---
_id: '7864'
abstract:
- lang: eng
text: "Purpose of review: Cancer is one of the leading causes of death and the incidence
rates are constantly rising. The heterogeneity of tumors poses a big challenge
for the treatment of the disease and natural antibodies additionally affect disease
progression. The introduction of engineered mAbs for anticancer immunotherapies
has substantially improved progression-free and overall survival of cancer patients,
but little efforts have been made to exploit other antibody isotypes than IgG.\r\nRecent
findings: In order to improve these therapies, ‘next-generation antibodies’ were
engineered to enhance a specific feature of classical antibodies and form a group
of highly effective and precise therapy compounds. Advanced antibody approaches
include among others antibody-drug conjugates, glyco-engineered and Fc-engineered
antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies
and alternative (non-IgG) immunoglobulin classes, especially IgE.\r\nSummary:
The current review describes solutions for the needs of next-generation antibody
therapies through different approaches. Careful selection of the best-suited engineering
methodology is a key factor in developing personalized, more specific and more
efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight
here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential
next-generation anticancer immunotherapy."
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Singer
orcid: 0000-0002-8777-3502
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Singer J, Singer J, Jensen-Jarolim E. Precision medicine in clinical oncology:
the journey from IgG antibody to IgE. Current opinion in allergy and clinical
immunology. 2020;20(3):282-289. doi:10.1097/ACI.0000000000000637'
apa: 'Singer, J., Singer, J., & Jensen-Jarolim, E. (2020). Precision medicine
in clinical oncology: the journey from IgG antibody to IgE. Current Opinion
in Allergy and Clinical Immunology. Wolters Kluwer. https://doi.org/10.1097/ACI.0000000000000637'
chicago: 'Singer, Judit, Josef Singer, and Erika Jensen-Jarolim. “Precision Medicine
in Clinical Oncology: The Journey from IgG Antibody to IgE.” Current Opinion
in Allergy and Clinical Immunology. Wolters Kluwer, 2020. https://doi.org/10.1097/ACI.0000000000000637.'
ieee: 'J. Singer, J. Singer, and E. Jensen-Jarolim, “Precision medicine in clinical
oncology: the journey from IgG antibody to IgE,” Current opinion in allergy
and clinical immunology, vol. 20, no. 3. Wolters Kluwer, pp. 282–289, 2020.'
ista: 'Singer J, Singer J, Jensen-Jarolim E. 2020. Precision medicine in clinical
oncology: the journey from IgG antibody to IgE. Current opinion in allergy and
clinical immunology. 20(3), 282–289.'
mla: 'Singer, Judit, et al. “Precision Medicine in Clinical Oncology: The Journey
from IgG Antibody to IgE.” Current Opinion in Allergy and Clinical Immunology,
vol. 20, no. 3, Wolters Kluwer, 2020, pp. 282–89, doi:10.1097/ACI.0000000000000637.'
short: J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical
Immunology 20 (2020) 282–289.
date_created: 2020-05-17T22:00:44Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-21T06:28:52Z
day: '01'
department:
- _id: Bio
doi: 10.1097/ACI.0000000000000637
external_id:
isi:
- '000561358300010'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 282-289
publication: Current opinion in allergy and clinical immunology
publication_identifier:
eissn:
- '14736322'
publication_status: published
publisher: Wolters Kluwer
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Precision medicine in clinical oncology: the journey from IgG antibody to
IgE'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
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
license: https://creativecommons.org/licenses/by/4.0/
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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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: '13999'
abstract:
- lang: eng
text: Attosecond chronoscopy has revealed small but measurable delays in photoionization,
characterized by the ejection of an electron on absorption of a single photon.
Ionization-delay measurements in atomic targets provide a wealth of information
about the timing of the photoelectric effect, resonances, electron correlations
and transport. However, extending this approach to molecules presents challenges,
such as identifying the correct ionization channels and the effect of the anisotropic
molecular landscape on the measured delays. Here, we measure ionization delays
from ethyl iodide around a giant dipole resonance. By using the theoretical value
for the iodine atom as a reference, we disentangle the contribution from the functional
ethyl group, which is responsible for the characteristic chemical reactivity of
a molecule. We find a substantial additional delay caused by the presence of a
functional group, which encodes the effect of the molecular potential on the departing
electron. Such information is inaccessible to the conventional approach of measuring
photoionization cross-sections. The results establish ionization-delay measurements
as a valuable tool in investigating the electronic properties of molecules.
article_processing_charge: No
article_type: original
author:
- first_name: Shubhadeep
full_name: Biswas, Shubhadeep
last_name: Biswas
- first_name: Benjamin
full_name: Förg, Benjamin
last_name: Förg
- first_name: Lisa
full_name: Ortmann, Lisa
last_name: Ortmann
- first_name: Johannes
full_name: Schötz, Johannes
last_name: Schötz
- first_name: Wolfgang
full_name: Schweinberger, Wolfgang
last_name: Schweinberger
- first_name: Tomáš
full_name: Zimmermann, Tomáš
last_name: Zimmermann
- first_name: Liangwen
full_name: Pi, Liangwen
last_name: Pi
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hafiz A.
full_name: Masood, Hafiz A.
last_name: Masood
- first_name: Ioannis
full_name: Liontos, Ioannis
last_name: Liontos
- first_name: Amgad M.
full_name: Kamal, Amgad M.
last_name: Kamal
- first_name: Nora G.
full_name: Kling, Nora G.
last_name: Kling
- first_name: Abdullah F.
full_name: Alharbi, Abdullah F.
last_name: Alharbi
- first_name: Meshaal
full_name: Alharbi, Meshaal
last_name: Alharbi
- first_name: Abdallah M.
full_name: Azzeer, Abdallah M.
last_name: Azzeer
- first_name: Gregor
full_name: Hartmann, Gregor
last_name: Hartmann
- first_name: Hans J.
full_name: Wörner, Hans J.
last_name: Wörner
- first_name: Alexandra S.
full_name: Landsman, Alexandra S.
last_name: Landsman
- first_name: Matthias F.
full_name: Kling, Matthias F.
last_name: Kling
citation:
ama: Biswas S, Förg B, Ortmann L, et al. Probing molecular environment through photoemission
delays. Nature Physics. 2020;16(7):778-783. doi:10.1038/s41567-020-0887-8
apa: Biswas, S., Förg, B., Ortmann, L., Schötz, J., Schweinberger, W., Zimmermann,
T., … Kling, M. F. (2020). Probing molecular environment through photoemission
delays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0887-8
chicago: Biswas, Shubhadeep, Benjamin Förg, Lisa Ortmann, Johannes Schötz, Wolfgang
Schweinberger, Tomáš Zimmermann, Liangwen Pi, et al. “Probing Molecular Environment
through Photoemission Delays.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0887-8.
ieee: S. Biswas et al., “Probing molecular environment through photoemission
delays,” Nature Physics, vol. 16, no. 7. Springer Nature, pp. 778–783,
2020.
ista: Biswas S, Förg B, Ortmann L, Schötz J, Schweinberger W, Zimmermann T, Pi L,
Baykusheva DR, Masood HA, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M,
Azzeer AM, Hartmann G, Wörner HJ, Landsman AS, Kling MF. 2020. Probing molecular
environment through photoemission delays. Nature Physics. 16(7), 778–783.
mla: Biswas, Shubhadeep, et al. “Probing Molecular Environment through Photoemission
Delays.” Nature Physics, vol. 16, no. 7, Springer Nature, 2020, pp. 778–83,
doi:10.1038/s41567-020-0887-8.
short: S. Biswas, B. Förg, L. Ortmann, J. Schötz, W. Schweinberger, T. Zimmermann,
L. Pi, D.R. Baykusheva, H.A. Masood, I. Liontos, A.M. Kamal, N.G. Kling, A.F.
Alharbi, M. Alharbi, A.M. Azzeer, G. Hartmann, H.J. Wörner, A.S. Landsman, M.F.
Kling, Nature Physics 16 (2020) 778–783.
date_created: 2023-08-09T13:10:07Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T07:38:04Z
day: '01'
doi: 10.1038/s41567-020-0887-8
extern: '1'
intvolume: ' 16'
issue: '7'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '07'
oa_version: None
page: 778-783
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing molecular environment through photoemission delays
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
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: '8040'
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 form—a 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
article_type: original
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun Kit
full_name: Chan, Chun Kit
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 CK, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230.
doi:10.1021/jacs.9b13450
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.9b13450
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit 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.” Journal of
the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I,” Journal of the American Chemical Society, vol.
142, no. 20. American Chemical Society, pp. 9220–9230, 2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. 142(20), 9220–9230.
mla: Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory
Complex I.” Journal of the American Chemical Society, vol. 142, no. 20,
American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142
(2020) 9220–9230.
date_created: 2020-06-29T07:59:35Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:38Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450
external_id:
isi:
- '000537415600020'
pmid:
- '32347721'
intvolume: ' 142'
isi: 1
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
page: 9220-9230
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- '15205126'
issn:
- '00027863'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '9326'
relation: research_data
status: public
- id: '9713'
relation: research_data
status: public
- id: '9878'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 142
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: '9713'
abstract:
- lang: eng
text: Additional analyses of the trajectories
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 Kit
full_name: Chan, Chun Kit
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 CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar,
M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting
Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001.
ieee: C. Gupta et al., “Supporting information.” American Chemical Society
, 2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001.
mla: Gupta, Chitrak, et al. Supporting Information. American Chemical Society
, 2020, doi:10.1021/jacs.9b13450.s001.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, (2020).
date_created: 2021-07-23T12:02:39Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:38Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s001
month: '05'
oa_version: Published Version
publisher: 'American Chemical Society '
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9878'
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 Kit
full_name: Chan, Chun Kit
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 CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar,
M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.”
American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.
ieee: C. Gupta et al., “Movies.” American Chemical Society, 2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002.
mla: Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, (2020).
date_created: 2021-08-11T09:18:54Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:38Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s002
month: '05'
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Movies
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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:
- access_level: open_access
checksum: 05a8e65d49c3f5b8e37ac4afe68287e2
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-02T12:35:12Z
date_updated: 2021-12-02T12:35:12Z
file_id: '10398'
file_name: 2020_BrJournalCancer_Hippe.pdf
file_size: 3620691
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success: 1
file_date_updated: 2021-12-02T12:35:12Z
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language:
- iso: eng
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:
- access_level: open_access
checksum: 5cbeef52caf18d0d952f17fed7b5545a
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T15:05:04Z
date_updated: 2020-11-25T15:05:04Z
file_id: '8812'
file_name: 2020_JourStatPhysics_Seiringer.pdf
file_size: 404778
relation: main_file
success: 1
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: '8039'
abstract:
- lang: eng
text: In the present work, we report a solution-based strategy to produce crystallographically
textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric
performance in the direction normal to the substrate. Our strategy is based on
the formulation of a molecular precursor that can be continuously decomposed to
produce a SnSe powder or printed into predefined patterns. The precursor formulation
and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates.
The printed layer and the bulk material obtained after hot press displays a clear
preferential orientation of the crystallographic domains, resulting in an ultralow
thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate.
Such textured nanomaterials present highly anisotropic properties with the best
thermoelectric performance in plane, i.e., in the directions parallel to the substrate,
which coincide with the crystallographic bc plane of SnSe. This is an unfortunate
characteristic because thermoelectric devices are designed to create/harvest temperature
gradients in the direction normal to the substrate. We further demonstrate that
this limitation can be overcome with the introduction of small amounts of tellurium
in the precursor. The presence of tellurium allows one to reduce the band gap
and increase both the charge carrier concentration and the mobility, especially
the cross plane, with a minimal decrease of the Seebeck coefficient. These effects
translate into record out of plane ZT values at 800 K.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Ting
full_name: Zhang, Ting
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Mercè
full_name: Pacios, Mercè
last_name: Pacios
- first_name: Xiaoting
full_name: Yu, Xiaoting
last_name: Yu
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Zhang Y, Liu Y, Xing C, et al. Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices. ACS Applied Materials and
Interfaces. 2020;12(24):27104-27111. doi:10.1021/acsami.0c04331
apa: Zhang, Y., Liu, Y., Xing, C., Zhang, T., Li, M., Pacios, M., … Cabot, A. (2020).
