.'
ista: 'Götberg YLL, Korol V, Lamberts A, Kupfer T, Breivik K, Ludwig B, Drout MR.
2020. Stars stripped in binaries: The living gravitational-wave sources. The Astrophysical
Journal. 904(1), 56.'
mla: 'Götberg, Ylva Louise Linsdotter, et al. “Stars Stripped in Binaries: The Living
Gravitational-Wave Sources.” The Astrophysical Journal, vol. 904, no. 1,
56, American Astronomical Society, 2020, doi:10.3847/1538-4357/abbda5.'
short: Y.L.L. Götberg, V. Korol, A. Lamberts, T. Kupfer, K. Breivik, B. Ludwig,
M.R. Drout, The Astrophysical Journal 904 (2020).
date_created: 2023-08-03T10:12:07Z
date_published: 2020-11-20T00:00:00Z
date_updated: 2023-08-21T11:32:40Z
day: '20'
doi: 10.3847/1538-4357/abbda5
extern: '1'
external_id:
arxiv:
- '2006.07382'
intvolume: ' 904'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2006.07382
month: '11'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Stars stripped in binaries: The living gravitational-wave sources'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 904
year: '2020'
...
---
_id: '7999'
abstract:
- lang: eng
text: 'Linking epigenetic marks to clinical outcomes improves insight into molecular
processes, disease prediction, and therapeutic target identification. Here, a
statistical approach is presented to infer the epigenetic architecture of complex
disease, determine the variation captured by epigenetic effects, and estimate
phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe
correlations, data structure (cell-count or relatedness), and single-nucleotide
polymorphism (SNP) marker effects, improves association estimates and in 9,448
individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and
45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole
blood methylation array data. Pathway-linked probes of blood cholesterol, lipid
transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking,
showed >1.5 times larger associations with >95% posterior inclusion probability.
Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO
model, with age-, and tissue-specificity, implying associations are a phenotypic
consequence rather than causal. '
article_number: '2865'
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Trejo Banos, D
last_name: Trejo Banos
- first_name: DL
full_name: McCartney, DL
last_name: McCartney
- first_name: M
full_name: Patxot, M
last_name: Patxot
- first_name: L
full_name: Anchieri, L
last_name: Anchieri
- first_name: T
full_name: Battram, T
last_name: Battram
- first_name: C
full_name: Christiansen, C
last_name: Christiansen
- first_name: R
full_name: Costeira, R
last_name: Costeira
- first_name: RM
full_name: Walker, RM
last_name: Walker
- first_name: SW
full_name: Morris, SW
last_name: Morris
- first_name: A
full_name: Campbell, A
last_name: Campbell
- first_name: Q
full_name: Zhang, Q
last_name: Zhang
- first_name: DJ
full_name: Porteous, DJ
last_name: Porteous
- first_name: AF
full_name: McRae, AF
last_name: McRae
- first_name: NR
full_name: Wray, NR
last_name: Wray
- first_name: PM
full_name: Visscher, PM
last_name: Visscher
- first_name: CS
full_name: Haley, CS
last_name: Haley
- first_name: KL
full_name: Evans, KL
last_name: Evans
- first_name: IJ
full_name: Deary, IJ
last_name: Deary
- first_name: AM
full_name: McIntosh, AM
last_name: McIntosh
- first_name: G
full_name: Hemani, G
last_name: Hemani
- first_name: JT
full_name: Bell, JT
last_name: Bell
- first_name: RE
full_name: Marioni, RE
last_name: Marioni
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic
architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1
apa: Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen,
C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture
of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1
chicago: Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen,
R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex
Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1.
ieee: D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture
of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen
C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray
N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni
R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of
complex traits. Nature Communications. 11, 2865.
mla: Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture
of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature,
2020, doi:10.1038/s41467-020-16520-1.
short: D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen,
R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae,
N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J.
Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020).
date_created: 2020-06-22T11:18:25Z
date_published: 2020-06-08T00:00:00Z
date_updated: 2023-08-22T07:13:09Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1038/s41467-020-16520-1
external_id:
isi:
- '000541702400004'
pmid:
- '32513961'
file:
- access_level: open_access
checksum: 4c96babd4cfb0d153334f6c598c0bacb
content_type: application/pdf
creator: dernst
date_created: 2020-06-22T11:24:32Z
date_updated: 2020-07-14T12:48:07Z
file_id: '8000'
file_name: 2020_NatureComm_Bayesian.pdf
file_size: 1475657
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-020-19099-9
scopus_import: '1'
status: public
title: Bayesian reassessment of the epigenetic architecture of complex traits
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '7995'
abstract:
- lang: eng
text: When divergent populations are connected by gene flow, the establishment of
complete reproductive isolation usually requires the joint action of multiple
barrier effects. One example where multiple barrier effects are coupled consists
of a single trait that is under divergent natural selection and also mediates
assortative mating. Such multiple‐effect traits can strongly reduce gene flow.
However, there are few cases where patterns of assortative mating have been described
quantitatively and their impact on gene flow has been determined. Two ecotypes
of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore
habitats dominated by either crab predation or wave action. There is evidence
for divergent natural selection acting on size, and size‐assortative mating has
previously been documented. Here, we analyze the mating pattern in L. saxatilis
with respect to size in intensively sampled transects across boundaries between
the habitats. We show that the mating pattern is mostly conserved between ecotypes
and that it generates both assortment and directional sexual selection for small
male size. Using simulations, we show that the mating pattern can contribute to
reproductive isolation between ecotypes but the barrier to gene flow is likely
strengthened more by sexual selection than by assortment.
acknowledgement: We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J.
Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating
experiments. This work was funded by the Natural Environment Research Council, European
Research Council and Swedish Research Council VR and we are also very grateful for
the support of the Linnaeus Centre for Marine Evolutionary Biology at the University
of Gothenburg. The simulations were performed on resources at Chalmers Centre for
Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure
for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research
and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.
article_processing_charge: No
article_type: original
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating,
sexual selection, and their consequences for gene flow in Littorina. Evolution.
2020;74(7):1482-1497. doi:10.1111/evo.14027
apa: Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin,
R. K. (2020). Assortative mating, sexual selection, and their consequences for
gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027
chicago: Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson,
and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences
for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027.
ieee: S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin,
“Assortative mating, sexual selection, and their consequences for gene flow in
Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.
ista: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative
mating, sexual selection, and their consequences for gene flow in Littorina. Evolution.
74(7), 1482–1497.
mla: Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences
for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp.
1482–97, doi:10.1111/evo.14027.
short: S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
74 (2020) 1482–1497.
date_created: 2020-06-22T09:14:21Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T07:13:38Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14027
ec_funded: 1
external_id:
isi:
- '000539780800001'
file:
- access_level: open_access
checksum: 56235bf1e2a9e25f96196bb13b6b754d
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T10:49:48Z
date_updated: 2020-11-25T10:49:48Z
file_id: '8808'
file_name: 2020_Evolution_Perini.pdf
file_size: 1080810
relation: main_file
success: 1
file_date_updated: 2020-11-25T10:49:48Z
has_accepted_license: '1'
intvolume: ' 74'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1482-1497
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution
publication_identifier:
eissn:
- '15585646'
issn:
- '00143820'
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '8809'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Assortative mating, sexual selection, and their consequences for gene flow
in Littorina
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: 74
year: '2020'
...
---
_id: '8809'
abstract:
- lang: eng
text: When divergent populations are connected by gene flow, the establishment of
complete reproductive isolation usually requires the joint action of multiple
barrier effects. One example where multiple barrier effects are coupled consists
of a single trait that is under divergent natural selection and also mediates
assortative mating. Such multiple-effect traits can strongly reduce gene flow.
However, there are few cases where patterns of assortative mating have been described
quantitatively and their impact on gene flow has been determined. Two ecotypes
of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore
habitats dominated by either crab predation or wave action. There is evidence
for divergent natural selection acting on size, and size-assortative mating has
previously been documented. Here, we analyze the mating pattern in L. saxatilis
with respect to size in intensively-sampled transects across boundaries between
the habitats. We show that the mating pattern is mostly conserved between ecotypes
and that it generates both assortment and directional sexual selection for small
male size. Using simulations, we show that the mating pattern can contribute to
reproductive isolation between ecotypes but the barrier to gene flow is likely
strengthened more by sexual selection than by assortment.
article_processing_charge: No
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Marina
full_name: Rafajlovic, Marina
last_name: Rafajlovic
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative
mating, sexual selection and their consequences for gene flow in Littorina. 2020.
doi:10.5061/dryad.qrfj6q5cn'
apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin,
R. (2020). Data from: Assortative mating, sexual selection and their consequences
for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn'
chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson,
and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences
for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.'
ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data
from: Assortative mating, sexual selection and their consequences for gene flow
in Littorina.” Dryad, 2020.'
ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from:
Assortative mating, sexual selection and their consequences for gene flow in Littorina,
Dryad, 10.5061/dryad.qrfj6q5cn.'
mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection
and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.'
short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).
date_created: 2020-11-25T11:07:25Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T07:13:37Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.qrfj6q5cn
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.qrfj6q5cn
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7995'
relation: used_in_publication
status: public
status: public
title: 'Data from: Assortative mating, sexual selection and their consequences for
gene flow in Littorina'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '8001'
abstract:
- lang: eng
text: Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent
short-term memory. Although PTP has a uniquely large magnitude at hippocampal
mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced
by natural activity and whether its lifetime is sufficient to support short-term
memory. We combined in vivo recordings from granule cells (GCs), in vitro paired
recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash
and freeze” electron microscopy. PTP was induced at single synapses and showed
a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly
generated by enlargement of the readily releasable pool of synaptic vesicles,
allowing multiplicative interaction with other plasticity forms. PTP was associated
with an increase in the docked vesicle pool, suggesting formation of structural
“pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation,
enabling prolonged information storage in the hippocampal network.
acknowledged_ssus:
- _id: SSU
acknowledgement: This project received funding from the European Research Council
(ERC) under the European Union Horizon 2020 Research and Innovation Program (grant
agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs.
Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting
on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel
Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian
Marr for excellent technical assistance and cell reconstruction; Christina Altmutter
for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen
for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of
IST Austria for support.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal
mossy fiber synapses is induced by natural activity patterns and associated with
vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013
apa: Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term
plasticity at hippocampal mossy fiber synapses is induced by natural activity
patterns and associated with vesicle pool engram formation. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2020.05.013
chicago: Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas.
“Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural
Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013.
ieee: D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity
at hippocampal mossy fiber synapses is induced by natural activity patterns and
associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3.
Elsevier, pp. 509–521, 2020.
ista: Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity
at hippocampal mossy fiber synapses is induced by natural activity patterns and
associated with vesicle pool engram formation. Neuron. 107(3), 509–521.
mla: Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber
Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool
Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21,
doi:10.1016/j.neuron.2020.05.013.
short: D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020)
509–521.
date_created: 2020-06-22T13:29:05Z
date_published: 2020-08-05T00:00:00Z
date_updated: 2023-08-22T07:45:25Z
day: '05'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2020.05.013
ec_funded: 1
external_id:
isi:
- '000556135600004'
pmid:
- '32492366'
file:
- access_level: open_access
checksum: 4030b2be0c9625d54694a1e9fb00305e
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T11:23:02Z
date_updated: 2020-11-25T11:23:02Z
file_id: '8811'
file_name: 2020_Neuron_Vandael.pdf
file_size: 4390833
relation: main_file
success: 1
file_date_updated: 2020-11-25T11:23:02Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 509-521
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: Neuron
publication_identifier:
eissn:
- '10974199'
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/possible-physical-trace-of-short-term-memory-found/
scopus_import: '1'
status: public
title: Short-term plasticity at hippocampal mossy fiber synapses is induced by natural
activity patterns and associated with vesicle pool engram formation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '13998'
abstract:
- lang: eng
text: The interaction of strong near-infrared (NIR) laser pulses with wide-bandgap
dielectrics produces high harmonics in the extreme ultraviolet (XUV) wavelength
range. These observations have opened up the possibility of attosecond metrology
in solids, which would benefit from a precise measurement of the emission times
of individual harmonics with respect to the NIR laser field. Here we show that,
when high-harmonics are detected from the input surface of a magnesium oxide crystal,
a bichromatic probing of the XUV emission shows a clear synchronization largely
consistent with a semiclassical model of electron–hole recollisions in bulk solids.
On the other hand, the bichromatic spectrogram of harmonics originating from the
exit surface of the 200 μm-thick crystal is strongly modified, indicating the
influence of laser field distortions during propagation. Our tracking of sub-cycle
electron and hole re-collisions at XUV energies is relevant to the development
of solid-state sources of attosecond pulses.
article_number: '144003'
article_processing_charge: No
article_type: original
author:
- first_name: Giulio
full_name: Vampa, Giulio
last_name: Vampa
- first_name: Jian
full_name: Lu, Jian
last_name: Lu
- first_name: Yong Sing
full_name: You, Yong Sing
last_name: You
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Mengxi
full_name: Wu, Mengxi
last_name: Wu
- first_name: Hanzhe
full_name: Liu, Hanzhe
last_name: Liu
- first_name: Kenneth J
full_name: Schafer, Kenneth J
last_name: Schafer
- first_name: Mette B
full_name: Gaarde, Mette B
last_name: Gaarde
- first_name: David A
full_name: Reis, David A
last_name: Reis
- first_name: Shambhu
full_name: Ghimire, Shambhu
last_name: Ghimire
citation:
ama: 'Vampa G, Lu J, You YS, et al. Attosecond synchronization of extreme ultraviolet
high harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical
Physics. 2020;53(14). doi:10.1088/1361-6455/ab8e56'
apa: 'Vampa, G., Lu, J., You, Y. S., Baykusheva, D. R., Wu, M., Liu, H., … Ghimire,
S. (2020). Attosecond synchronization of extreme ultraviolet high harmonics from
crystals. Journal of Physics B: Atomic, Molecular and Optical Physics.
IOP Publishing. https://doi.org/10.1088/1361-6455/ab8e56'
chicago: 'Vampa, Giulio, Jian Lu, Yong Sing You, Denitsa Rangelova Baykusheva, Mengxi
Wu, Hanzhe Liu, Kenneth J Schafer, Mette B Gaarde, David A Reis, and Shambhu Ghimire.
“Attosecond Synchronization of Extreme Ultraviolet High Harmonics from Crystals.”
Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing,
2020. https://doi.org/10.1088/1361-6455/ab8e56.'
ieee: 'G. Vampa et al., “Attosecond synchronization of extreme ultraviolet
high harmonics from crystals,” Journal of Physics B: Atomic, Molecular and
Optical Physics, vol. 53, no. 14. IOP Publishing, 2020.'
ista: 'Vampa G, Lu J, You YS, Baykusheva DR, Wu M, Liu H, Schafer KJ, Gaarde MB,
Reis DA, Ghimire S. 2020. Attosecond synchronization of extreme ultraviolet high
harmonics from crystals. Journal of Physics B: Atomic, Molecular and Optical Physics.
53(14), 144003.'
mla: 'Vampa, Giulio, et al. “Attosecond Synchronization of Extreme Ultraviolet High
Harmonics from Crystals.” Journal of Physics B: Atomic, Molecular and Optical
Physics, vol. 53, no. 14, 144003, IOP Publishing, 2020, doi:10.1088/1361-6455/ab8e56.'
short: 'G. Vampa, J. Lu, Y.S. You, D.R. Baykusheva, M. Wu, H. Liu, K.J. Schafer,
M.B. Gaarde, D.A. Reis, S. Ghimire, Journal of Physics B: Atomic, Molecular and
Optical Physics 53 (2020).'
date_created: 2023-08-09T13:09:51Z
date_published: 2020-06-17T00:00:00Z
date_updated: 2023-08-22T07:36:36Z
day: '17'
doi: 10.1088/1361-6455/ab8e56
extern: '1'
external_id:
arxiv:
- '2001.09951'
intvolume: ' 53'
issue: '14'
keyword:
- Condensed Matter Physics
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.09951
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics'
publication_identifier:
eissn:
- 1361-6455
issn:
- 0953-4075
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attosecond synchronization of extreme ultraviolet high harmonics from crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2020'
...
---
_id: '8038'
abstract:
- lang: eng
text: Microelectromechanical systems and integrated photonics provide the basis
for many reliable and compact circuit elements in modern communication systems.
Electro-opto-mechanical devices are currently one of the leading approaches to
realize ultra-sensitive, low-loss transducers for an emerging quantum information
technology. Here we present an on-chip microwave frequency converter based on
a planar aluminum on silicon nitride platform that is compatible with slot-mode
coupled photonic crystal cavities. We show efficient frequency conversion between
two propagating microwave modes mediated by the radiation pressure interaction
with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent
conversion with a total device efficiency of up to ~60%, a dynamic range of 2
× 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity
quantum state transfer would be possible if the drive dependent output noise of
currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based
transducer is in situ reconfigurable and could be used for on-chip classical and
quantum signal routing and filtering, both for microwave and hybrid microwave-optical
applications.
article_number: '034011'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: M.
full_name: Kalaee, M.
last_name: Kalaee
- first_name: R.
full_name: Norte, R.
last_name: Norte
- first_name: A.
full_name: Pitanti, A.
last_name: Pitanti
- first_name: O.
full_name: Painter, O.
last_name: Painter
citation:
ama: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency
conversion mediated by a photonics compatible silicon nitride nanobeam oscillator.
Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce
apa: Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020).
Efficient microwave frequency conversion mediated by a photonics compatible silicon
nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing.
https://doi.org/10.1088/2058-9565/ab8dce
chicago: Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient
Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride
Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020.
https://doi.org/10.1088/2058-9565/ab8dce.
ieee: J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave
frequency conversion mediated by a photonics compatible silicon nitride nanobeam
oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing,
2020.
ista: Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave
frequency conversion mediated by a photonics compatible silicon nitride nanobeam
oscillator. Quantum Science and Technology. 5(3), 034011.
mla: Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated
by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science
and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce.
short: J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and
Technology 5 (2020).
date_created: 2020-06-29T07:59:35Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2023-08-22T07:49:01Z
day: '25'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1088/2058-9565/ab8dce
ec_funded: 1
external_id:
isi:
- '000539300800001'
file:
- access_level: open_access
checksum: 8f25f05053f511f892ae8fa93f341e61
content_type: application/pdf
creator: cziletti
date_created: 2020-06-30T10:29:10Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8072'
file_name: 2020_QuantumSciTechnol_Fink.pdf
file_size: 2600967
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 26927A52-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F07105
name: Integrating superconducting quantum circuits
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 2622978C-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
publication: Quantum Science and Technology
publication_identifier:
eissn:
- '20589565'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient microwave frequency conversion mediated by a photonics compatible
silicon nitride nanobeam oscillator
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: 5
year: '2020'
...