Tin selenide molecular precursor for the solution processing of thermoelectric
materials and devices. ACS Applied Materials and Interfaces. American Chemical
Society. https://doi.org/10.1021/acsami.0c04331
chicago: Zhang, Yu, Yu Liu, Congcong Xing, Ting Zhang, Mengyao Li, Mercè Pacios,
Xiaoting Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing
of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces.
American Chemical Society, 2020. https://doi.org/10.1021/acsami.0c04331.
ieee: Y. Zhang et al., “Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices,” ACS Applied Materials
and Interfaces, vol. 12, no. 24. American Chemical Society, pp. 27104–27111,
2020.
ista: Zhang Y, Liu Y, Xing C, Zhang T, Li M, Pacios M, Yu X, Arbiol J, Llorca J,
Cadavid D, Ibáñez M, Cabot A. 2020. Tin selenide molecular precursor for the solution
processing of thermoelectric materials and devices. ACS Applied Materials and
Interfaces. 12(24), 27104–27111.
mla: Zhang, Yu, et al. “Tin Selenide Molecular Precursor for the Solution Processing
of Thermoelectric Materials and Devices.” ACS Applied Materials and Interfaces,
vol. 12, no. 24, American Chemical Society, 2020, pp. 27104–11, doi:10.1021/acsami.0c04331.
short: Y. Zhang, Y. Liu, C. Xing, T. Zhang, M. Li, M. Pacios, X. Yu, J. Arbiol,
J. Llorca, D. Cadavid, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces
12 (2020) 27104–27111.
date_created: 2020-06-29T07:59:35Z
date_published: 2020-06-17T00:00:00Z
date_updated: 2023-08-22T07:50:08Z
day: '17'
department:
- _id: MaIb
doi: 10.1021/acsami.0c04331
ec_funded: 1
external_id:
isi:
- '000542925300032'
pmid:
- '32437128'
intvolume: ' 12'
isi: 1
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
page: 27104-27111
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- '19448252'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tin selenide molecular precursor for the solution processing of thermoelectric
materials and devices
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2020'
...
---
_id: '8133'
abstract:
- lang: eng
text: The molecular factors which control circulating levels of inflammatory proteins
are not well understood. Furthermore, association studies between molecular probes
and human traits are often performed by linear model-based methods which may fail
to account for complex structure and interrelationships within molecular datasets.In
this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS)
on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy
older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel).
We employ a Bayesian framework (BayesR+) which can account for issues pertaining
to data structure and unknown confounding variables (with sensitivity analyses
using ordinary least squares- (OLS) and mixed model-based approaches). We identified
13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and
Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG
each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged
genetic variants accounted for up to 45% of variance in protein levels (for MCP2,
36% of variance alone attributable to 1 polymorphism). Methylation data accounted
for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation
in protein levels (for VEGFA) was explained using genetic and epigenetic data
combined. We demonstrated putative causal relationships between CD6 and IL18R1
with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data
may aid understanding of the molecular regulation of the circulating inflammatory
proteome as well as causal relationships between inflammatory mediators and disease.
article_number: '60'
article_processing_charge: No
article_type: original
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Allan F.
full_name: Mcrae, Allan F.
last_name: Mcrae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
2020;12(1). doi:10.1186/s13073-020-00754-1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide
studies of inflammatory protein levels in healthy older adults. Genome Medicine.
Springer Nature. https://doi.org/10.1186/s13073-020-00754-1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method
Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older
Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.
ieee: R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies
of inflammatory protein levels in healthy older adults,” Genome Medicine,
vol. 12, no. 1. Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Genome Medicine. 12(1), 60.
mla: Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies
of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine,
vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T07:55:37Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-020-00754-1
external_id:
isi:
- '000551778400001'
pmid:
- '32641083'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:27:38Z
date_updated: 2020-07-22T06:27:38Z
file_id: '8145'
file_name: 2020_GenomeMedicine_Hillary.pdf
file_size: 1136983
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:27:38Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Medicine
publication_identifier:
eissn:
- 1756994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '9706'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-method genome- and epigenome-wide studies of inflammatory protein levels
in healthy older adults
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2020'
...
---
_id: '8127'
abstract:
- lang: eng
text: Mechanistic modeling in neuroscience aims to explain observed phenomena in
terms of underlying causes. However, determining which model parameters agree
with complex and stochastic neural data presents a significant challenge. We address
this challenge with a machine learning tool which uses deep neural density estimators—trained
using model simulations—to carry out Bayesian inference and retrieve the full
space of parameters compatible with raw data or selected data features. Our method
is scalable in parameters and data features and can rapidly analyze new data after
initial training. We demonstrate the power and flexibility of our approach on
receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize
the space of circuit configurations giving rise to rhythmic activity in the crustacean
stomatogastric ganglion, and use these results to derive hypotheses for underlying
compensation mechanisms. Our approach will help close the gap between data-driven
and theory-driven models of neural dynamics.
acknowledgement: We thank Mahmood S Hoseini and Michael Stryker for sharing their
data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham,
Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid
Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the
manuscript. This work was supported by the German Research Foundation (DFG) through
SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041
‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1
– Project number 390727645 and the German Federal Ministry of Education and Research
(BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome
Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant
(SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological
Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge
the Leibniz Supercomputing Centre for funding this project by providing computing
time on its Linux-Cluster.
article_number: e56261
article_processing_charge: No
article_type: original
author:
- first_name: Pedro J.
full_name: Gonçalves, Pedro J.
last_name: Gonçalves
orcid: 0000-0002-6987-4836
- first_name: Jan-Matthis
full_name: Lueckmann, Jan-Matthis
last_name: Lueckmann
orcid: 0000-0003-4320-4663
- first_name: Michael
full_name: Deistler, Michael
last_name: Deistler
orcid: 0000-0002-3573-0404
- first_name: Marcel
full_name: Nonnenmacher, Marcel
last_name: Nonnenmacher
orcid: 0000-0001-6044-6627
- first_name: Kaan
full_name: Öcal, Kaan
last_name: Öcal
orcid: 0000-0002-8528-6858
- first_name: Giacomo
full_name: Bassetto, Giacomo
last_name: Bassetto
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Sara A.
full_name: Haddad, Sara A.
last_name: Haddad
orcid: 0000-0003-0807-0823
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: David S.
full_name: Greenberg, David S.
last_name: Greenberg
- first_name: Jakob H.
full_name: Macke, Jakob H.
last_name: Macke
orcid: 0000-0001-5154-8912
citation:
ama: Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density
estimators to identify mechanistic models of neural dynamics. eLife. 2020;9.
doi:10.7554/eLife.56261
apa: Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K.,
Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to
identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.56261
chicago: Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher,
Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural
Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.
ieee: P. J. Gonçalves et al., “Training deep neural density estimators to
identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto
G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020.
Training deep neural density estimators to identify mechanistic models of neural
dynamics. eLife. 9, e56261.
mla: Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify
Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences
Publications, 2020, doi:10.7554/eLife.56261.
short: P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G.
Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg,
J.H. Macke, ELife 9 (2020).
date_created: 2020-07-16T12:26:04Z
date_published: 2020-09-17T00:00:00Z
date_updated: 2023-08-22T07:54:52Z
day: '17'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.7554/eLife.56261
ec_funded: 1
external_id:
isi:
- '000584989400001'
pmid:
- '32940606'
file:
- access_level: open_access
checksum: c4300ddcd93ed03fc9c6cdf1f77890be
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T11:37:32Z
date_updated: 2020-10-27T11:37:32Z
file_id: '8709'
file_name: 2020_eLife_Gonçalves.pdf
file_size: 17355867
relation: main_file
success: 1
file_date_updated: 2020-10-27T11:37:32Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Training deep neural density estimators to identify mechanistic models of neural
dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8126'
abstract:
- lang: eng
text: Cortical areas comprise multiple types of inhibitory interneurons with stereotypical
connectivity motifs, but their combined effect on postsynaptic dynamics has been
largely unexplored. Here, we analyse the response of a single postsynaptic model
neuron receiving tuned excitatory connections alongside inhibition from two plastic
populations. Depending on the inhibitory plasticity rule, synapses remain unspecific
(flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the
neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on
the modulatory state of inhibition. When both inhibitory populations are active,
inhibition balances excitation, resulting in uncorrelated postsynaptic responses
regardless of the inhibitory tuning profiles. Modulating the activity of a given
inhibitory population produces strong correlations to either preferred or non-preferred
inputs, in line with recent experimental findings showing dramatic context-dependent
changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive
field doesn’t follow directly from the weight profiles of its presynaptic afferents.
article_processing_charge: No
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Andrea I.
full_name: Luppi, Andrea I.
last_name: Luppi
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge
from plasticity and allow attentional switching of receptive fields. The Journal
of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020
apa: Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory
weight profiles emerge from plasticity and allow attentional switching of receptive
fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020
chicago: Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory
Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive
Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.
ieee: E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight
profiles emerge from plasticity and allow attentional switching of receptive fields,”
The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience,
pp. 9634–9649, 2020.
ista: Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles
emerge from plasticity and allow attentional switching of receptive fields. The
Journal of Neuroscience. 40(50), 9634–9649.
mla: Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge
from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal
of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49,
doi:10.1523/JNEUROSCI.0276-20.2020.
short: E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020)
9634–9649.
date_created: 2020-07-16T12:25:04Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T07:54:26Z
day: '09'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0276-20.2020
external_id:
isi:
- '000606706400009'
pmid:
- '33168622'
file:
- access_level: open_access
checksum: 7977e4dd6b89357d1a5cc88babac56da
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:31:47Z
date_updated: 2020-12-28T08:31:47Z
file_id: '8977'
file_name: 2020_JourNeuroscience_Agnes.pdf
file_size: 2750920
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:31:47Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 9634-9649
pmid: 1
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complementary inhibitory weight profiles emerge from plasticity and allow attentional
switching of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2020'
...
---
_id: '8132'
abstract:
- lang: eng
text: The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral
branched actin network constituting one of the main drivers of eukaryotic cell
migration. Here, we uncover an essential role of the hematopoietic-specific WRC
component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies
an inborn error of immunity with systemic autoimmunity, at cellular level marked
by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia.
Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In
the absence of Hem1, B cells become deprived of extracellular stimuli necessary
to maintain the strength of B cell receptor signaling at a level permissive for
survival of non-autoreactive B cells. This shifts the balance of B cell fate choices
toward autoreactive B cells and thus autoimmunity.
article_number: eabc3979
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Samaneh
full_name: Zoghi, Samaneh
last_name: Zoghi
- first_name: Máté G.
full_name: Kiss, Máté G.
last_name: Kiss
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Christina
full_name: Rashkova, Christina
last_name: Rashkova
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Matthias
full_name: Haimel, Matthias
last_name: Haimel
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Rico Chandra
full_name: Ardy, Rico Chandra
last_name: Ardy
- first_name: Birgit
full_name: Hoeger, Birgit
last_name: Hoeger
- first_name: Jana
full_name: Block, Jana
last_name: Block
- first_name: David
full_name: Medgyesi, David
last_name: Medgyesi
- first_name: Celine
full_name: Sin, Celine
last_name: Sin
- first_name: Sepideh
full_name: Shahkarami, Sepideh
last_name: Shahkarami
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Vahid
full_name: Ziaee, Vahid
last_name: Ziaee
- first_name: Peter
full_name: Hammerl, Peter
last_name: Hammerl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Loïc
full_name: Dupré, Loïc
last_name: Dupré
- first_name: Johannes B.
full_name: Huppa, Johannes B.
last_name: Huppa
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alexis
full_name: Lomakin, Alexis
last_name: Lomakin
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Christoph J.
full_name: Binder, Christoph J.
last_name: Binder
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
- first_name: Nima
full_name: Rezaei, Nima
last_name: Rezaei
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs
B cell development and prevents autoimmunity. Science Immunology. 2020;5(49).
doi:10.1126/sciimmunol.abc3979
apa: Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., …
Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979
chicago: Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina
Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator
HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology.
AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.
ieee: E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.
ista: Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer
R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain
R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A,
Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal
regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology.
5(49), eabc3979.
mla: Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development
and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979,
AAAS, 2020, doi:10.1126/sciimmunol.abc3979.
short: E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel,
R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S.
Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B.
Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei,
K. Boztug, Science Immunology 5 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-10T00:00:00Z
date_updated: 2023-08-22T07:56:04Z
day: '10'
department:
- _id: MiSi
doi: 10.1126/sciimmunol.abc3979
external_id:
isi:
- '000546994600004'
pmid:
- '32646852'
intvolume: ' 5'
isi: 1
issue: '49'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Science Immunology
publication_identifier:
eissn:
- '24709468'
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '9706'
abstract:
- lang: eng
text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted
protein levels with biological and technical covariates. Protein levels were adjusted
for age, sex, array plate and four genetic principal components (population structure)
prior to analyses. Significant associations are emboldened. (Table S1). pQTLs
associated with inflammatory biomarker levels from Bayesian penalised regression
model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated
with inflammatory biomarker levels from ordinary least squares regression model
(P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary
least squares GWAS and EWAS performed on inflammatory protein levels (n = 70)
in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs
associated with inflammatory biomarker levels from ordinary least squares regression
model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary
least squares and Bayesian penalised regression models for concordantly identified
SNPs. (Table S6). Estimate of heritability for blood protein levels as well as
proportion of variance explained attributable to different prior mixtures. (Table
S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood)
and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant
SNPs identified by linear model and Bayesian penalised regression and whether
they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation
for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression
are putatively associated with circulating inflammatory proteins that harbour
pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified
by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table
S12). CpGs associated with inflammatory protein biomarkers as identified by linear
model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory
protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10.
(Table S14). Estimate of variance explained for blood protein levels by DNA methylation
as well as proportion of explained attributable to different prior mixtures -
BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide
DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression
model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker
levels explained by common genetic and methylation data (joint and conditional
estimates from BayesR+). Ordered by combined variance explained by genetic and
epigenetic data - smallest to largest. Significant results from t-tests comparing
distributions for variance explained by methylation or genetics alone versus combined
estimate are emboldened. (Table S17). Genetic and epigenetic factors identified
by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian
Randomisation analyses to assess whether proteins with concordantly identified
genetic signals are causally associated with Alzheimer’s disease risk. (Table
S19).'
article_processing_charge: No
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: McCartney, Daniel L.
last_name: McCartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: 'Allan F. '
full_name: 'McRae, Allan F. '
last_name: McRae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: 'Riccardo E. '
full_name: 'Marioni, Riccardo E. '
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. 2020. doi:10.6084/m9.figshare.12629697.v1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional
File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein
Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.
ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and
epigenome-wide studies of inflammatory protein levels in healthy older adults.”
Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional
file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein
levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.
mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and
Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.
Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, (2020).
date_created: 2021-07-23T08:59:15Z
date_published: 2020-07-09T00:00:00Z
date_updated: 2023-08-22T07:55:36Z
day: '09'
department:
- _id: MaRo
doi: 10.6084/m9.figshare.12629697.v1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.12629697.v1
month: '07'
oa: 1
oa_version: Published Version
other_data_license: CC0 + CC BY (4.0)
publisher: Springer Nature
related_material:
record:
- id: '8133'
relation: used_in_publication
status: public
status: public
title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory
protein levels in healthy older adults
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '8134'
abstract:
- lang: eng
text: We prove an upper bound on the free energy of a two-dimensional homogeneous
Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the
free energy per unit volume differs from the one of the non-interacting system
by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering
length of the two-body interaction potential, ρ is the density, β is the inverse
temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature
for superfluidity. In combination with the corresponding matching lower bound
proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality
in the asymptotic expansion.
article_number: '061901'
article_processing_charge: No
article_type: original
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas.
II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950
apa: Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional
dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP
Publishing. https://doi.org/10.1063/5.0005950
chicago: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP
Publishing, 2020. https://doi.org/10.1063/5.0005950.
ieee: S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute
Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no.
6. AIP Publishing, 2020.
ista: Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute
Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.
mla: Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional
Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol.
61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.
short: S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).
date_created: 2020-07-19T22:00:59Z
date_published: 2020-06-22T00:00:00Z
date_updated: 2023-08-22T08:12:40Z
day: '22'
department:
- _id: RoSe
doi: 10.1063/5.0005950
ec_funded: 1
external_id:
arxiv:
- '2002.08281'
isi:
- '000544595100001'
intvolume: ' 61'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.08281
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The free energy of the two-dimensional dilute Bose gas. II. Upper bound
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8112'
article_number: '20190530'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. On the completion of speciation. Philosophical Transactions
of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530'
apa: 'Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530'
chicago: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0530.'
ieee: 'N. H. Barton, “On the completion of speciation,” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The
Royal Society, 2020.'
ista: 'Barton NH. 2020. On the completion of speciation. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.'
mla: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530,
The Royal Society, 2020, doi:10.1098/rstb.2019.0530.'
short: 'N.H. Barton, Philosophical Transactions of the Royal Society. Series B:
Biological Sciences 375 (2020).'
date_created: 2020-07-13T03:41:39Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T07:53:52Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0530
external_id:
isi:
- '000552662100002'
pmid:
- '32654647'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the completion of speciation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8162'
abstract:
- lang: eng
text: In mammalian genomes, a subset of genes is regulated by genomic imprinting,
resulting in silencing of one parental allele. Imprinting is essential for cerebral
cortex development, but prevalence and functional impact in individual cells is
unclear. Here, we determined allelic expression in cortical cell types and established
a quantitative platform to interrogate imprinting in single cells. We created
cells with uniparental chromosome disomy (UPD) containing two copies of either
the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold
overexpressed or not expressed. By genetic labeling of UPD, we determined cellular
phenotypes and transcriptional responses to deregulated imprinted gene expression
at unprecedented single-cell resolution. We discovered an unexpected degree of
cell-type specificity and a novel function of imprinting in the regulation of
cortical astrocyte survival. More generally, our results suggest functional relevance
of imprinted gene expression in glial astrocyte lineage and thus for generating
cortical cell-type diversity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical
support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen
for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of
the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo
for comments on earlier versions of the manuscript. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical
Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian
Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031).
R.B. received support from the FWF Meitner-Programm (M 2416). This work was also
supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers
Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement 618444 to S.H.; and the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro)
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Thomas
full_name: Penz, Thomas
last_name: Penz
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
orcid: 0000-0001-6091-3088
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting
in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031
apa: Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher,
C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031
chicago: Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi
H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer.
“Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.
ieee: S. Laukoter et al., “Cell-type specificity of genomic imprinting in
cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.
ista: Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T,
Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral
cortex. Neuron. 107(6), 1160–1179.e9.
mla: Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral
Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.
short: S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher,
T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.
date_created: 2020-07-23T16:03:12Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:20:11Z
day: '23'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2020.06.031
ec_funded: 1
external_id:
isi:
- '000579698700006'
file:
- access_level: open_access
checksum: 7becdc16a6317304304631087ae7dd7f
content_type: application/pdf
creator: dernst
date_created: 2020-12-02T09:26:46Z
date_updated: 2020-12-02T09:26:46Z
file_id: '8828'
file_name: 2020_Neuron_Laukoter.pdf
file_size: 8911830
relation: main_file
success: 1
file_date_updated: 2020-12-02T09:26:46Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1160-1179.e9
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
- _id: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/
scopus_import: '1'
status: public
title: Cell-type specificity of genomic imprinting in cerebral cortex
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '8138'
abstract:
- lang: eng
text: Directional transport of the phytohormone auxin is a versatile, plant-specific
mechanism regulating many aspects of plant development. The recently identified
plant hormones, strigolactones (SLs), are implicated in many plant traits; among
others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters
for fine-tuning of growth and developmental responses. Here, we show in pea and
Arabidopsis that SLs target processes dependent on the canalization of auxin flow,
which involves auxin feedback on PIN subcellular distribution. D14 receptor- and
MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels
after wounding or from artificial auxin sources, during vasculature de novo formation
and regeneration. At the cellular level, SLs interfere with auxin effects on PIN
polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis.
Our results identify a non-transcriptional mechanism of SL action, uncoupling
auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue
formation and regeneration.
acknowledgement: We are grateful to David Nelson for providing published materials
and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful
discussions. The research leading to these results has received funding from the
European Research Council (ERC) under the European Union's Horizon 2020 research
and innovation programme (742985). This work was also supported by the Beijing Municipal
Natural Science Foundation (5192011), Beijing Outstanding University Discipline
Program, the National Natural Science Foundation of China (31370309), CEITEC 2020
(LQ1601) project with financial contribution made by the Ministry of Education,
Youth and Sports of the Czech Republic within special support paid from the National
Program of Sustainability II funds, Australian Research Council (FT180100081), and
China Postdoctoral Science Foundation (2019M660864).
article_processing_charge: No
article_type: original
author:
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: J
full_name: Balla, J
last_name: Balla
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: P
full_name: Kalousek, P
last_name: Kalousek
- first_name: Z
full_name: Medveďová, Z
last_name: Medveďová
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: V
full_name: Reinöhl, V
last_name: Reinöhl
- first_name: S
full_name: Procházka, S
last_name: Procházka
- first_name: R
full_name: Halouzka, R
last_name: Halouzka
- first_name: P
full_name: Tarkowski, P
last_name: Tarkowski
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
- first_name: PB
full_name: Brewer, PB
last_name: Brewer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on
PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508.
doi:10.1038/s41467-020-17252-y
apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z.,
… Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin
transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y
chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová,
Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport
Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.
ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer
Nature, p. 3508, 2020.
ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang
Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig
C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization. Nature Communications. 11(1), 3508.
mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin
Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer
Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.
short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y.
Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P.
Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.
date_created: 2020-07-21T08:58:07Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2023-08-22T08:13:44Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17252-y
ec_funded: 1
external_id:
isi:
- '000550062200004'
pmid:
- '32665554'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T08:32:55Z
date_updated: 2020-07-22T08:32:55Z
file_id: '8148'
file_name: 2020_NatureComm_Zhang.pdf
file_size: 1759490
relation: main_file
success: 1
file_date_updated: 2020-07-22T08:32:55Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '3508'
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8168'
abstract:
- lang: eng
text: Speciation, that is, the evolution of reproductive barriers eventually leading
to complete isolation, is a crucial process generating biodiversity. Recent work
has contributed much to our understanding of how reproductive barriers begin to
evolve, and how they are maintained in the face of gene flow. However, little
is known about the transition from partial to strong reproductive isolation (RI)
and the completion of speciation. We argue that the evolution of strong RI is
likely to involve different processes, or new interactions among processes, compared
with the evolution of the first reproductive barriers. Transition to strong RI
may be brought about by changing external conditions, for example, following secondary
contact. However, the increasing levels of RI themselves create opportunities
for new barriers to evolve and, and interaction or coupling among barriers. These
changing processes may depend on genomic architecture and leave detectable signals
in the genome. We outline outstanding questions and suggest more theoretical and
empirical work, considering both patterns and processes associated with strong
RI, is needed to understand how speciation is completed.
article_number: '20190528'
article_processing_charge: No
article_type: original
author:
- first_name: Jonna
full_name: Kulmuni, Jonna
last_name: Kulmuni
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Kay
full_name: Lucek, Kay
last_name: Lucek
- first_name: Vincent
full_name: Savolainen, Vincent
last_name: Savolainen
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion
of speciation: The evolution of reproductive isolation beyond the first barriers.
Philosophical Transactions of the Royal Society Series B: Biological sciences.
2020;375(1806). doi:10.1098/rstb.2019.0528'
apa: 'Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M.
(2020). Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers. Philosophical Transactions of the Royal Society.
Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528'
chicago: 'Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja
M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive
Isolation beyond the First Barriers.” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.'
ieee: 'J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards
the completion of speciation: The evolution of reproductive isolation beyond the
first barriers,” Philosophical Transactions of the Royal Society. Series B:
Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.'
ista: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the
completion of speciation: The evolution of reproductive isolation beyond the first
barriers. Philosophical Transactions of the Royal Society. Series B: Biological
sciences. 375(1806), 20190528.'
mla: 'Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution
of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions
of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528,
The Royal Society, 2020, doi:10.1098/rstb.2019.0528.'
short: 'J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical
Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:21:31Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0528
ec_funded: 1
external_id:
isi:
- '000552662100001'
pmid:
- '32654637'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0528
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Towards the completion of speciation: The evolution of reproductive isolation
beyond the first barriers'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8167'
abstract:
- lang: eng
text: The evolution of strong reproductive isolation (RI) is fundamental to the
origins and maintenance of biological diversity, especially in situations where
geographical distributions of taxa broadly overlap. But what is the history behind
strong barriers currently acting in sympatry? Using whole-genome sequencing and
single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships,
(ii) the strength of RI, and (iii) the demographic history of divergence between
two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on
external morphology, Littorina arcana and Littorina saxatilis differ in their
mode of female reproduction (egg-laying versus brooding), which may generate a
strong post-zygotic barrier. We show that egg-laying and brooding snails are closely
related, but genetically distinct. Genotyping of 3092 snails from three locations
failed to recover any recent hybrid or backcrossed individuals, confirming that
RI is strong. There was, however, evidence for a very low level of asymmetrical
introgression, suggesting that isolation remains incomplete. The presence of strong,
asymmetrical RI was further supported by demographic analysis of these populations.