---
_id: '8037'
abstract:
- lang: eng
text: 'Genetic perturbations that affect bacterial resistance to antibiotics have
been characterized genome-wide, but how do such perturbations interact with subsequent
evolutionary adaptation to the drug? Here, we show that strong epistasis between
resistance mutations and systematically identified genes can be exploited to control
spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12
mutant populations in parallel, using a robotic platform that tightly controls
population size and selection pressure. We find a global diminishing-returns epistasis
pattern: strains that are initially more sensitive generally undergo larger resistance
gains. However, some gene deletion strains deviate from this general trend and
curtail the evolvability of resistance, including deletions of genes for membrane
transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force
evolution on inferior mutational paths, not explored in the wild type, and some
of these essentially block resistance evolution. This effect is due to strong
negative epistasis with resistance mutations. The identified genes and cellular
functions provide potential targets for development of adjuvants that may block
spontaneous resistance evolution when combined with antibiotics.'
article_number: '3105'
article_processing_charge: No
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Booshini
full_name: Fernando, Booshini
last_name: Fernando
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisinova M, Fernando B, Bollenbach MT. Highly parallel lab evolution reveals
that epistasis can curb the evolution of antibiotic resistance. Nature Communications.
2020;11. doi:10.1038/s41467-020-16932-z
apa: Lukacisinova, M., Fernando, B., & Bollenbach, M. T. (2020). Highly parallel
lab evolution reveals that epistasis can curb the evolution of antibiotic resistance.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16932-z
chicago: Lukacisinova, Marta, Booshini Fernando, and Mark Tobias Bollenbach. “Highly
Parallel Lab Evolution Reveals That Epistasis Can Curb the Evolution of Antibiotic
Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16932-z.
ieee: M. Lukacisinova, B. Fernando, and M. T. Bollenbach, “Highly parallel lab evolution
reveals that epistasis can curb the evolution of antibiotic resistance,” Nature
Communications, vol. 11. Springer Nature, 2020.
ista: Lukacisinova M, Fernando B, Bollenbach MT. 2020. Highly parallel lab evolution
reveals that epistasis can curb the evolution of antibiotic resistance. Nature
Communications. 11, 3105.
mla: Lukacisinova, Marta, et al. “Highly Parallel Lab Evolution Reveals That Epistasis
Can Curb the Evolution of Antibiotic Resistance.” Nature Communications,
vol. 11, 3105, Springer Nature, 2020, doi:10.1038/s41467-020-16932-z.
short: M. Lukacisinova, B. Fernando, M.T. Bollenbach, Nature Communications 11 (2020).
date_created: 2020-06-29T07:59:35Z
date_published: 2020-06-19T00:00:00Z
date_updated: 2023-08-22T07:48:30Z
day: '19'
ddc:
- '570'
doi: 10.1038/s41467-020-16932-z
extern: '1'
external_id:
isi:
- '000545685100002'
pmid:
- '32561723'
file:
- access_level: open_access
checksum: 4f5f49d63add331d5eb8a2bae477b396
content_type: application/pdf
creator: cziletti
date_created: 2020-06-30T09:58:50Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8071'
file_name: 2020_NatureComm_Lukacisinova.pdf
file_size: 1546491
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly parallel lab evolution reveals that epistasis can curb the evolution
of antibiotic resistance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8036'
abstract:
- lang: eng
text: When tiny soft ferromagnetic particles are placed along a liquid interface
and exposed to a vertical magnetic field, the balance between capillary attraction
and magnetic repulsion leads to self-organization into well-defined patterns.
Here, we demonstrate experimentally that precessing magnetic fields induce metachronal
waves on the periphery of these assemblies, similar to the ones observed in ciliates
and some arthropods. The outermost layer of particles behaves like an array of
cilia or legs whose sequential movement causes a net and controllable locomotion.
This bioinspired many-particle swimming strategy is effective even at low Reynolds
number, using only spatially uniform fields to generate the waves.
article_number: '112'
article_processing_charge: No
article_type: original
author:
- first_name: Ylona
full_name: Collard, Ylona
last_name: Collard
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Nicolas
full_name: Vandewalle, Nicolas
last_name: Vandewalle
citation:
ama: Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves
induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9
apa: Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered
metachronal waves induce locomotion in self-assemblies. Communications Physics.
Springer Nature. https://doi.org/10.1038/s42005-020-0380-9
chicago: Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically
Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications
Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9.
ieee: Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal
waves induce locomotion in self-assemblies,” Communications Physics, vol.
3. Springer Nature, 2020.
ista: Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal
waves induce locomotion in self-assemblies. Communications Physics. 3, 112.
mla: Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion
in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature,
2020, doi:10.1038/s42005-020-0380-9.
short: Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020).
date_created: 2020-06-29T07:59:35Z
date_published: 2020-06-19T00:00:00Z
date_updated: 2023-08-22T07:47:30Z
day: '19'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1038/s42005-020-0380-9
ec_funded: 1
external_id:
isi:
- '000543328000002'
file:
- access_level: open_access
checksum: ed984f7a393f19140b5279a54a3336ad
content_type: application/pdf
creator: cziletti
date_created: 2020-06-29T13:21:24Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8045'
file_name: 2020_CommunicationsPhysics_Collard.pdf
file_size: 1907821
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Communications Physics
publication_identifier:
eissn:
- '23993650'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetically powered metachronal waves induce locomotion in self-assemblies
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: 3
year: '2020'
...
---
_id: '8043'
abstract:
- lang: eng
text: With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally
intermittent and self-organises into solitary stripes oblique to the mean flow
direction. We report here the existence of localised nonlinear travelling wave
solutions of the Navier–Stokes equations possessing this obliqueness property.
Such solutions are identified numerically using edge tracking coupled with arclength
continuation. All solutions emerge in saddle-node bifurcations at values of Re
lower than the non-localised solutions. Relative periodic orbit solutions bifurcating
from branches of travelling waves have also been computed. A complete parametric
study is performed, including their stability, the investigation of their large-scale
flow, and the robustness to changes of the numerical domain.
acknowledgement: The authors thank S. Zammert and B. Budanur for useful discussions.
J. F. Gibson is gratefully acknowledged for the development and the maintenance
of the code Channelflow. Y.D. would like to thank P. Schlatter and D. S. Henningson
for an early collaboration on a similar topic in the case of plane Couette flow
during the years 2008–2013.
article_number: A7
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Chaitanya S
full_name: Paranjape, Chaitanya S
id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87
last_name: Paranjape
- first_name: Yohann
full_name: Duguet, Yohann
last_name: Duguet
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Paranjape CS, Duguet Y, Hof B. Oblique stripe solutions of channel flow. Journal
of Fluid Mechanics. 2020;897. doi:10.1017/jfm.2020.322
apa: Paranjape, C. S., Duguet, Y., & Hof, B. (2020). Oblique stripe solutions
of channel flow. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2020.322
chicago: Paranjape, Chaitanya S, Yohann Duguet, and Björn Hof. “Oblique Stripe Solutions
of Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press,
2020. https://doi.org/10.1017/jfm.2020.322.
ieee: C. S. Paranjape, Y. Duguet, and B. Hof, “Oblique stripe solutions of channel
flow,” Journal of Fluid Mechanics, vol. 897. Cambridge University Press,
2020.
ista: Paranjape CS, Duguet Y, Hof B. 2020. Oblique stripe solutions of channel flow.
Journal of Fluid Mechanics. 897, A7.
mla: Paranjape, Chaitanya S., et al. “Oblique Stripe Solutions of Channel Flow.”
Journal of Fluid Mechanics, vol. 897, A7, Cambridge University Press, 2020,
doi:10.1017/jfm.2020.322.
short: C.S. Paranjape, Y. Duguet, B. Hof, Journal of Fluid Mechanics 897 (2020).
date_created: 2020-06-29T07:59:35Z
date_published: 2020-08-25T00:00:00Z
date_updated: 2023-08-22T07:48:02Z
day: '25'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2020.322
external_id:
isi:
- '000539132300001'
file:
- access_level: open_access
checksum: 3f487bf6d9286787096306eaa18702e8
content_type: application/pdf
creator: cziletti
date_created: 2020-06-30T08:37:37Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8070'
file_name: 2020_JournalOfFluidMech_Paranjape.pdf
file_size: 767873
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 897'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- '14697645'
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Oblique stripe solutions of channel flow
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 897
year: '2020'
...
---
_id: '9326'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes
energy from catabolic processes to synthesize ATP. Complex I, the first and the
largest protein complex of the chain, harvests electrons from NADH to reduce quinone,
while pumping protons across the mitochondrial membrane. Detailed knowledge of
the working principle of such coupled charge-transfer processes remains, however,
fragmentary due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus
thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons
from NADH. Here, employing the latest crystal structure of T. thermophilus complex
I, we have used microsecond-scale molecular dynamics simulations to study the
chemo-mechanical coupling between redox changes of the iron–sulfur clusters and
conformational transitions across complex I. First, we identify the redox switches
within complex I, which allosterically couple the dynamics of the quinone binding
pocket to the site of NADH reduction. Second, our free-energy calculations reveal
that the affinity of the quinone, specifically menaquinone, for the binding-site
is higher than that of its reduced, menaquinol forma design essential for menaquinol
release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser
than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup
of the former furnishes stronger binding interactions with the pocket, favoring
menaquinone for charge transport in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues into
three functional classes, identifying new mutation targets. Third, long-range
hydrogen-bond networks connecting the quinone-binding site to the transmembrane
subunits are found to be responsible for proton pumping. Put together, the simulations
reveal the molecular design principles linking redox reactions to quinone turnover
to proton translocation in complex I.
article_processing_charge: No
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun
full_name: Chan, Chun
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M. R.
full_name: Gunner, M. R.
last_name: Gunner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002
apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., …
Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar,
M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge
Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical
Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I.” American Chemical Society, 2020.
ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.
mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in
Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.
short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov,
C. Chipot, A. Singharoy, (2020).
date_created: 2021-04-14T12:05:20Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:37Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s002
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
month: '05'
oa: 1
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8042'
abstract:
- lang: eng
text: We consider systems of N bosons in a box of volume one, interacting through
a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for
sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov
theory, identifying the ground state energy and the low-lying excitation spectrum
up to errors that vanish in the limit of large N.
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Christian
full_name: Brennecke, Christian
last_name: Brennecke
- first_name: Serena
full_name: Cenatiempo, Serena
last_name: Cenatiempo
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of
Bose gases interacting through singular potentials. Journal of the European
Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966
apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation
spectrum of Bose gases interacting through singular potentials. Journal of
the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966
chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein.
“The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.”
Journal of the European Mathematical Society. European Mathematical Society,
2020. https://doi.org/10.4171/JEMS/966.
ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum
of Bose gases interacting through singular potentials,” Journal of the European
Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403,
2020.
ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum
of Bose gases interacting through singular potentials. Journal of the European
Mathematical Society. 22(7), 2331–2403.
mla: Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting
through Singular Potentials.” Journal of the European Mathematical Society,
vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966.
short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European
Mathematical Society 22 (2020) 2331–2403.
date_created: 2020-06-29T07:59:35Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T07:47:04Z
day: '01'
department:
- _id: RoSe
doi: 10.4171/JEMS/966
external_id:
arxiv:
- '1704.04819'
isi:
- '000548174700006'
intvolume: ' 22'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.04819
month: '07'
oa: 1
oa_version: Preprint
page: 2331-2403
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- '14359855'
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitation spectrum of Bose gases interacting through singular potentials
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2020'
...
---
_id: '8093'
abstract:
- lang: eng
text: "Background: The activation of the EGFR/Ras-signalling pathway in tumour cells
induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods:
The effects of EGFR/Ras on the expression and translation of CCL20 were analysed
in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and
ELISA in vitro. CCL20 production was verified by immunohistochemistry in different
tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial
cell migration and tumour-associated vascularisation were comprehensively analysed
with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults:
Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression
of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased
lymph node metastasis and decreased survival in patients. Microvascular endothelial
cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in
endothelial cells induces angiogenesis. CCR6-deficient mice show significantly
decreased tumour growth and tumour-associated vascularisation. The observed phenotype
is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion:
We propose that the chemokine axis CCL20–CCR6 represents a novel and promising
target to interfere with the tumour microenvironment, and opens an innovative
multimodal strategy for cancer therapy."
acknowledgement: "The authors would like to thank A. van Lierop for technical assistance.
In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and
assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K.
Horst for advice on performing matrigel plug assays. This study has also been partially
presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190
‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis
project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1
of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was
supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and
J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research
Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia."
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Hippe, Andreas
last_name: Hippe
- first_name: Stephan Alexander
full_name: Braun, Stephan Alexander
last_name: Braun
- first_name: Péter
full_name: Oláh, Péter
last_name: Oláh
- first_name: Peter Arne
full_name: Gerber, Peter Arne
last_name: Gerber
- first_name: Anne
full_name: Schorr, Anne
last_name: Schorr
- first_name: Stephan
full_name: Seeliger, Stephan
last_name: Seeliger
- first_name: Stephanie
full_name: Holtz, Stephanie
last_name: Holtz
- first_name: Katharina
full_name: Jannasch, Katharina
last_name: Jannasch
- first_name: Andor
full_name: Pivarcsi, Andor
last_name: Pivarcsi
- first_name: Bettina
full_name: Buhren, Bettina
last_name: Buhren
- first_name: Holger
full_name: Schrumpf, Holger
last_name: Schrumpf
- first_name: Andreas
full_name: Kislat, Andreas
last_name: Kislat
- first_name: Erich
full_name: Bünemann, Erich
last_name: Bünemann
- first_name: Martin
full_name: Steinhoff, Martin
last_name: Steinhoff
- first_name: Jens
full_name: Fischer, Jens
last_name: Fischer
- first_name: Sérgio A.
full_name: Lira, Sérgio A.
last_name: Lira
- first_name: Petra
full_name: Boukamp, Petra
last_name: Boukamp
- first_name: Peter
full_name: Hevezi, Peter
last_name: Hevezi
- first_name: Nikolas Hendrik
full_name: Stoecklein, Nikolas Hendrik
last_name: Stoecklein
- first_name: Thomas
full_name: Hoffmann, Thomas
last_name: Hoffmann
- first_name: Frauke
full_name: Alves, Frauke
last_name: Alves
- first_name: Jonathan
full_name: Sleeman, Jonathan
last_name: Sleeman
- first_name: Thomas
full_name: Bauer, Thomas
last_name: Bauer
- first_name: Jörg
full_name: Klufa, Jörg
last_name: Klufa
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Maria
full_name: Sibilia, Maria
last_name: Sibilia
- first_name: Albert
full_name: Zlotnik, Albert
last_name: Zlotnik
- first_name: Anja
full_name: Müller-Homey, Anja
last_name: Müller-Homey
- first_name: Bernhard
full_name: Homey, Bernhard
last_name: Homey
citation:
ama: Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates
the tumour microenvironment. British Journal of Cancer. 2020;123:942-954.
doi:10.1038/s41416-020-0943-2
apa: Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S.,
… Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment.
British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2
chicago: Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber,
Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20
Production Modulates the Tumour Microenvironment.” British Journal of Cancer.
Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.
ieee: A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour
microenvironment,” British Journal of Cancer, vol. 123. Springer Nature,
pp. 942–954, 2020.
ista: Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch
K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer
J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J,
Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020.
EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British
Journal of Cancer. 123, 942–954.
mla: Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour
Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature,
2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.
short: A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz,
K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff,
J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F.
Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey,
B. Homey, British Journal of Cancer 123 (2020) 942–954.
date_created: 2020-07-05T22:00:46Z
date_published: 2020-09-15T00:00:00Z
date_updated: 2023-08-22T07:51:12Z
day: '15'
ddc:
- '610'
department:
- _id: SiHi
doi: 10.1038/s41416-020-0943-2
external_id:
isi:
- '000544152500001'
pmid:
- '32601464'
file:
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checksum: 05a8e65d49c3f5b8e37ac4afe68287e2
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creator: cchlebak
date_created: 2021-12-02T12:35:12Z
date_updated: 2021-12-02T12:35:12Z
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file_name: 2020_BrJournalCancer_Hippe.pdf
file_size: 3620691
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month: '09'
oa: 1
oa_version: Published Version
page: 942-954
pmid: 1
publication: British Journal of Cancer
publication_identifier:
eissn:
- 1532-1827
issn:
- 0007-0920
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41416-021-01563-y
record:
- id: '10170'
relation: later_version
status: deleted
scopus_import: '1'
status: public
title: EGFR/Ras-induced CCL20 production modulates the tumour microenvironment
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: 123
year: '2020'
...
---
_id: '8091'
abstract:
- lang: eng
text: In the setting of the fractional quantum Hall effect we study the effects
of strong, repulsive two-body interaction potentials of short range. We prove
that Haldane’s pseudo-potential operators, including their pre-factors, emerge
as mathematically rigorous limits of such interactions when the range of the potential
tends to zero while its strength tends to infinity. In a common approach the interaction
potential is expanded in angular momentum eigenstates in the lowest Landau level,
which amounts to taking the pre-factors to be the moments of the potential. Such
a procedure is not appropriate for very strong interactions, however, in particular
not in the case of hard spheres. We derive the formulas valid in the short-range
case, which involve the scattering lengths of the interaction potential in different
angular momentum channels rather than its moments. Our results hold for bosons
and fermions alike and generalize previous results in [6], which apply to bosons
in the lowest angular momentum channel. Our main theorem asserts the convergence
in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after
appropriate energy scalings, to Hamiltonians with contact interactions in the
lowest Landau level.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria).\r\nThe work of R.S. was supported by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC
Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. "
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems
with short-range interactions. Journal of Statistical Physics. 2020;181:448-464.
doi:10.1007/s10955-020-02586-0
apa: Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials
in systems with short-range interactions. Journal of Statistical Physics.
Springer. https://doi.org/10.1007/s10955-020-02586-0
chicago: Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials
in Systems with Short-Range Interactions.” Journal of Statistical Physics.
Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.
ieee: R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems
with short-range interactions,” Journal of Statistical Physics, vol. 181.
Springer, pp. 448–464, 2020.
ista: Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems
with short-range interactions. Journal of Statistical Physics. 181, 448–464.
mla: Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials
in Systems with Short-Range Interactions.” Journal of Statistical Physics,
vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.
short: R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.
date_created: 2020-07-05T22:00:46Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T07:51:47Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s10955-020-02586-0
ec_funded: 1
external_id:
arxiv:
- '2001.07144'
isi:
- '000543030000002'
file:
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creator: dernst
date_created: 2020-11-25T15:05:04Z
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file_id: '8812'
file_name: 2020_JourStatPhysics_Seiringer.pdf
file_size: 404778
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file_date_updated: 2020-11-25T15:05:04Z
has_accepted_license: '1'
intvolume: ' 181'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 448-464
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- '15729613'
issn:
- '00224715'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of Haldane pseudo-potentials in systems with short-range interactions
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: 181
year: '2020'
...