Although the taxa are currently broadly sympatric, demographic modelling suggests
that they initially diverged during a short period of geographical separation
involving very low gene flow. Our study suggests that some geographical separation
may kick-start the evolution of strong RI, facilitating subsequent coexistence
of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent
effect of sympatry on RI remain open questions.
acknowledgement: Funding was provided by the Natural Environment Research Council
(NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin
Garlovsky and Hernan Morales for advice and/or useful discussion during the project.
Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton
participated in the collection and processing of samples. Mark Dunning helped with
the development of bioinformatic pipelines. The analysis of genomic data was conducted
on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and
an anonymous reviewer provided comments that improved the manuscript.
article_number: '20190545'
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Isobel
full_name: Eyres, Isobel
last_name: Eyres
- first_name: Thomas
full_name: Broquet, Thomas
last_name: Broquet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545'
apa: 'Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T.,
Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive
isolation between sympatric intertidal snails. Philosophical Transactions of
the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545'
chicago: 'Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres,
Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong
Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0545.'
ieee: 'S. Stankowski et al., “The evolution of strong reproductive isolation
between sympatric intertidal snails,” Philosophical Transactions of the Royal
Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society,
2020.'
ista: 'Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K,
Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric
intertidal snails. Philosophical Transactions of the Royal Society. Series B:
Biological Sciences. 375(1806), 20190545.'
mla: 'Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between
Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society.
Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society,
2020, doi:10.1098/rstb.2019.0545.'
short: 'S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson,
R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological
Sciences 375 (2020).'
date_created: 2020-07-26T22:01:01Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:22:13Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0545
external_id:
isi:
- '000552662100014'
pmid:
- '32654639'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rstb.2019.0545
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- 1471-2970
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolution of strong reproductive isolation between sympatric intertidal
snails
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8170'
abstract:
- lang: eng
text: "Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is
measured as a function\r\nof time following rotational excitation by a nonresonant,
comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra,
obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal
distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy.
For\r\nCS2 and I2, they are the first experimental results reported. The alignment
dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using
the experimental in-droplet B and D values, agree in\r\ndetail with the measurement
for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium
droplets introduced here should apply to a range of molecules and complexes."
acknowledgement: "H. S. acknowledges support from the European Research Council-AdG
(Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a
Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian
Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC)
Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian
Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by
the European Union’s Horizon 2020 research and\r\ninnovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe
PIMC simulations were provided by the division for scientific computing at the Johannes
Kepler University."
article_number: '013001'
article_processing_charge: No
article_type: original
author:
- first_name: Adam S.
full_name: Chatterley, Adam S.
last_name: Chatterley
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Anders V.
full_name: Jørgensen, Anders V.
last_name: Jørgensen
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Robert E.
full_name: Zillich, Robert E.
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001'
apa: 'Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson,
B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy
of molecules in Helium nanodroplets: Reconciling the time and the frequency domains.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001'
chicago: 'Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V.
Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich,
Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of
Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.”
Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.'
ieee: 'A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules
in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical
Review Letters, vol. 125, no. 1. American Physical Society, 2020.'
ista: 'Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov
I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence
spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the
frequency domains. Physical Review Letters. 125(1), 013001.'
mla: 'Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules
in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical
Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020,
doi:10.1103/PhysRevLett.125.013001.'
short: A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson,
I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical
Review Letters 125 (2020).
date_created: 2020-07-26T22:01:02Z
date_published: 2020-07-03T00:00:00Z
date_updated: 2023-08-22T08:22:43Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.125.013001
ec_funded: 1
external_id:
arxiv:
- '2006.02694'
isi:
- '000544526900006'
intvolume: ' 125'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.02694
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling
the time and the frequency domains'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 125
year: '2020'
...
---
_id: '8194'
abstract:
- lang: eng
text: 'Fixed-point arithmetic is a popular alternative to floating-point arithmetic
on embedded systems. Existing work on the verification of fixed-point programs
relies on custom formalizations of fixed-point arithmetic, which makes it hard
to compare the described techniques or reuse the implementations. In this paper,
we address this issue by proposing and formalizing an SMT theory of fixed-point
arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point
theory, and provide formal semantics for it based on rational arithmetic. We also
describe two decision procedures for this theory: one based on the theory of bit-vectors
and the other on the theory of reals. We implement the two decision procedures,
and evaluate our implementations using existing mature SMT solvers on a benchmark
suite we created. Finally, we perform a case study of using the theory we propose
to verify properties of quantized neural networks.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Baranowski, Marek
last_name: Baranowski
- first_name: Shaobo
full_name: He, Shaobo
last_name: He
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Thanh Son
full_name: Nguyen, Thanh Son
last_name: Nguyen
- first_name: Zvonimir
full_name: Rakamarić, Zvonimir
last_name: Rakamarić
citation:
ama: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point
arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31.
doi:10.1007/978-3-030-51074-9_2'
apa: 'Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020).
An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166,
pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2'
chicago: Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir
Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning,
12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.
ieee: M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT
theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France,
2020, vol. 12166, pp. 13–31.
ista: 'Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory
of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference
on Automated Reasoning, LNCS, vol. 12166, 13–31.'
mla: Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated
Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.
short: M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated
Reasoning, Springer Nature, 2020, pp. 13–31.
conference:
end_date: 2020-07-04
location: Paris, France
name: 'IJCAR: International Joint Conference on Automated Reasoning'
start_date: 2020-07-01
date_created: 2020-08-02T22:00:59Z
date_published: 2020-06-24T00:00:00Z
date_updated: 2023-08-22T08:27:25Z
day: '24'
department:
- _id: ToHe
doi: 10.1007/978-3-030-51074-9_2
external_id:
isi:
- '000884318000002'
intvolume: ' 12166'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-030-51074-9_2
month: '06'
oa: 1
oa_version: Published Version
page: 13-31
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Automated Reasoning
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030510732'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An SMT theory of fixed-point arithmetic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12166
year: '2020'
...
---
_id: '8169'
abstract:
- lang: eng
text: Many recent studies have addressed the mechanisms operating during the early
stages of speciation, but surprisingly few studies have tested theoretical predictions
on the evolution of strong reproductive isolation (RI). To help address this gap,
we first undertook a quantitative review of the hybrid zone literature for flowering
plants in relation to reproductive barriers. Then, using Populus as an exemplary
model group, we analysed genome-wide variation for phylogenetic tree topologies
in both early- and late-stage speciation taxa to determine how these patterns
may be related to the genomic architecture of RI. Our plant literature survey
revealed variation in barrier complexity and an association between barrier number
and introgressive gene flow. Focusing on Populus, our genome-wide analysis of
tree topologies in speciating poplar taxa points to unusually complex genomic
architectures of RI, consistent with earlier genome-wide association studies.
These architectures appear to facilitate the ‘escape’ of introgressed genome segments
from polygenic barriers even with strong RI, thus affecting their relationships
with recombination rates. Placed within the context of the broader literature,
our data illustrate how phylogenomic approaches hold great promise for addressing
the evolution and temporary breakdown of RI during late stages of speciation.
acknowledgement: This work was supported by a fellowship from the China Scholarship
Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306
to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and
the University of Vienna. We thank members of J.L.’s lab for collecting samples,
Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation
Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific
Cluster (VSC) for access to computational resources, and Claus Vogel and members
of the PopGen Vienna graduate school for helpful discussions.
article_number: '20190544'
article_processing_charge: No
article_type: original
author:
- first_name: Huiying
full_name: Shang, Huiying
last_name: Shang
- first_name: Jaqueline
full_name: Hess, Jaqueline
last_name: Hess
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Pär K.
full_name: Ingvarsson, Pär K.
last_name: Ingvarsson
- first_name: Jianquan
full_name: Liu, Jianquan
last_name: Liu
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
citation:
ama: 'Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation
in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical
Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806).
doi:10.1098/rstb.2019.0544'
apa: 'Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &
Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale
patterns and lessons from a perennial model group. Philosophical Transactions
of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544'
chicago: 'Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson,
Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation
in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences. The Royal
Society, 2020. https://doi.org/10.1098/rstb.2019.0544.'
ieee: 'H. Shang et al., “Evolution of strong reproductive isolation in plants:
Broad-scale patterns and lessons from a perennial model group,” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences, vol. 375,
no. 1806. The Royal Society, 2020.'
ista: 'Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020.
Evolution of strong reproductive isolation in plants: Broad-scale patterns and
lessons from a perennial model group. Philosophical Transactions of the Royal
Society. Series B: Biological Sciences. 375(1806), 20190544.'
mla: 'Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants:
Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical
Transactions of the Royal Society. Series B: Biological Sciences, vol. 375,
no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.'
short: 'H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer,
Philosophical Transactions of the Royal Society. Series B: Biological Sciences
375 (2020).'
date_created: 2020-07-26T22:01:02Z
date_published: 2020-07-12T00:00:00Z
date_updated: 2023-08-22T08:23:24Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2019.0544
external_id:
isi:
- '000552662100013'
pmid:
- '32654641'
intvolume: ' 375'
isi: 1
issue: '1806'
language:
- iso: eng
month: '07'
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society. Series B: Biological
Sciences'
publication_identifier:
eissn:
- '14712970'
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Evolution of strong reproductive isolation in plants: Broad-scale patterns
and lessons from a perennial model group'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2020'
...
---
_id: '8189'
abstract:
- lang: eng
text: Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric
vehicles and portable electronics, but their deployment is currently limited by
the unavailability of proper electrocatalysis for the ethanol oxidation reaction
(EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous
into a palladium-tin alloy and demonstrate a significant performance improvement
toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals
that incorporate 35% of phosphorus. These nanoparticles are supported on carbon
black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up
to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts.
Furthermore, a twofold lower Tafel slope and a much longer durability are revealed
for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is
rationalized with the aid of density functional theory (DFT) calculations considering
different phosphorous chemical environments. Depending on its oxidation state,
surface phosphorus introduces sites with low energy OH− adsorption and/or strongly
influences the electronic structure of palladium and tin to facilitate the oxidation
of the acetyl to acetic acid, which is considered the EOR rate limiting step.
DFT calculations also points out that the durability improvement of Pd2Sn:P/C
catalyst is associated to the promotion of OH adsorption that accelerates the
oxidation of intermediate poisoning COads, reactivating the catalyst surface.
acknowledgement: This work was supported by the European Regional Development Funds
and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP,
ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship
Council for the scholarship support. J. Liu acknowledges support from the Jiangsu
University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange
Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the
project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors
acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246,
and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme
(MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat
de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER
RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.
article_number: '105116'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoting
full_name: Yu, Xiaoting
last_name: Yu
- first_name: Junfeng
full_name: Liu, Junfeng
last_name: Liu
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Zhishan
full_name: Luo, Zhishan
last_name: Luo
- first_name: Yong
full_name: Zuo, Yong
last_name: Zuo
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Déspina
full_name: Nasiou, Déspina
last_name: Nasiou
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Kai
full_name: Pan, Kai
last_name: Pan
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Ying
full_name: Xie, Ying
last_name: Xie
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic
ethanol oxidation. Nano Energy. 2020;77(11). doi:10.1016/j.nanoen.2020.105116
apa: Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous
incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano
Energy. Elsevier. https://doi.org/10.1016/j.nanoen.2020.105116
chicago: Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong
Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic
Ethanol Oxidation.” Nano Energy. Elsevier, 2020. https://doi.org/10.1016/j.nanoen.2020.105116.
ieee: X. Yu et al., “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic
ethanol oxidation,” Nano Energy, vol. 77, no. 11. Elsevier, 2020.
ista: Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan
K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys
for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.
mla: Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic
Ethanol Oxidation.” Nano Energy, vol. 77, no. 11, 105116, Elsevier, 2020,
doi:10.1016/j.nanoen.2020.105116.
short: X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol,
K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).
date_created: 2020-08-02T22:00:57Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T08:24:05Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.nanoen.2020.105116
external_id:
isi:
- '000581738300030'
intvolume: ' 77'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
publication: Nano Energy
publication_identifier:
issn:
- 2211-2855
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 77
year: '2020'
...