---
_id: '8077'
abstract:
- lang: eng
text: The projection methods with vanilla inertial extrapolation step for variational
inequalities have been of interest to many authors recently due to the improved
convergence speed contributed by the presence of inertial extrapolation step.
However, it is discovered that these projection methods with inertial steps lose
the Fejér monotonicity of the iterates with respect to the solution, which is
being enjoyed by their corresponding non-inertial projection methods for variational
inequalities. This lack of Fejér monotonicity makes projection methods with vanilla
inertial extrapolation step for variational inequalities not to converge faster
than their corresponding non-inertial projection methods at times. Also, it has
recently been proved that the projection methods with vanilla inertial extrapolation
step may provide convergence rates that are worse than the classical projected
gradient methods for strongly convex functions. In this paper, we introduce projection
methods with alternated inertial extrapolation step for solving variational inequalities.
We show that the sequence of iterates generated by our methods converges weakly
to a solution of the variational inequality under some appropriate conditions.
The Fejér monotonicity of even subsequence is recovered in these methods and linear
rate of convergence is obtained. The numerical implementations of our methods
compared with some other inertial projection methods show that our method is more
efficient and outperforms some of these inertial projection methods.
acknowledgement: The authors are grateful to the two anonymous referees for their
insightful comments and suggestions which have improved the earlier version of the
manuscript greatly. The first author has received funding from the European Research
Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013)
(Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
citation:
ama: 'Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for
variational inequalities: Weak and linear convergence. Applied Numerical Mathematics.
2020;157:315-337. doi:10.1016/j.apnum.2020.06.009'
apa: 'Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating
inertial steps for variational inequalities: Weak and linear convergence. Applied
Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009'
chicago: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating
Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied
Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009.'
ieee: 'Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial
steps for variational inequalities: Weak and linear convergence,” Applied Numerical
Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.'
ista: 'Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps
for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics.
157, 315–337.'
mla: 'Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating
Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied
Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009.'
short: Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.
date_created: 2020-07-02T09:02:33Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T07:50:43Z
day: '01'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1016/j.apnum.2020.06.009
ec_funded: 1
external_id:
isi:
- '000564648400018'
file:
- access_level: open_access
checksum: 87d81324a62c82baa925c009dfcb0200
content_type: application/pdf
creator: dernst
date_created: 2020-07-02T09:08:59Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8078'
file_name: 2020_AppliedNumericalMath_Shehu.pdf
file_size: 2874203
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 315-337
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Applied Numerical Mathematics
publication_identifier:
issn:
- 0168-9274
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Projection methods with alternating inertial steps for variational inequalities:
Weak and linear convergence'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 157
year: '2020'
...
---
_id: '8133'
abstract:
- lang: eng
text: The molecular factors which control circulating levels of inflammatory proteins
are not well understood. Furthermore, association studies between molecular probes
and human traits are often performed by linear model-based methods which may fail
to account for complex structure and interrelationships within molecular datasets.In
this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS)
on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy
older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel).
We employ a Bayesian framework (BayesR+) which can account for issues pertaining
to data structure and unknown confounding variables (with sensitivity analyses
using ordinary least squares- (OLS) and mixed model-based approaches). We identified
13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and
Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG
each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged
genetic variants accounted for up to 45% of variance in protein levels (for MCP2,
36% of variance alone attributable to 1 polymorphism). Methylation data accounted
for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation
in protein levels (for VEGFA) was explained using genetic and epigenetic data
combined. We demonstrated putative causal relationships between CD6 and IL18R1
with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data
may aid understanding of the molecular regulation of the circulating inflammatory
proteome as well as causal relationships between inflammatory mediators and disease.
article_number: '60'
article_processing_charge: No
article_type: original
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Allan F.
full_name: Mcrae, Allan F.
last_name: Mcrae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
2020;12(1). doi:10.1186/s13073-020-00754-1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
Springer Nature. https://doi.org/10.1186/s13073-020-00754-1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method
Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older
Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.
ieee: R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies
of inflammatory protein levels in healthy older adults,” Genome Medicine,
vol. 12, no. 1. Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Genome Medicine. 12(1), 60.
mla: Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies
of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine,
vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T07:55:37Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-020-00754-1
external_id:
isi:
- '000551778400001'
pmid:
- '32641083'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:27:38Z
date_updated: 2020-07-22T06:27:38Z
file_id: '8145'
file_name: 2020_GenomeMedicine_Hillary.pdf
file_size: 1136983
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:27:38Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Medicine
publication_identifier:
eissn:
- 1756994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9706'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-method genome- and epigenome-wide studies of inflammatory protein levels
in healthy older adults
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2020'
...
---
_id: '8127'
abstract:
- lang: eng
text: Mechanistic modeling in neuroscience aims to explain observed phenomena in
terms of underlying causes. However, determining which model parameters agree
with complex and stochastic neural data presents a significant challenge. We address
this challenge with a machine learning tool which uses deep neural density estimators—trained
using model simulations—to carry out Bayesian inference and retrieve the full
space of parameters compatible with raw data or selected data features. Our method
is scalable in parameters and data features and can rapidly analyze new data after
initial training. We demonstrate the power and flexibility of our approach on
receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize
the space of circuit configurations giving rise to rhythmic activity in the crustacean
stomatogastric ganglion, and use these results to derive hypotheses for underlying
compensation mechanisms. Our approach will help close the gap between data-driven
and theory-driven models of neural dynamics.
acknowledgement: We thank Mahmood S Hoseini and Michael Stryker for sharing their
data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham,
Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid
Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the
manuscript. This work was supported by the German Research Foundation (DFG) through
SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041
‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1
– Project number 390727645 and the German Federal Ministry of Education and Research
(BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome
Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant
(SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological
Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge
the Leibniz Supercomputing Centre for funding this project by providing computing
time on its Linux-Cluster.
article_number: e56261
article_processing_charge: No
article_type: original
author:
- first_name: Pedro J.
full_name: Gonçalves, Pedro J.
last_name: Gonçalves
orcid: 0000-0002-6987-4836
- first_name: Jan-Matthis
full_name: Lueckmann, Jan-Matthis
last_name: Lueckmann
orcid: 0000-0003-4320-4663
- first_name: Michael
full_name: Deistler, Michael
last_name: Deistler
orcid: 0000-0002-3573-0404
- first_name: Marcel
full_name: Nonnenmacher, Marcel
last_name: Nonnenmacher
orcid: 0000-0001-6044-6627
- first_name: Kaan
full_name: Öcal, Kaan
last_name: Öcal
orcid: 0000-0002-8528-6858
- first_name: Giacomo
full_name: Bassetto, Giacomo
last_name: Bassetto
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Sara A.
full_name: Haddad, Sara A.
last_name: Haddad
orcid: 0000-0003-0807-0823
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: David S.
full_name: Greenberg, David S.
last_name: Greenberg
- first_name: Jakob H.
full_name: Macke, Jakob H.
last_name: Macke
orcid: 0000-0001-5154-8912
citation:
ama: Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density
estimators to identify mechanistic models of neural dynamics. eLife. 2020;9.
doi:10.7554/eLife.56261
apa: Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K.,
Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to
identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.56261
chicago: Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher,
Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural
Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.
ieee: P. J. Gonçalves et al., “Training deep neural density estimators to
identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto
G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020.
Training deep neural density estimators to identify mechanistic models of neural
dynamics. eLife. 9, e56261.
mla: Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify
Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences
Publications, 2020, doi:10.7554/eLife.56261.
short: P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G.
Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg,
J.H. Macke, ELife 9 (2020).
date_created: 2020-07-16T12:26:04Z
date_published: 2020-09-17T00:00:00Z
date_updated: 2023-08-22T07:54:52Z
day: '17'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.7554/eLife.56261
ec_funded: 1
external_id:
isi:
- '000584989400001'
pmid:
- '32940606'
file:
- access_level: open_access
checksum: c4300ddcd93ed03fc9c6cdf1f77890be
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T11:37:32Z
date_updated: 2020-10-27T11:37:32Z
file_id: '8709'
file_name: 2020_eLife_Gonçalves.pdf
file_size: 17355867
relation: main_file
success: 1
file_date_updated: 2020-10-27T11:37:32Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Training deep neural density estimators to identify mechanistic models of neural
dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8126'
abstract:
- lang: eng
text: Cortical areas comprise multiple types of inhibitory interneurons with stereotypical
connectivity motifs, but their combined effect on postsynaptic dynamics has been
largely unexplored. Here, we analyse the response of a single postsynaptic model
neuron receiving tuned excitatory connections alongside inhibition from two plastic
populations. Depending on the inhibitory plasticity rule, synapses remain unspecific
(flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the
neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on
the modulatory state of inhibition. When both inhibitory populations are active,
inhibition balances excitation, resulting in uncorrelated postsynaptic responses
regardless of the inhibitory tuning profiles. Modulating the activity of a given
inhibitory population produces strong correlations to either preferred or non-preferred
inputs, in line with recent experimental findings showing dramatic context-dependent
changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive
field doesn’t follow directly from the weight profiles of its presynaptic afferents.
article_processing_charge: No
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Andrea I.
full_name: Luppi, Andrea I.
last_name: Luppi
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge
from plasticity and allow attentional switching of receptive fields. The Journal
of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020
apa: Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory
weight profiles emerge from plasticity and allow attentional switching of receptive
fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020
chicago: Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory
Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive
Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.
ieee: E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight
profiles emerge from plasticity and allow attentional switching of receptive fields,”
The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience,
pp. 9634–9649, 2020.
ista: Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles
emerge from plasticity and allow attentional switching of receptive fields. The
Journal of Neuroscience. 40(50), 9634–9649.
mla: Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge
from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal
of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49,
doi:10.1523/JNEUROSCI.0276-20.2020.
short: E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020)
9634–9649.
date_created: 2020-07-16T12:25:04Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T07:54:26Z
day: '09'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0276-20.2020
external_id:
isi:
- '000606706400009'
pmid:
- '33168622'
file:
- access_level: open_access
checksum: 7977e4dd6b89357d1a5cc88babac56da
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:31:47Z
date_updated: 2020-12-28T08:31:47Z
file_id: '8977'
file_name: 2020_JourNeuroscience_Agnes.pdf
file_size: 2750920
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:31:47Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 9634-9649
pmid: 1
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complementary inhibitory weight profiles emerge from plasticity and allow attentional
switching of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2020'
...
---
_id: '9706'
abstract:
- lang: eng
text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted
protein levels with biological and technical covariates. Protein levels were adjusted
for age, sex, array plate and four genetic principal components (population structure)
prior to analyses. Significant associations are emboldened. (Table S1). pQTLs
associated with inflammatory biomarker levels from Bayesian penalised regression
model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated
with inflammatory biomarker levels from ordinary least squares regression model
(P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary
least squares GWAS and EWAS performed on inflammatory protein levels (n = 70)
in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs
associated with inflammatory biomarker levels from ordinary least squares regression
model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary
least squares and Bayesian penalised regression models for concordantly identified
SNPs. (Table S6). Estimate of heritability for blood protein levels as well as
proportion of variance explained attributable to different prior mixtures. (Table
S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood)
and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant
SNPs identified by linear model and Bayesian penalised regression and whether
they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation
for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression
are putatively associated with circulating inflammatory proteins that harbour
pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified
by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table
S12). CpGs associated with inflammatory protein biomarkers as identified by linear
model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory
protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10.
(Table S14). Estimate of variance explained for blood protein levels by DNA methylation
as well as proportion of explained attributable to different prior mixtures -
BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide
DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression
model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker
levels explained by common genetic and methylation data (joint and conditional
estimates from BayesR+). Ordered by combined variance explained by genetic and
epigenetic data - smallest to largest. Significant results from t-tests comparing
distributions for variance explained by methylation or genetics alone versus combined
estimate are emboldened. (Table S17). Genetic and epigenetic factors identified
by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian
Randomisation analyses to assess whether proteins with concordantly identified
genetic signals are causally associated with Alzheimer’s disease risk. (Table
S19).'
article_processing_charge: No
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: McCartney, Daniel L.
last_name: McCartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: 'Allan F. '
full_name: 'McRae, Allan F. '
last_name: McRae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: 'Riccardo E. '
full_name: 'Marioni, Riccardo E. '
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. 2020. doi:10.6084/m9.figshare.12629697.v1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional
File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein
Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.
ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and
epigenome-wide studies of inflammatory protein levels in healthy older adults.”
Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional
file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein
levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.
mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and
Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.
Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, (2020).
date_created: 2021-07-23T08:59:15Z
date_published: 2020-07-09T00:00:00Z
date_updated: 2023-08-22T07:55:36Z
day: '09'
department:
- _id: MaRo
doi: 10.6084/m9.figshare.12629697.v1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.12629697.v1
month: '07'
oa: 1
oa_version: Published Version
other_data_license: CC0 + CC BY (4.0)
publisher: Springer Nature
related_material:
record:
- id: '8133'
relation: used_in_publication
status: public
status: public
title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory
protein levels in healthy older adults
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '8134'
abstract:
- lang: eng
text: We prove an upper bound on the free energy of a two-dimensional homogeneous
Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the
free energy per unit volume differs from the one of the non-interacting system
by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering
length of the two-body interaction potential, ρ is the density, β is the inverse
temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature
for superfluidity. In combination with the corresponding matching lower bound
proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality
in the asymptotic expansion.
article_number: '061901'
article_processing_charge: No
article_type: original
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas.
II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950
apa: Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional
dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP
Publishing. https://doi.org/10.1063/5.0005950
chicago: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP
Publishing, 2020. https://doi.org/10.1063/5.0005950.
ieee: S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute
Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no.
6. AIP Publishing, 2020.
ista: Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute
Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.
mla: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol.
61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.
short: S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).
date_created: 2020-07-19T22:00:59Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-08-22T08:12:40Z
day: '22'
department:
- _id: RoSe
doi: 10.1063/5.0005950
ec_funded: 1
external_id:
arxiv:
- '2002.08281'
isi:
- '000544595100001'
intvolume: ' 61'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.08281
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free energy of the two-dimensional dilute Bose gas. II. Upper bound
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8162'
abstract:
- lang: eng
text: In mammalian genomes, a subset of genes is regulated by genomic imprinting,
resulting in silencing of one parental allele. Imprinting is essential for cerebral
cortex development, but prevalence and functional impact in individual cells is
unclear. Here, we determined allelic expression in cortical cell types and established
a quantitative platform to interrogate imprinting in single cells. We created
cells with uniparental chromosome disomy (UPD) containing two copies of either
the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold
overexpressed or not expressed. By genetic labeling of UPD, we determined cellular
phenotypes and transcriptional responses to deregulated imprinted gene expression
at unprecedented single-cell resolution. We discovered an unexpected degree of
cell-type specificity and a novel function of imprinting in the regulation of
cortical astrocyte survival. More generally, our results suggest functional relevance
of imprinted gene expression in glial astrocyte lineage and thus for generating
cortical cell-type diversity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical
support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen
for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of
the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo
for comments on earlier versions of the manuscript. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical
Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian
Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031).
R.B. received support from the FWF Meitner-Programm (M 2416). This work was also
supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers
Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement 618444 to S.H.; and the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro)
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Thomas
full_name: Penz, Thomas
last_name: Penz
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
orcid: 0000-0001-6091-3088
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting
in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031
apa: Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher,
C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031
chicago: Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi
H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer.
“Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.
ieee: S. Laukoter et al., “Cell-type specificity of genomic imprinting in
cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.
ista: Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T,
Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. 107(6), 1160–1179.e9.
mla: Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral
Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.
short: S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher,
T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.
date_created: 2020-07-23T16:03:12Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:20:11Z
day: '23'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2020.06.031
ec_funded: 1
external_id:
isi:
- '000579698700006'
file:
- access_level: open_access
checksum: 7becdc16a6317304304631087ae7dd7f
content_type: application/pdf
creator: dernst
date_created: 2020-12-02T09:26:46Z
date_updated: 2020-12-02T09:26:46Z
file_id: '8828'
file_name: 2020_Neuron_Laukoter.pdf
file_size: 8911830
relation: main_file
success: 1
file_date_updated: 2020-12-02T09:26:46Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1160-1179.e9
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/
scopus_import: '1'
status: public
title: Cell-type specificity of genomic imprinting in cerebral cortex
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '8138'
abstract:
- lang: eng
text: Directional transport of the phytohormone auxin is a versatile, plant-specific
mechanism regulating many aspects of plant development. The recently identified
plant hormones, strigolactones (SLs), are implicated in many plant traits; among
others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters
for fine-tuning of growth and developmental responses. Here, we show in pea and
Arabidopsis that SLs target processes dependent on the canalization of auxin flow,
which involves auxin feedback on PIN subcellular distribution. D14 receptor- and
MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels
after wounding or from artificial auxin sources, during vasculature de novo formation
and regeneration. At the cellular level, SLs interfere with auxin effects on PIN
polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis.
Our results identify a non-transcriptional mechanism of SL action, uncoupling
auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue
formation and regeneration.
acknowledgement: We are grateful to David Nelson for providing published materials
and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful
discussions. The research leading to these results has received funding from the
European Research Council (ERC) under the European Union's Horizon 2020 research
and innovation programme (742985). This work was also supported by the Beijing Municipal
Natural Science Foundation (5192011), Beijing Outstanding University Discipline
Program, the National Natural Science Foundation of China (31370309), CEITEC 2020
(LQ1601) project with financial contribution made by the Ministry of Education,
Youth and Sports of the Czech Republic within special support paid from the National
Program of Sustainability II funds, Australian Research Council (FT180100081), and
China Postdoctoral Science Foundation (2019M660864).
article_processing_charge: No
article_type: original
author:
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: J
full_name: Balla, J
last_name: Balla
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: P
full_name: Kalousek, P
last_name: Kalousek
- first_name: Z
full_name: Medveďová, Z
last_name: Medveďová
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: V
full_name: Reinöhl, V
last_name: Reinöhl
- first_name: S
full_name: Procházka, S
last_name: Procházka
- first_name: R
full_name: Halouzka, R
last_name: Halouzka
- first_name: P
full_name: Tarkowski, P
last_name: Tarkowski
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
- first_name: PB
full_name: Brewer, PB
last_name: Brewer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on
PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508.
doi:10.1038/s41467-020-17252-y
apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z.,
… Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin
transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y
chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová,
Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport
Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.
ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer
Nature, p. 3508, 2020.
ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang
Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig
C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization. Nature Communications. 11(1), 3508.
mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin
Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer
Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.
short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y.
Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P.
Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.
date_created: 2020-07-21T08:58:07Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2023-08-22T08:13:44Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17252-y
ec_funded: 1
external_id:
isi:
- '000550062200004'
pmid:
- '32665554'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T08:32:55Z
date_updated: 2020-07-22T08:32:55Z
file_id: '8148'
file_name: 2020_NatureComm_Zhang.pdf
file_size: 1759490
relation: main_file
success: 1
file_date_updated: 2020-07-22T08:32:55Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '3508'
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8168'
abstract:
- lang: eng
text: Speciation, that is, the evolution of reproductive barriers eventually leading
to complete isolation, is a crucial process generating biodiversity. Recent work
has contributed much to our understanding of how reproductive barriers begin to
evolve, and how they are maintained in the face of gene flow. However, little
is known about the transition from partial to strong reproductive isolation (RI)
and the completion of speciation. We argue that the evolution of strong RI is
likely to involve different processes, or new interactions among processes, compared
with the evolution of the first reproductive barriers. Transition to strong RI
may be brought about by changing external conditions, for example, following secondary
contact. However, the increasing levels of RI themselves create opportunities
for new barriers to evolve and, and interaction or coupling among barriers. These
changing processes may depend on genomic architecture and leave detectable signals
in the genome. We outline outstanding questions and suggest more theoretical and
empirical work, considering both patterns and processes associated with strong
RI, is needed to understand how speciation is completed.
article_number: '20190528'
article_processing_charge: No
article_type: original
author:
- first_name: Jonna
full_name: Kulmuni, Jonna
last_name: Kulmuni
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Kay
full_name: Lucek, Kay
last_name: Lucek
- first_name: Vincent
full_name: Savolainen, Vincent
last_name: Savolainen
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion
of speciation: The evolution of reproductive isolation beyond the first barriers.
Philosophical Transactions of the Royal Society Series B: Biological sciences.
2020;375(1806). doi:10.1098/rstb.2019.0528'
apa: 'Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M.
(2020). Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers. Philosophical Transactions of the Royal Society.
Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528'
chicago: 'Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja
M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive
Isolation beyond the First Barriers.” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.'
ieee: 'J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards
the completion of speciation: The evolution of reproductive isolation beyond the
first barriers,” Philosophical Transactions of the Royal Society. Series B:
Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.'
ista: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the
completion of speciation: The evolution of reproductive isolation beyond the first
barriers. Philosophical Transactions of the Royal Society. Series B: Biological
sciences. 375(1806), 20190528.'
mla: 'Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution
of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528,
The Royal Society, 2020, doi:10.1098/rstb.2019.0528.'
short: 'J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical
Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:21:31Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0528
ec_funded: 1
external_id:
isi:
- '000552662100001'
pmid:
- '32654637'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0528
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8167'
abstract:
- lang: eng
text: The evolution of strong reproductive isolation (RI) is fundamental to the
origins and maintenance of biological diversity, especially in situations where
geographical distributions of taxa broadly overlap. But what is the history behind
strong barriers currently acting in sympatry? Using whole-genome sequencing and
single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships,
(ii) the strength of RI, and (iii) the demographic history of divergence between
two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on
external morphology, Littorina arcana and Littorina saxatilis differ in their
mode of female reproduction (egg-laying versus brooding), which may generate a
strong post-zygotic barrier. We show that egg-laying and brooding snails are closely
related, but genetically distinct. Genotyping of 3092 snails from three locations
failed to recover any recent hybrid or backcrossed individuals, confirming that
RI is strong. There was, however, evidence for a very low level of asymmetrical
introgression, suggesting that isolation remains incomplete. The presence of strong,
asymmetrical RI was further supported by demographic analysis of these populations.
Although the taxa are currently broadly sympatric, demographic modelling suggests
that they initially diverged during a short period of geographical separation
involving very low gene flow. Our study suggests that some geographical separation
may kick-start the evolution of strong RI, facilitating subsequent coexistence
of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent
effect of sympatry on RI remain open questions.
acknowledgement: Funding was provided by the Natural Environment Research Council
(NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin
Garlovsky and Hernan Morales for advice and/or useful discussion during the project.
Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton
participated in the collection and processing of samples. Mark Dunning helped with
the development of bioinformatic pipelines. The analysis of genomic data was conducted
on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and
an anonymous reviewer provided comments that improved the manuscript.
article_number: '20190545'
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Isobel
full_name: Eyres, Isobel
last_name: Eyres
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545'
apa: 'Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T.,
Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545'
chicago: 'Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres,
Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong
Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0545.'
ieee: 'S. Stankowski et al., “The evolution of strong reproductive isolation
between sympatric intertidal snails,” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society,
2020.'
ista: 'Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K,
Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric
intertidal snails. Philosophical Transactions of the Royal Society. Series B:
Biological Sciences. 375(1806), 20190545.'
mla: 'Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between
Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society.
Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society,
2020, doi:10.1098/rstb.2019.0545.'
short: 'S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson,
R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological
Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:22:13Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0545
external_id:
isi:
- '000552662100014'
pmid:
- '32654639'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0545
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolution of strong reproductive isolation between sympatric intertidal
snails
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8170'
abstract:
- lang: eng
text: "Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is
measured as a function\r\nof time following rotational excitation by a nonresonant,
comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra,
obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal
distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy.
For\r\nCS2 and I2, they are the first experimental results reported. The alignment
dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using
the experimental in-droplet B and D values, agree in\r\ndetail with the measurement
for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium
droplets introduced here should apply to a range of molecules and complexes."
acknowledgement: "H. S. acknowledges support from the European Research Council-AdG
(Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a
Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian
Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC)
Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian
Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by
the European Union’s Horizon 2020 research and\r\ninnovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe
PIMC simulations were provided by the division for scientific computing at the Johannes
Kepler University."
article_number: '013001'
article_processing_charge: No
article_type: original
author:
- first_name: Adam S.
full_name: Chatterley, Adam S.
last_name: Chatterley
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Anders V.
full_name: Jørgensen, Anders V.
last_name: Jørgensen
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Robert E.
full_name: Zillich, Robert E.
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001'
apa: 'Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson,
B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001'
chicago: 'Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V.
Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich,
Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of
Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.”
Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.'
ieee: 'A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules
in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical
Review Letters, vol. 125, no. 1. American Physical Society, 2020.'
ista: 'Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov
I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence
spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the
frequency domains. Physical Review Letters. 125(1), 013001.'
mla: 'Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules
in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical
Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020,
doi:10.1103/PhysRevLett.125.013001.'
short: A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson,
I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical
Review Letters 125 (2020).
date_created: 2020-07-26T22:01:02Z
date_published: 2020-07-03T00:00:00Z
date_updated: 2023-08-22T08:22:43Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.125.013001
ec_funded: 1
external_id:
arxiv:
- '2006.02694'
isi:
- '000544526900006'
intvolume: ' 125'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.02694
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling
the time and the frequency domains'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 125
year: '2020'
...
---
_id: '8194'
abstract:
- lang: eng
text: 'Fixed-point arithmetic is a popular alternative to floating-point arithmetic
on embedded systems. Existing work on the verification of fixed-point programs
relies on custom formalizations of fixed-point arithmetic, which makes it hard
to compare the described techniques or reuse the implementations. In this paper,
we address this issue by proposing and formalizing an SMT theory of fixed-point
arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point
theory, and provide formal semantics for it based on rational arithmetic. We also
describe two decision procedures for this theory: one based on the theory of bit-vectors
and the other on the theory of reals. We implement the two decision procedures,
and evaluate our implementations using existing mature SMT solvers on a benchmark
suite we created. Finally, we perform a case study of using the theory we propose
to verify properties of quantized neural networks.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Baranowski, Marek
last_name: Baranowski
- first_name: Shaobo
full_name: He, Shaobo
last_name: He
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Thanh Son
full_name: Nguyen, Thanh Son
last_name: Nguyen
- first_name: Zvonimir
full_name: Rakamarić, Zvonimir
last_name: Rakamarić
citation:
ama: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point
arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31.
doi:10.1007/978-3-030-51074-9_2'
apa: 'Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020).
An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166,
pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2'
chicago: Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir
Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning,
12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.
ieee: M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT
theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France,
2020, vol. 12166, pp. 13–31.
ista: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory
of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference
on Automated Reasoning, LNCS, vol. 12166, 13–31.'
mla: Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated
Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.
short: M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated
Reasoning, Springer Nature, 2020, pp. 13–31.
conference:
end_date: 2020-07-04
location: Paris, France
name: 'IJCAR: International Joint Conference on Automated Reasoning'
start_date: 2020-07-01
date_created: 2020-08-02T22:00:59Z
date_published: 2020-06-24T00:00:00Z
date_updated: 2023-08-22T08:27:25Z
day: '24'
department:
- _id: ToHe
doi: 10.1007/978-3-030-51074-9_2
external_id:
isi:
- '000884318000002'
intvolume: ' 12166'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-030-51074-9_2
month: '06'
oa: 1
oa_version: Published Version
page: 13-31
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Automated Reasoning
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030510732'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An SMT theory of fixed-point arithmetic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12166
year: '2020'
...