---
_id: '8220'
abstract:
- lang: eng
text: Understanding to what extent stem cell potential is a cell-intrinsic property
or an emergent behavior coming from global tissue dynamics and geometry is a key
outstanding question of systems and stem cell biology. Here, we propose a theory
of stem cell dynamics as a stochastic competition for access to a spatially localized
niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce
a steady cellular stream which advects cells away from the niche, while random
rearrangements enable cells away from the niche to be favorably repositioned.
Importantly, even when assuming that all cells in a tissue are molecularly equivalent,
we predict a common (“universal”) functional dependence of the long-term clonal
survival probability on distance from the niche, as well as the emergence of a
well-defined number of functional stem cells, dependent only on the rate of random
movements vs. mitosis-driven advection. We test the predictions of this theory
on datasets of pubertal mammary gland tips and embryonic kidney tips, as well
as homeostatic intestinal crypts. Importantly, we find good agreement for the
predicted functional dependency of the competition as a function of position,
and thus functional stem cell number in each organ. This argues for a key role
of positional fluctuations in dictating stem cell number and dynamics, and we
discuss the applicability of this theory to other settings.
acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for
stimulating discussions. This project was supported by\r\nthe European Research
Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from
the CancerGenomics.nl (Netherlands Organization for Scientific Research) program
(J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by
Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust
Grant 098357/Z/12/Z."
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Saskia I.J.
full_name: Ellenbroek, Saskia I.J.
last_name: Ellenbroek
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival
as a noisy competition for niche access. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117
apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J.,
Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage
survival as a noisy competition for niche access. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1921205117
chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia
I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo.
“Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.
ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy
competition for niche access,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 117, no. 29. National Academy of Sciences,
pp. 16969–16975, 2020.
ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van
Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition
for niche access. Proceedings of the National Academy of Sciences of the United
States of America. 117(29), 16969–16975.
mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition
for Niche Access.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp.
16969–75, doi:10.1073/pnas.1921205117.
short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D.
Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences
of the United States of America 117 (2020) 16969–16975.
date_created: 2020-08-09T22:00:52Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2023-08-22T08:29:30Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1921205117
ec_funded: 1
external_id:
isi:
- '000553292900014'
pmid:
- '32611816'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T06:50:28Z
date_updated: 2020-08-10T06:50:28Z
file_id: '8223'
file_name: 2020_PNAS_Corominas.pdf
file_size: 1111604
relation: main_file
success: 1
file_date_updated: 2020-08-10T06:50:28Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16969-16975
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/order-from-noise/
scopus_import: '1'
status: public
title: Stem cell lineage survival as a noisy competition for niche access
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2020'
...
---
_id: '8199'
abstract:
- lang: eng
text: We investigate a mechanism to transiently stabilize topological phenomena
in long-lived quasi-steady states of isolated quantum many-body systems driven
at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady
states which is exponentially large in the inverse driving frequency. Within this
lifetime, the quasi-steady state is characterized by maximum entropy subject to
the constraint of fixed number of particles in the system's Floquet-Bloch bands.
In such a state, all the non-universal properties of these bands are washed out,
hence only the topological properties persist.
acknowledgement: "N.L., T.G. and E.B. acknowledge support from the European Research
Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme
(Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship
at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and
Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research
and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No.
754411. N.L. acknowledges support from the People Programme (Marie Curie Actions)
of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA
Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence
(I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12).
M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC)
under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement
No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B.
acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft"
article_number: '015'
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Gulden, Tobias
id: 1083E038-9F73-11E9-A4B5-532AE6697425
last_name: Gulden
orcid: 0000-0001-6814-7541
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Mark Spencer
full_name: Rudner, Mark Spencer
last_name: Rudner
- first_name: Netanel
full_name: Lindner, Netanel
last_name: Lindner
citation:
ama: Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal
quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9.
doi:10.21468/scipostphys.9.1.015
apa: Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially
long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015
chicago: Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially
Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.”
SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015.
ieee: T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps,” SciPost Physics,
vol. 9. SciPost Foundation, 2020.
ista: Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime
of universal quasi-steady states in topological Floquet pumps. SciPost Physics.
9, 015.
mla: Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady
States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost
Foundation, 2020, doi:10.21468/scipostphys.9.1.015.
short: T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).
date_created: 2020-08-04T13:04:15Z
date_published: 2020-07-29T00:00:00Z
date_updated: 2023-08-22T08:28:24Z
day: '29'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.21468/scipostphys.9.1.015
ec_funded: 1
external_id:
isi:
- '000557362300008'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-06T08:56:06Z
date_updated: 2020-08-06T08:56:06Z
file_id: '8202'
file_name: 2020_SciPostPhys_Gulden.pdf
file_size: 531137
relation: main_file
success: 1
file_date_updated: 2020-08-06T08:56:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exponentially long lifetime of universal quasi-steady states in topological
Floquet pumps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
_id: '8261'
abstract:
- lang: eng
text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal
CA3 region, but how they process spatial information remains enigmatic. To examine
the role of GCs in spatial coding, we measured excitatory postsynaptic potentials
(EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt.
Intracellular recording from morphologically identified GCs revealed that most
cells were active, but activity level varied over a wide range. Whereas only ∼5%
of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus,
the GC population broadly encodes spatial information, but only a subset relays
this information to the CA3 network. Fourier analysis indicated that GCs received
conjunctive place-grid-like synaptic input, suggesting code conversion in single
neurons. GC firing was correlated with dendritic complexity and intrinsic excitability,
but not extrinsic excitatory input or dendritic cable properties. Thus, functional
maturation may control input-output transformation and spatial code conversion.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari,
Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of
this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery
Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp
recording. We are grateful to Florian Marr for cell labeling, cell reconstruction,
and technical assistance; Ben Suter for helpful discussions; Christina Altmutter
for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor
Asenov (Machine Shop) for device construction. We also thank the Scientific Service
Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical
Facility) for efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow
from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225.
doi:10.1016/j.neuron.2020.07.006
apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial
information flow from input to output in hippocampal granule cells. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006
chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of
Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.
ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information
flow from input to output in hippocampal granule cells,” Neuron, vol. 107,
no. 6. Elsevier, pp. 1212–1225, 2020.
ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information
flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.
mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from
Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6,
Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.
short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.
date_created: 2020-08-14T09:36:05Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T08:30:55Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.neuron.2020.07.006
ec_funded: 1
external_id:
isi:
- '000579698700009'
pmid:
- '32763145'
file:
- access_level: open_access
checksum: 44a5960fc083a4cb3488d22224859fdc
content_type: application/pdf
creator: dernst
date_created: 2020-12-04T09:29:21Z
date_updated: 2020-12-04T09:29:21Z
file_id: '8920'
file_name: 2020_Neuron_Zhang.pdf
file_size: 3011120
relation: main_file
success: 1
file_date_updated: 2020-12-04T09:29:21Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1212-1225
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/
status: public
title: Selective routing of spatial information flow from input to output in hippocampal
granule cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_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'
...
---
_id: '8271'
acknowledgement: We thank Dr. Gai Huang for his comments and help. We apologize to
authors whose work could not be cited due to space limitation. No conflict of interest
declared.
article_processing_charge: No
article_type: original
author:
- first_name: Peng
full_name: He, Peng
last_name: He
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Guanghui
full_name: Xiao, Guanghui
last_name: Xiao
citation:
ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid
cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006
apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome
evolution of allotetraploid cotton species. Molecular Plant. Elsevier.
https://doi.org/10.1016/j.molp.2020.07.006
chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome
Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier,
2020. https://doi.org/10.1016/j.molp.2020.07.006.
ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution
of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier,
pp. 1238–1240, 2020.
ista: He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of
allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.
mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid
Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40,
doi:10.1016/j.molp.2020.07.006.
short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.
date_created: 2020-08-16T22:00:57Z
date_published: 2020-09-07T00:00:00Z
date_updated: 2023-08-22T08:40:35Z
day: '07'
department:
- _id: JiFr
doi: 10.1016/j.molp.2020.07.006
external_id:
isi:
- '000566895400007'
pmid:
- '32688032'
intvolume: ' 13'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 1238-1240
pmid: 1
publication: Molecular Plant
publication_identifier:
eissn:
- '17529867'
issn:
- '16742052'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Origin of a subgenome and genome evolution of allotetraploid cotton species
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2020'
...
---
_id: '8101'
abstract:
- lang: eng
text: By rigorously accounting for mesoscale spatial correlations in donor/acceptor
surface properties, we develop a scale-spanning model for same-material tribocharging.
We find that mesoscale correlations affect not only the magnitude of charge transfer
but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability
that is not observed experimentally. We furthermore propose a generic theoretical
mechanism by which the mesoscale features might emerge, which is qualitatively
consistent with other proposals in the literature.
acknowledgement: "We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin,
and Bilge Baytekin for helpful discussions.\r\nThis project has received funding
from the European Unions Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411."
article_number: '082602'
article_processing_charge: Yes
article_type: original
author:
- 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: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
- first_name: Juan Carlos A
full_name: Sobarzo Ponce, Juan Carlos A
id: 4B807D68-AE37-11E9-AC72-31CAE5697425
last_name: Sobarzo Ponce
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent
scale-spanning model for same-material tribocharging. Physical Review Materials.
2020;4(8). doi:10.1103/PhysRevMaterials.4.082602
apa: Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R.
(2020). Quantitatively consistent scale-spanning model for same-material tribocharging.
Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602
chicago: Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott
R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material
Tribocharging.” Physical Review Materials. American Physical Society, 2020.
https://doi.org/10.1103/PhysRevMaterials.4.082602.
ieee: G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively
consistent scale-spanning model for same-material tribocharging,” Physical
Review Materials, vol. 4, no. 8. American Physical Society, 2020.
ista: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively
consistent scale-spanning model for same-material tribocharging. Physical Review
Materials. 4(8), 082602.
mla: Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model
for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no.
8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.
short: G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical
Review Materials 4 (2020).
date_created: 2020-07-07T11:33:54Z
date_published: 2020-08-17T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '17'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevMaterials.4.082602
ec_funded: 1
external_id:
arxiv:
- '2006.07120'
isi:
- '000561897000001'
file:
- access_level: open_access
checksum: 288fef1eeb6540c6344bb8f7c8159dc9
content_type: application/pdf
creator: ggrosjea
date_created: 2020-08-17T15:54:20Z
date_updated: 2020-08-17T15:54:20Z
file_id: '8277'
file_name: Grosjean2020.pdf
file_size: 853753
relation: main_file
success: 1
file_date_updated: 2020-08-17T15:54:20Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '8'
keyword:
- electric charge
- tribocharging
- soft matter
- granular materials
- polymers
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Materials
publication_identifier:
issn:
- 2475-9953
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '12697'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Quantitatively consistent scale-spanning model for same-material tribocharging
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: 4
year: '2020'
...
---
_id: '8325'
abstract:
- lang: eng
text: "Let \U0001D439:ℤ2→ℤ be the pointwise minimum of several linear functions.
The theory of smoothing allows us to prove that under certain conditions there
exists the pointwise minimal function among all integer-valued superharmonic functions
coinciding with F “at infinity”. We develop such a theory to prove existence of
so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo,
G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the
phenomena of the identity in the sandpile group for planar domains where solitons
appear according to experiments. We prove that sandpile states, defined using
our smoothing procedure, move changeless when we apply the wave operator (that
is why we call them solitons), and can interact, forming triads and nodes. "
acknowledgement: We thank Andrea Sportiello for sharing his insights on perturbative
regimes of the Abelian sandpile model which was the starting point of our work.
We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We
thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who
participated on the initial state of this project, when we had nothing except the
computer simulation and pictures. We thank Mikhail Raskin for providing us the code
on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max
Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak,
Danila Cherkashin asked us a lot of questions and listened to us; not all of their
questions found answers here, but we are going to treat them in subsequent papers.
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions.
Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8
apa: Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of
superharmonic functions. Communications in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s00220-020-03828-8
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing
of Superharmonic Functions.” Communications in Mathematical Physics. Springer
Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.
ieee: N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic
functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer
Nature, pp. 1649–1675, 2020.
ista: Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic
functions. Communications in Mathematical Physics. 378(9), 1649–1675.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of
Superharmonic Functions.” Communications in Mathematical Physics, vol.
378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.
short: N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020)
1649–1675.
date_created: 2020-08-30T22:01:13Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T09:00:03Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00220-020-03828-8
ec_funded: 1
external_id:
arxiv:
- '1711.04285'
isi:
- '000560620600001'
intvolume: ' 378'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.04285
month: '09'
oa: 1
oa_version: Preprint
page: 1649-1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- '14320916'
issn:
- '00103616'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sandpile solitons via smoothing of superharmonic functions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 378
year: '2020'
...
---
_id: '8318'
abstract:
- lang: eng
text: Complex I is the first and the largest enzyme of respiratory chains in bacteria
and mitochondria. The mechanism which couples spatially separated transfer of
electrons to proton translocation in complex I is not known. Here we report five
crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like
compounds. We also determined cryo-EM structures of major and minor native states
of the complex, differing in the position of the peripheral arm. Crystal structures
show that binding of quinone-like compounds (but not of NADH) leads to a related
global conformational change, accompanied by local re-arrangements propagating
from the quinone site to the nearest proton channel. Normal mode and molecular
dynamics analyses indicate that these are likely to represent the first steps
in the proton translocation mechanism. Our results suggest that quinone binding
and chemistry play a key role in the coupling mechanism of complex I.
acknowledgement: This work was funded by the Medical Research Council, UK and IST
Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light
Source for provision of synchrotron radiation facilities. We are grateful to the
staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light
Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance
computing cluster.
article_number: '4135'
article_processing_charge: No
article_type: original
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Gurdeep S.
full_name: Minhas, Gurdeep S.
last_name: Minhas
- first_name: Rozbeh
full_name: Baradaran, Rozbeh
last_name: Baradaran
- first_name: Margherita
full_name: Tambalo, Margherita
id: 4187dfe4-ec23-11ea-ae46-f08ab378313a
last_name: Tambalo
- first_name: David T.
full_name: Gallagher, David T.
last_name: Gallagher
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in
the mechanism of respiratory complex I. Nature Communications. 2020;11(1).
doi:10.1038/s41467-020-17957-0
apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo,
M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the
mechanism of respiratory complex I. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-17957-0
chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran,
Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone
in the Mechanism of Respiratory Complex I.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.
ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism
of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer
Nature, 2020.
ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher
DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex
I. Nature Communications. 11(1), 4135.
mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of
Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer
Nature, 2020, doi:10.1038/s41467-020-17957-0.
short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo,
D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2023-08-22T09:03:00Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-020-17957-0
external_id:
isi:
- '000607072900001'
pmid:
- '32811817'
file:
- access_level: open_access
checksum: 52b96f41d7d0db9728064c08da00d030
content_type: application/pdf
creator: cziletti
date_created: 2020-08-31T13:40:00Z
date_updated: 2020-08-31T13:40:00Z
file_id: '8326'
file_name: 2020_NatComm_Gutierrez-Fernandez.pdf
file_size: 7527373
relation: main_file
success: 1
file_date_updated: 2020-08-31T13:40:00Z
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issue: '1'
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month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/
scopus_import: '1'
status: public
title: Key role of quinone in the mechanism of respiratory complex I
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: '8320'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
acknowledgement: We would like to thank our co-workers and members of the Alkalaeva
lab for participating in discussions about the topics covered in this essay.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molecular Biology.
2020;54(4):475-484. doi:10.1134/S0026893320040111'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological
Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484,
2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molecular
Biology. 54(4), 475–484.'
mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in
Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature,
2020, pp. 475–84, doi:10.1134/S0026893320040111.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molecular Biology 54 (2020) 475–484.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-08-19T00:00:00Z
date_updated: 2023-08-22T09:01:03Z
day: '19'
department:
- _id: FyKo
doi: 10.1134/S0026893320040111
external_id:
isi:
- '000562110300001'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 475-484
publication: Molecular Biology
publication_identifier:
eissn:
- '16083245'
issn:
- '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8321'
relation: original
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8321'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences.
https://doi.org/10.31857/S0026898420040126'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological
systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.
https://doi.org/10.31857/S0026898420040126.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of
Sciences, pp. 531–541, 2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 54(4), 531–541.'
mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in
biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian
Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molekuliarnaia biologiia 54 (2020) 531–541.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T09:01:02Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420040126
external_id:
pmid:
- '32799218'
intvolume: ' 54'
issue: '4'
language:
- iso: rus
month: '07'
oa_version: None
page: 531-541
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8320'
relation: translation
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_id: '8323'
article_processing_charge: No
article_type: letter_note
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
citation:
ama: Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry.
2020;64:571-574. doi:10.1007/s00454-020-00237-5
apa: Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational
Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5
chicago: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational
Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.
ieee: J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry,
vol. 64. Springer Nature, pp. 571–574, 2020.
ista: Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry.
64, 571–574.
mla: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry,
vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.
short: J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.
date_created: 2020-08-30T22:01:12Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T09:05:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00237-5
external_id:
isi:
- '000561483500001'
intvolume: ' 64'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-020-00237-5
month: '10'
oa: 1
oa_version: None
page: 571-574
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
scopus_import: '1'
status: public
title: A farewell to Ricky Pollack
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2020'
...
---
_id: '8336'
abstract:
- lang: eng
text: Plant hormone cytokinins are perceived by a subfamily of sensor histidine
kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional
responses in the nucleus. Subcellular localization of the receptors proposed the
endoplasmic reticulum (ER) membrane as a principal cytokinin perception site,
while study of cytokinin transport pointed to the plasma membrane (PM)-mediated
cytokinin signalling. Here, by detailed monitoring of subcellular localizations
of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS
HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the
ER-located cytokinin receptors can enter the secretory pathway and reach the PM
in cells of the root apical meristem, and the cell plate of dividing meristematic
cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor
and its accumulation in BFA compartments. We provide a revised view on cytokinin
signalling and the possibility of multiple sites of perception at PM and ER.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This paper is dedicated to deceased P. Galuszka for his support and
contribution to the project. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility
(BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký
University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical
assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material.
The work was supported from ERDF project “Plants as a tool for sustainable global
development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation
via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S
(K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term
Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences
at the Institute of Science and Technology, Austria (H.S.).
article_number: '4285'
article_processing_charge: No
article_type: original
author:
- first_name: Karolina
full_name: Kubiasova, Karolina
id: 946011F4-3E71-11EA-860B-C7A73DDC885E
last_name: Kubiasova
orcid: 0000-0001-5630-9419
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Jaroslav
full_name: Nisler, Jaroslav
last_name: Nisler
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Hana
full_name: Semeradova, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semeradova
- first_name: Lucie
full_name: Plíhalová, Lucie
last_name: Plíhalová
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Peter
full_name: Marhavý, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavý
orcid: 0000-0001-5227-5741
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: David
full_name: Zalabák, David
last_name: Zalabák
- first_name: Karel
full_name: Berka, Karel
last_name: Berka
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Petr
full_name: Galuszka, Petr
last_name: Galuszka
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
citation:
ama: Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe
reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic
reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0
apa: Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V.,
Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0
chicago: Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler,
Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals
Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.
ieee: K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature
Communications, vol. 11. Springer Nature, 2020.
ista: Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová
H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K,
Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin
fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane
and endoplasmic reticulum. Nature Communications. 11, 4285.
mla: Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of
Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature
Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.
short: K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová,
L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal,
P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications
11 (2020).
date_created: 2020-09-06T22:01:12Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2023-08-22T09:09:06Z
day: '27'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1038/s41467-020-17949-0
ec_funded: 1
external_id:
isi:
- '000567931000002'
pmid:
- '32855390'
file:
- access_level: open_access
checksum: 7494b7665b3d2bf2d8edb13e4f12b92d
content_type: application/pdf
creator: dernst
date_created: 2020-09-10T08:05:19Z
date_updated: 2020-09-10T08:05:19Z
file_id: '8357'
file_name: 2020_NatureComm_Kubiasova.pdf
file_size: 3455704
relation: main_file
success: 1
file_date_updated: 2020-09-10T08:05:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
- _id: 253E54C8-B435-11E9-9278-68D0E5697425
grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma
membrane and endoplasmic reticulum
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: '8337'
abstract:
- lang: eng
text: Cytokinins are mobile multifunctional plant hormones with roles in development
and stress resilience. Although their Histidine Kinase receptors are substantially
localised to the endoplasmic reticulum, cellular sites of cytokinin perception
and importance of spatially heterogeneous cytokinin distribution continue to be
debated. Here we show that cytokinin perception by plasma membrane receptors is
an effective additional path for cytokinin response. Readout from a Two Component
Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular
cytokinin content in roots, yet we also find cytokinins in extracellular fluid,
potentially enabling action at the cell surface. Cytokinins covalently linked
to beads that could not pass the plasma membrane increased expression of both
TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled
receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin
receptor mutants, further indicate that receptors can function at the cell surface.
We argue that dual intracellular and surface locations may augment flexibility
of cytokinin responses.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank Bruno Müller and Aaron Rashotte for critical discussions
and provision of plant lines used in this work, Roger Granbom and Tamara Hernández
Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana
Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic)
for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký
University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing
CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre
and the IST Austria Bio-Imaging facility are acknowledged for support. The work
was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.),
Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the
International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.),
the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest
Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811)
(E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic
via the European Regional Development Fund-Project “Plants as a tool for sustainable
global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M.,
L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did
the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P.,
K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.),
Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J.
was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading
to these results received funding from European Union’s Horizon 2020 programme (ERC
grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.'
article_number: '4284'
article_processing_charge: No
article_type: original
author:
- first_name: Ioanna
full_name: Antoniadi, Ioanna
last_name: Antoniadi
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Radim
full_name: Simerský, Radim
last_name: Simerský
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Eduardo
full_name: Mateo-Bonmatí, Eduardo
last_name: Mateo-Bonmatí
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Lenka
full_name: Plačková, Lenka
last_name: Plačková
- first_name: Korawit
full_name: Opassathian, Korawit
last_name: Opassathian
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Colin
full_name: Turnbull, Colin
last_name: Turnbull
citation:
ama: Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception
of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9
apa: Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský,
R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular
cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9
chicago: Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej
Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception
of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-17700-9.
ieee: I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular
cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain
T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko
J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors
enable perception of extracellular cytokinins. Nature Communications. 11, 4284.
mla: Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular
Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020,
doi:10.1038/s41467-020-17700-9.
short: I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský,
V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian,
J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications
11 (2020).
date_created: 2020-09-06T22:01:13Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2023-08-22T09:10:32Z
day: '27'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17700-9
ec_funded: 1
external_id:
isi:
- '000567931000001'
file:
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file_name: 2020_NatureComm_Antoniadi.pdf
file_size: 3526415
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month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _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:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-surface receptors enable perception of extracellular cytokinins
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: '8067'
abstract:
- lang: eng
text: "With the lithium-ion technology approaching its intrinsic limit with graphite-based
anodes, lithium metal is recently receiving renewed interest from the battery
community as potential high capacity anode for next-generation rechargeable batteries.
In this focus paper, we review the main advances in this field since the first
attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding
dendrite growth are thoroughly discussed, including specific applications in all-solid-state
(polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular
attention is paid to review recent developments in regard of prototype manufacturing
and current state-ofthe-art of these battery technologies with respect to the
2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan)
Action 7."
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Alberto
full_name: Varzi, Alberto
last_name: Varzi
- first_name: Katharina
full_name: Thanner, Katharina
last_name: Thanner
- first_name: Roberto
full_name: Scipioni, Roberto
last_name: Scipioni
- first_name: Daniele
full_name: Di Lecce, Daniele
last_name: Di Lecce
- first_name: Jusef
full_name: Hassoun, Jusef
last_name: Hassoun
- first_name: Susanne
full_name: Dörfler, Susanne
last_name: Dörfler
- first_name: Holger
full_name: Altheus, Holger
last_name: Altheus
- first_name: Stefan
full_name: Kaskel, Stefan
last_name: Kaskel
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives
of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067
apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S.,
… Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium
metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067
chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce,
Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal,
and Stefan Alexander Freunberger. Current Status and Future Perspectives of
Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067.
ieee: A. Varzi et al., Current status and future perspectives of Lithium
metal batteries. IST Austria.
ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus
H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives
of Lithium metal batteries, IST Austria, 63p.
mla: Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium
Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067.
short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H.
Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives
of Lithium Metal Batteries, IST Austria, n.d.
date_created: 2020-06-30T07:37:39Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T09:20:36Z
day: '01'
ddc:
- '540'
department:
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doi: 10.15479/AT:ISTA:8067
file:
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checksum: d183ca1465a1cbb4f8db27875cd156f7
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creator: dernst
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file_size: 2612498
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
keyword:
- Battery
- Lithium metal
- Lithium-sulphur
- Lithium-air
- All-solid-state
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '63'
publication_identifier:
issn:
- 2664-1690
publication_status: submitted
publisher: IST Austria
related_material:
record:
- id: '8361'
relation: later_version
status: public
status: public
title: Current status and future perspectives of Lithium metal batteries
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '8361'
abstract:
- lang: eng
text: With the lithium-ion technology approaching its intrinsic limit with graphite-based
anodes, Li metal is recently receiving renewed interest from the battery community
as potential high capacity anode for next-generation rechargeable batteries. In
this focus paper, we review the main advances in this field since the first attempts
in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite
growth are thoroughly discussed, including specific applications in all-solid-state
(inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries.
A particular attention is paid to recent developments of these battery technologies
and their current state with respect to the 2030 targets of the EU Integrated
Strategic Energy Technology Plan (SET-Plan) Action 7.
acknowledgement: A.V. and K.T. acknowledge, respectively, the financial support of
the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project
“Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department
of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department
of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische
Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon
2020 research and innovation programme under grant agree-ment No 814471. S.A.F.
and C.P. are indebted to the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement no. 636069)
and IST Austria.
article_number: '228803'
article_processing_charge: No
article_type: original
author:
- first_name: Alberto
full_name: Varzi, Alberto
last_name: Varzi
orcid: 0000-0001-5069-0589
- first_name: Katharina
full_name: Thanner, Katharina
last_name: Thanner
orcid: 0000-0001-5394-2323
- first_name: Roberto
full_name: Scipioni, Roberto
last_name: Scipioni
orcid: 0000-0003-1926-421X
- first_name: Daniele
full_name: Di Lecce, Daniele
last_name: Di Lecce
- first_name: Jusef
full_name: Hassoun, Jusef
last_name: Hassoun
- first_name: Susanne
full_name: Dörfler, Susanne
last_name: Dörfler
- first_name: Holger
full_name: Altheus, Holger
last_name: Altheus
- first_name: Stefan
full_name: Kaskel, Stefan
last_name: Kaskel
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
orcid: 0000-0003-0654-0940
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives
of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803
apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S.,
… Freunberger, S. A. (2020). Current status and future perspectives of lithium
metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803
chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce,
Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal,
and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium
Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.
ieee: A. Varzi et al., “Current status and future perspectives of lithium
metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier,
2020.
ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus
H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives
of lithium metal batteries. Journal of Power Sources. 480(12), 228803.
mla: Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal
Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier,
2020, doi:10.1016/j.jpowsour.2020.228803.
short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H.
Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480
(2020).
date_created: 2020-09-10T10:48:40Z
date_published: 2020-12-31T00:00:00Z
date_updated: 2023-08-22T09:20:37Z
day: '31'
department:
- _id: StFr
doi: 10.1016/j.jpowsour.2020.228803
external_id:
isi:
- '000593857300001'
intvolume: ' 480'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jpowsour.2020.228803
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Power Sources
publication_identifier:
issn:
- 0378-7753
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8067'
relation: earlier_version
status: public
status: public
title: Current status and future perspectives of lithium metal batteries
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2020'
...
---
_id: '14028'
abstract:
- lang: eng
text: 'The present review addresses the technical advances and the theoretical developments
to realize and rationalize attosecond-science experiments that reveal a new dynamical
time scale (10−15-10−18 s), with a particular emphasis on molecular systems and
the implications of attosecond processes for chemical dynamics. After a brief
outline of the theoretical framework for treating non-perturbative phenomena in
Section 2, we introduce the physical mechanisms underlying high-harmonic generation
and attosecond technology. The relevant technological developments and experimental
schemes are covered in Section 3. Throughout the remainder of the chapter, we
report on selected applications in molecular attosecond physics, thereby addressing
specific phenomena mediated by purely electronic dynamics: charge localization
in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic
spectroscopy, and delays in molecular photoionization.'
article_processing_charge: No
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. doi:10.48550/arXiv.2002.02111
apa: Baykusheva, D. R., & Wörner, H. J. (n.d.). Attosecond molecular spectroscopy
and dynamics. https://doi.org/10.48550/arXiv.2002.02111
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Spectroscopy and Dynamics,” n.d. https://doi.org/10.48550/arXiv.2002.02111.
ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond molecular spectroscopy and
dynamics.” .
ista: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics.
10.48550/arXiv.2002.02111.
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. Attosecond Molecular
Spectroscopy and Dynamics. doi:10.48550/arXiv.2002.02111.
short: D.R. Baykusheva, H.J. Wörner, (n.d.).
date_created: 2023-08-10T06:47:45Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-22T09:17:34Z
day: '01'
doi: 10.48550/arXiv.2002.02111
extern: '1'
external_id:
arxiv:
- '2002.02111'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2002.02111
month: '02'
oa: 1
oa_version: Preprint
page: '2002.02111'
publication_status: submitted
status: public
title: Attosecond molecular spectroscopy and dynamics
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8529'
abstract:
- lang: eng
text: Practical quantum networks require low-loss and noise-resilient optical interconnects
as well as non-Gaussian resources for entanglement distillation and distributed
quantum computation. The latter could be provided by superconducting circuits
but existing solutions to interface the microwave and optical domains lack either
scalability or efficiency, and in most cases the conversion noise is not known.
In this work we utilize the unique opportunities of silicon photonics, cavity
optomechanics and superconducting circuits to demonstrate a fully integrated,
coherent transducer interfacing the microwave X and the telecom S bands with a
total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin
temperatures. The coupling relies solely on the radiation pressure interaction
mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ
as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical
gain, we achieve a total (internal) pure conversion efficiency of up to 0.019%
(1.6%), relevant for future noise-free operation on this qubit-compatible platform.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank Yuan Chen for performing supplementary FEM simulations and
Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable
discussions. This work was supported by IST Austria, the IST nanofabrication facility
(NFF), the European Union’s Horizon 2020 research and innovation program under grant
agreement no. 732894 (FET Proactive HOT) and the European Research Council under
grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an
ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020
research and innovation program under the Marie Sklodowska-Curie grant agreement
no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through
BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research
and innovation program under grant agreement no. 862644 (FET Open QUARTET).
article_number: '4460'
article_processing_charge: No
article_type: original
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons
with a silicon photonic nanomechanical interface. Nature Communications.
2020;11. doi:10.1038/s41467-020-18269-z
apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R.,
Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with
a silicon photonic nanomechanical interface. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-020-18269-z
chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo
R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting
Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.
ieee: G. M. Arnold et al., “Converting microwave and telecom photons with
a silicon photonic nanomechanical interface,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani
F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic
nanomechanical interface. Nature Communications. 11, 4460.
mla: Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon
Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460,
Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.
short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J.
Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).
date_created: 2020-09-18T10:56:20Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-08-22T09:27:12Z
day: '08'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-020-18269-z
ec_funded: 1
external_id:
isi:
- '000577280200001'
file:
- access_level: open_access
checksum: 88f92544889eb18bb38e25629a422a86
content_type: application/pdf
creator: dernst
date_created: 2020-09-18T13:02:37Z
date_updated: 2020-09-18T13:02:37Z
file_id: '8530'
file_name: 2020_NatureComm_Arnold.pdf
file_size: 1002818
relation: main_file
success: 1
file_date_updated: 2020-09-18T13:02:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
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/s41467-020-18912-9
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/
record:
- id: '13056'
relation: research_data
status: public
status: public
title: Converting microwave and telecom photons with a silicon photonic nanomechanical
interface
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: '8535'
abstract:
- lang: eng
text: We propose a method to enhance the visual detail of a water surface simulation.
Our method works as a post-processing step which takes a simulation as input and
increases its apparent resolution by simulating many detailed Lagrangian water
waves on top of it. We extend linear water wave theory to work in non-planar domains
which deform over time, and we discretize the theory using Lagrangian wave packets
attached to spline curves. The method is numerically stable and trivially parallelizable,
and it produces high frequency ripples with dispersive wave-like behaviors customized
to the underlying fluid simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual
Computing Group at IST Austria for their valuable feedback. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.
article_number: '65'
article_processing_charge: No
article_type: original
author:
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Andreas
full_name: Soderstrom, Andreas
last_name: Soderstrom
- first_name: John
full_name: Johansson, John
last_name: Johansson
- first_name: Christoph
full_name: Sprenger, Christoph
last_name: Sprenger
- first_name: Ken
full_name: Museth, Ken
last_name: Museth
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave
curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM
Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466'
apa: 'Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &
Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically
deforming surfaces. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3386569.3392466'
chicago: 'Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger,
Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves
on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.'
ieee: 'T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan,
“Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,”
ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing
Machinery, 2020.'
ista: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020.
Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces.
ACM Transactions on Graphics. 39(4), 65.'
mla: 'Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on
Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39,
no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.'
short: T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan,
ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-20T22:01:37Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T09:28:27Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392466
ec_funded: 1
external_id:
isi:
- '000583700300038'
file:
- access_level: open_access
checksum: c3a680893f01cc4a9e961ff0a4cfa12f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T07:51:44Z
date_updated: 2020-09-21T07:51:44Z
file_id: '8541'
file_name: 2020_ACM_Skrivan.pdf
file_size: 20223953
relation: main_file
success: 1
file_date_updated: 2020-09-21T07:51:44Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8539'
abstract:
- lang: eng
text: Cohomological and K-theoretic stable bases originated from the study of quantum
cohomology and quantum K-theory. Restriction formula for cohomological stable
bases played an important role in computing the quantum connection of cotangent
bundle of partial flag varieties. In this paper we study the K-theoretic stable
bases of cotangent bundles of flag varieties. We describe these bases in terms
of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar.
Using this algebraic description and the method of root polynomials, we give a
restriction formula of the stable bases. We apply it to obtain the restriction
formula for partial flag varieties. We also build a relation between the stable
basis and the Casselman basis in the principal series representations of the Langlands
dual group. As an application, we give a closed formula for the transition matrix
between Casselman basis and the characteristic functions.
- lang: fre
text: "Les bases stables cohomologiques et K-théoriques proviennent de l’étude de
la cohomologie quantique et de la K-théorie quantique. La formule de restriction
pour les bases stables cohomologiques a joué un rôle important dans le calcul
de la connexion quantique du fibré cotangent de variétés de drapeaux partielles.
Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents
des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de
l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette
description algébrique et la méthode des polynômes de racine, nous donnons une
formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la
formule de restriction pour les variétés de drapeaux partielles. Nous construisons
également une relation entre la base stable et la base de Casselman dans les représentations
de la série principale du groupe dual de Langlands p-adique. Comme une application,
nous donnons une formule close pour la matrice de transition entre la base de
Casselman et les fonctions caractéristiques. "
article_processing_charge: No
article_type: original
author:
- first_name: C.
full_name: Su, C.
last_name: Su
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
- first_name: C.
full_name: Zhong, C.
last_name: Zhong
citation:
ama: Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution.
Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671.
doi:10.24033/asens.2431
apa: Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the
springer resolution. Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France. https://doi.org/10.24033/asens.2431
chicago: Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the
Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.
ieee: C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer
resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol.
53, no. 3. Société Mathématique de France, pp. 663–671, 2020.
ista: Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer
resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.
mla: Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales
Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique
de France, 2020, pp. 663–71, doi:10.24033/asens.2431.
short: C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure
53 (2020) 663–671.
date_created: 2020-09-20T22:01:38Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-22T09:27:57Z
day: '01'
department:
- _id: TaHa
doi: 10.24033/asens.2431
external_id:
arxiv:
- '1708.08013'
isi:
- '000592182600004'
intvolume: ' 53'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08013
month: '06'
oa: 1
oa_version: Preprint
page: 663-671
publication: Annales Scientifiques de l'Ecole Normale Superieure
publication_identifier:
issn:
- 0012-9593
publication_status: published
publisher: Société Mathématique de France
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the K-theory stable bases of the springer resolution
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2020'
...