---
_id: '8220'
abstract:
- lang: eng
text: Understanding to what extent stem cell potential is a cell-intrinsic property
or an emergent behavior coming from global tissue dynamics and geometry is a key
outstanding question of systems and stem cell biology. Here, we propose a theory
of stem cell dynamics as a stochastic competition for access to a spatially localized
niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce
a steady cellular stream which advects cells away from the niche, while random
rearrangements enable cells away from the niche to be favorably repositioned.
Importantly, even when assuming that all cells in a tissue are molecularly equivalent,
we predict a common (“universal”) functional dependence of the long-term clonal
survival probability on distance from the niche, as well as the emergence of a
well-defined number of functional stem cells, dependent only on the rate of random
movements vs. mitosis-driven advection. We test the predictions of this theory
on datasets of pubertal mammary gland tips and embryonic kidney tips, as well
as homeostatic intestinal crypts. Importantly, we find good agreement for the
predicted functional dependency of the competition as a function of position,
and thus functional stem cell number in each organ. This argues for a key role
of positional fluctuations in dictating stem cell number and dynamics, and we
discuss the applicability of this theory to other settings.
acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for
stimulating discussions. This project was supported by\r\nthe European Research
Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from
the CancerGenomics.nl (Netherlands Organization for Scientific Research) program
(J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by
Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust
Grant 098357/Z/12/Z."
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Saskia I.J.
full_name: Ellenbroek, Saskia I.J.
last_name: Ellenbroek
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival
as a noisy competition for niche access. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117
apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J.,
Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage
survival as a noisy competition for niche access. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1921205117
chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia
I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo.
“Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.
ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy
competition for niche access,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 117, no. 29. National Academy of Sciences,
pp. 16969–16975, 2020.
ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van
Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition
for niche access. Proceedings of the National Academy of Sciences of the United
States of America. 117(29), 16969–16975.
mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition
for Niche Access.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp.
16969–75, doi:10.1073/pnas.1921205117.
short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D.
Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences
of the United States of America 117 (2020) 16969–16975.
date_created: 2020-08-09T22:00:52Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2023-08-22T08:29:30Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1921205117
ec_funded: 1
external_id:
isi:
- '000553292900014'
pmid:
- '32611816'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T06:50:28Z
date_updated: 2020-08-10T06:50:28Z
file_id: '8223'
file_name: 2020_PNAS_Corominas.pdf
file_size: 1111604
relation: main_file
success: 1
file_date_updated: 2020-08-10T06:50:28Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16969-16975
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/order-from-noise/
scopus_import: '1'
status: public
title: Stem cell lineage survival as a noisy competition for niche access
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8199'
abstract:
- lang: eng
text: We investigate a mechanism to transiently stabilize topological phenomena
in long-lived quasi-steady states of isolated quantum many-body systems driven
at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady
states which is exponentially large in the inverse driving frequency. Within this
lifetime, the quasi-steady state is characterized by maximum entropy subject to
the constraint of fixed number of particles in the system's Floquet-Bloch bands.
In such a state, all the non-universal properties of these bands are washed out,
hence only the topological properties persist.
acknowledgement: "N.L., T.G. and E.B. acknowledge support from the European Research
Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme
(Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship
at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and
Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research
and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No.
754411. N.L. acknowledges support from the People Programme (Marie Curie Actions)
of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA
Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence
(I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12).
M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC)
under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement
No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B.
acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft"
article_number: '015'
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Mark Spencer
full_name: Rudner, Mark Spencer
last_name: Rudner
- first_name: Netanel
full_name: Lindner, Netanel
last_name: Lindner
citation:
ama: Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal
quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9.
doi:10.21468/scipostphys.9.1.015
apa: Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially
long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015
chicago: Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially
Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.”
SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.
ieee: T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps,” SciPost Physics,
vol. 9. SciPost Foundation, 2020.
ista: Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps. SciPost Physics.
9, 015.
mla: Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady
States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost
Foundation, 2020, doi:10.21468/scipostphys.9.1.015.
short: T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).
date_created: 2020-08-04T13:04:15Z
date_published: 2020-07-29T00:00:00Z
date_updated: 2023-08-22T08:28:24Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.9.1.015
ec_funded: 1
external_id:
isi:
- '000557362300008'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-06T08:56:06Z
date_updated: 2020-08-06T08:56:06Z
file_id: '8202'
file_name: 2020_SciPostPhys_Gulden.pdf
file_size: 531137
relation: main_file
success: 1
file_date_updated: 2020-08-06T08:56:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exponentially long lifetime of universal quasi-steady states in topological
Floquet pumps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8261'
abstract:
- lang: eng
text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal
CA3 region, but how they process spatial information remains enigmatic. To examine
the role of GCs in spatial coding, we measured excitatory postsynaptic potentials
(EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt.
Intracellular recording from morphologically identified GCs revealed that most
cells were active, but activity level varied over a wide range. Whereas only ∼5%
of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus,
the GC population broadly encodes spatial information, but only a subset relays
this information to the CA3 network. Fourier analysis indicated that GCs received
conjunctive place-grid-like synaptic input, suggesting code conversion in single
neurons. GC firing was correlated with dendritic complexity and intrinsic excitability,
but not extrinsic excitatory input or dendritic cable properties. Thus, functional
maturation may control input-output transformation and spatial code conversion.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari,
Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of
this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery
Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp
recording. We are grateful to Florian Marr for cell labeling, cell reconstruction,
and technical assistance; Ben Suter for helpful discussions; Christina Altmutter
for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor
Asenov (Machine Shop) for device construction. We also thank the Scientific Service
Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical
Facility) for efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow
from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225.
doi:10.1016/j.neuron.2020.07.006
apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial
information flow from input to output in hippocampal granule cells. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006
chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of
Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.
ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information
flow from input to output in hippocampal granule cells,” Neuron, vol. 107,
no. 6. Elsevier, pp. 1212–1225, 2020.
ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information
flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.
mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from
Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6,
Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.
short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.
date_created: 2020-08-14T09:36:05Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:30:55Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.neuron.2020.07.006
ec_funded: 1
external_id:
isi:
- '000579698700009'
pmid:
- '32763145'
file:
- access_level: open_access
checksum: 44a5960fc083a4cb3488d22224859fdc
content_type: application/pdf
creator: dernst
date_created: 2020-12-04T09:29:21Z
date_updated: 2020-12-04T09:29:21Z
file_id: '8920'
file_name: 2020_Neuron_Zhang.pdf
file_size: 3011120
relation: main_file
success: 1
file_date_updated: 2020-12-04T09:29:21Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1212-1225
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/
status: public
title: Selective routing of spatial information flow from input to output in hippocampal
granule cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '8268'
abstract:
- lang: eng
text: 'Modern scientific instruments produce vast amounts of data, which can overwhelm
the processing ability of computer systems. Lossy compression of data is an intriguing
solution, but comes with its own drawbacks, such as potential signal loss, and
the need for careful optimization of the compression ratio. In this work, we focus
on a setting where this problem is especially acute: compressive sensing frameworks
for interferometry and medical imaging. We ask the following question: can the
precision of the data representation be lowered for all inputs, with recovery
guarantees and practical performance Our first contribution is a theoretical analysis
of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data,
meaning both the measurement matrix and the observation vector are quantized aggressively.
We present a variant of low precision normalized IHT that, under mild conditions,
can still provide recovery guarantees. The second contribution is the application
of our quantization framework to radio astronomy and magnetic resonance imaging.
We show that lowering the precision of the data can significantly accelerate image
recovery. We evaluate our approach on telescope data and samples of brain images
using CPU and FPGA implementations achieving up to a 9x speedup with negligible
loss of recovery quality.'
acknowledgement: The authors would like to thank Dr. Michiel Brentjens at the Netherlands
Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and
Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology
of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab
gratefully acknowledge the support from the Swiss Data Science Center, Alibaba,
Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich
Insurance, Chinese Scholarship Council, and the Department of Computer Science at
ETH Zurich.
article_processing_charge: No
article_type: original
author:
- first_name: Nezihe Merve
full_name: Gurel, Nezihe Merve
last_name: Gurel
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler
full_name: Smith, Tyler
last_name: Smith
- first_name: Thomas
full_name: Lemmin, Thomas
last_name: Lemmin
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Puschel, Markus
last_name: Puschel
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard
thresholding with low precision data representation: Theory and applications.
IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355'
apa: 'Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A.,
… Zhang, C. (2020). Compressive sensing using iterative hard thresholding with
low precision data representation: Theory and applications. IEEE Transactions
on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355'
chicago: 'Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin,
Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using
Iterative Hard Thresholding with Low Precision Data Representation: Theory and
Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.'
ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding
with low precision data representation: Theory and applications,” IEEE Transactions
on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.'
ista: 'Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M,
Zhang C. 2020. Compressive sensing using iterative hard thresholding with low
precision data representation: Theory and applications. IEEE Transactions on Signal
Processing. 68, 4268–4282.'
mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding
with Low Precision Data Representation: Theory and Applications.” IEEE Transactions
on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.'
short: N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M.
Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.
date_created: 2020-08-16T22:00:56Z
date_published: 2020-07-20T00:00:00Z
date_updated: 2023-08-22T08:40:08Z
day: '20'
department:
- _id: DaAl
doi: 10.1109/TSP.2020.3010355
external_id:
arxiv:
- '1802.04907'
isi:
- '000562044500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.04907
month: '07'
oa: 1
oa_version: Preprint
page: 4268-4282
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- '19410476'
issn:
- 1053587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Compressive sensing using iterative hard thresholding with low precision data
representation: Theory and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2020'
...