---
_id: '14000'
abstract:
- lang: eng
text: This chapter presents an overview of the state of the art in attosecond time-resolved
spectroscopy. The theoretical foundations of strong-field light–matter interaction
and attosecond pulse generation are described. The enabling laser technologies
are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization
to the generation and characterization of attosecond pulses. The applications
of attosecond pulses and pulse trains in electron- or ion-imaging experiments
are presented, followed by attosecond electron spectroscopy in larger molecules.
After this, high-harmonic spectroscopy and its applications to probing charge
migration on attosecond time scales is reviewed. The rapidly evolving field of
molecular photoionization delays is discussed. Finally, the applications of attosecond
transient absorption to probing molecular dynamics are presented.
article_processing_charge: No
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy.
In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics.
1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x'
apa: Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics
and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy
and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics,
edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020.
https://doi.org/10.1016/b978-0-12-817234-6.00009-x.
ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,”
in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and
M. Quack, Eds. Elsevier, 2020, pp. 113–161.
ista: 'Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy.
In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.'
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics,
edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61,
doi:10.1016/b978-0-12-817234-6.00009-x.
short: D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular
Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161.
date_created: 2023-08-09T13:10:23Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2023-08-22T09:25:07Z
day: '25'
doi: 10.1016/b978-0-12-817234-6.00009-x
edition: '1'
editor:
- first_name: Roberto
full_name: Marquardt, Roberto
last_name: Marquardt
- first_name: Martin
full_name: Quack, Martin
last_name: Quack
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 113-161
publication: Molecular Spectroscopy and Quantum Dynamics
publication_identifier:
eisbn:
- '0128172355'
isbn:
- '9780128172353'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attosecond Molecular Dynamics and Spectroscopy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '13056'
abstract:
- lang: eng
text: This datasets comprises all data shown in plots of the submitted article "Converting
microwave and telecom photons with a silicon photonic nanomechanical interface".
Additional raw data are available from the corresponding author on reasonable
request.
article_processing_charge: No
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons
with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561
apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R.,
Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with
a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561
chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo
R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting
Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.”
Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.
ieee: G. M. Arnold et al., “Converting microwave and telecom photons with
a silicon photonic nanomechanical interface.” Zenodo, 2020.
ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani
F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic
nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.
mla: Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a
Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.
short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J.
Hease, F. Hassani, J.M. Fink, (2020).
date_created: 2023-05-23T13:37:41Z
date_published: 2020-07-27T00:00:00Z
date_updated: 2023-08-22T09:27:11Z
day: '27'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.3961561
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.3961562
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '8529'
relation: used_in_publication
status: public
status: public
title: Converting microwave and telecom photons with a silicon photonic nanomechanical
interface
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8579'
abstract:
- lang: eng
text: Copper (Cu) is an essential trace element for all living organisms and used
as cofactor in key enzymes of important biological processes, such as aerobic
respiration or superoxide dismutation. However, due to its toxicity, cells have
developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for
cuproprotein biogenesis with the need to remove excess Cu. This review summarizes
our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative
bacteria and describes the multiple strategies that bacteria use for uptake, storage
and export of Cu. We furthermore describe general mechanistic principles that
aid the bacterial response to toxic Cu concentrations and illustrate dedicated
Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress
in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu
quota for cell proliferation is of particular importance for microbial pathogens
because Cu is utilized by the host immune system for attenuating pathogen survival
in host cells.
article_number: '242'
article_processing_charge: No
article_type: original
author:
- first_name: Andreea
full_name: Andrei, Andreea
last_name: Andrei
- first_name: Yavuz
full_name: Öztürk, Yavuz
last_name: Öztürk
- first_name: Bahia
full_name: Khalfaoui-Hassani, Bahia
last_name: Khalfaoui-Hassani
- first_name: Juna
full_name: Rauch, Juna
last_name: Rauch
- first_name: Dorian
full_name: Marckmann, Dorian
last_name: Marckmann
- first_name: Petru Iulian
full_name: Trasnea, Petru Iulian
id: D560034C-10C4-11EA-ABF4-A4B43DDC885E
last_name: Trasnea
- first_name: Fevzi
full_name: Daldal, Fevzi
last_name: Daldal
- first_name: Hans-Georg
full_name: Koch, Hans-Georg
last_name: Koch
citation:
ama: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria:
The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242'
apa: 'Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea,
P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes.
MDPI. https://doi.org/10.3390/membranes10090242'
chicago: 'Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian
Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis
in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.'
ieee: 'A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,”
Membranes, vol. 10, no. 9. MDPI, 2020.'
ista: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI,
Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes.
10(9), 242.'
mla: 'Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes,
vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.'
short: A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I.
Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).
date_created: 2020-09-28T08:59:26Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T09:34:06Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/membranes10090242
external_id:
isi:
- '000581446000001'
file:
- access_level: open_access
checksum: ceb43d7554e712dea6f36f9287271737
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T11:36:50Z
date_updated: 2020-09-28T11:36:50Z
file_id: '8583'
file_name: 2020_Membranes_Andrei.pdf
file_size: 4612258
relation: main_file
success: 1
file_date_updated: 2020-09-28T11:36:50Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Membranes
publication_identifier:
eissn:
- '20770375'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cu homeostasis in bacteria: The ins and outs'
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: '8581'
abstract:
- lang: eng
text: The majority of adenosine triphosphate (ATP) powering cellular processes in
eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present
the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo,
determined by cryo-electron microscopy. Subunits in the membrane domain are arranged
in the ‘proton translocation cluster’ attached to the c-ring and a more distant
‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to
a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation
pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM
maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled
c-ring, suggesting permeability transition pore opening. We propose a model for
the permeability transition pore opening, whereby subunit e pulls the lipid plug
out of the c-ring. Our structure will allow the design of drugs for many emerging
applications in medicine.
acknowledged_ssus:
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance
with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC.
We thank the IST Austria EM facility for access and assistance with collecting the
FEI Glacios dataset. Data processing was performed at the IST high-performance computing
cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by
the Horizon 2020 Programme of the European Commission.
article_processing_charge: No
article_type: original
author:
- first_name: Gergely
full_name: Pinke, Gergely
id: 4D5303E6-F248-11E8-B48F-1D18A9856A87
last_name: Pinke
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type
ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085.
doi:10.1038/s41594-020-0503-8
apa: Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the
entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology.
Springer Nature. https://doi.org/10.1038/s41594-020-0503-8
chicago: Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of
the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular
Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.
ieee: G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian
F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27,
no. 11. Springer Nature, pp. 1077–1085, 2020.
ista: Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian
F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.
mla: Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP
Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer
Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8.
short: G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology
27 (2020) 1077–1085.
date_created: 2020-09-28T08:59:27Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T09:33:09Z
day: '01'
department:
- _id: LeSa
doi: 10.1038/s41594-020-0503-8
external_id:
isi:
- '000569299400004'
pmid:
- '32929284'
intvolume: ' 27'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1077-1085
pmid: 1
publication: Nature Structural and Molecular Biology
publication_identifier:
eissn:
- '15459985'
issn:
- '15459993'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/structure-of-atpase-solved/
scopus_import: '1'
status: public
title: Cryo-EM structure of the entire mammalian F-type ATP synthase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2020'
...
---
_id: '8580'
abstract:
- lang: eng
text: We evaluate the usefulness of persistent homology in the analysis of heart
rate variability. In our approach we extract several topological descriptors characterising
datasets of RR-intervals, which are later used in classical machine learning algorithms.
By this method we are able to differentiate the group of patients with the history
of transient ischemic attack and the group of hypertensive patients.
article_number: '9158054'
article_processing_charge: No
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Beata
full_name: Graff, Beata
last_name: Graff
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Krzysztof
full_name: Narkiewicz, Krzysztof
last_name: Narkiewicz
citation:
ama: 'Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent
homology in the analysis of heart rate variability. In: 11th Conference of
the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054'
apa: 'Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application
of persistent homology in the analysis of heart rate variability. In 11th Conference
of the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054'
chicago: 'Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz.
“The Application of Persistent Homology in the Analysis of Heart Rate Variability.”
In 11th Conference of the European Study Group on Cardiovascular Oscillations:
Computation and Modelling in Physiology: New Challenges and Opportunities, .
IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.'
ieee: 'G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of
persistent homology in the analysis of heart rate variability,” in 11th Conference
of the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.'
ista: 'Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent
homology in the analysis of heart rate variability. 11th Conference of the European
Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology:
New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular
Oscillations, 9158054.'
mla: 'Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis
of Heart Rate Variability.” 11th Conference of the European Study Group on
Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges
and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.'
short: 'G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of
the European Study Group on Cardiovascular Oscillations: Computation and Modelling
in Physiology: New Challenges and Opportunities, , IEEE, 2020.'
conference:
end_date: 2020-07-15
location: Pisa, Italy
name: 'ESGCO: European Study Group on Cardiovascular Oscillations'
start_date: 2020-07-15
date_created: 2020-09-28T08:59:27Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2023-08-22T09:33:34Z
day: '01'
department:
- _id: HeEd
doi: 10.1109/ESGCO49734.2020.9158054
external_id:
isi:
- '000621172600045'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
publication: '11th Conference of the European Study Group on Cardiovascular Oscillations:
Computation and Modelling in Physiology: New Challenges and Opportunities, '
publication_identifier:
isbn:
- '9781728157511'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: The application of persistent homology in the analysis of heart rate variability
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8592'
abstract:
- lang: eng
text: Glioblastoma is the most malignant cancer in the brain and currently incurable.
It is urgent to identify effective targets for this lethal disease. Inhibition
of such targets should suppress the growth of cancer cells and, ideally also precancerous
cells for early prevention, but minimally affect their normal counterparts. Using
genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor
cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility
of cells within the development hierarchy of glioma to the knockout of insulin‐like
growth factor I receptor (IGF1R) is determined not only by their oncogenic states,
but also by their cell identities/states. Knockout of IGF1R selectively disrupts
the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable
outcome of IGF1R knockout on cell growth requires the mutant cells to commit to
the OPC identity regardless of its development hierarchical status. At the molecular
level, oncogenic mutations reprogram the cellular network of OPCs and force them
to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally
available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed.
The findings reveal the cellular window of IGF1R targeting and establish IGF1R
as an effective target for the prevention and treatment of glioblastoma.
acknowledgement: The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo,
and Q. Wu for their critical comments on the manuscript. They also thank Dr. H.
Zong for providing the CKO_NG2‐CreER model. This work is supported by the National
Key Research and Development Program of China, Stem Cell and Translational Research
(2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science
Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science
Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001
to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and
2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists,
China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation programme
(725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.
article_number: '2001724'
article_processing_charge: No
article_type: original
author:
- first_name: Anhao
full_name: Tian, Anhao
last_name: Tian
- first_name: Bo
full_name: Kang, Bo
last_name: Kang
- first_name: Baizhou
full_name: Li, Baizhou
last_name: Li
- first_name: Biying
full_name: Qiu, Biying
last_name: Qiu
- first_name: Wenhong
full_name: Jiang, Wenhong
last_name: Jiang
- first_name: Fangjie
full_name: Shao, Fangjie
last_name: Shao
- first_name: Qingqing
full_name: Gao, Qingqing
last_name: Gao
- first_name: Rui
full_name: Liu, Rui
last_name: Liu
- first_name: Chengwei
full_name: Cai, Chengwei
last_name: Cai
- first_name: Rui
full_name: Jing, Rui
last_name: Jing
- first_name: Wei
full_name: Wang, Wei
last_name: Wang
- first_name: Pengxiang
full_name: Chen, Pengxiang
last_name: Chen
- first_name: Qinghui
full_name: Liang, Qinghui
last_name: Liang
- first_name: Lili
full_name: Bao, Lili
last_name: Bao
- first_name: Jianghong
full_name: Man, Jianghong
last_name: Man
- first_name: Yan
full_name: Wang, Yan
last_name: Wang
- first_name: Yu
full_name: Shi, Yu
last_name: Shi
- first_name: Jin
full_name: Li, Jin
last_name: Li
- first_name: Minmin
full_name: Yang, Minmin
last_name: Yang
- first_name: Lisha
full_name: Wang, Lisha
last_name: Wang
- first_name: Jianmin
full_name: Zhang, Jianmin
last_name: Zhang
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Junming
full_name: Zhu, Junming
last_name: Zhu
- first_name: Xiuwu
full_name: Bian, Xiuwu
last_name: Bian
- first_name: Ying‐Jie
full_name: Wang, Ying‐Jie
last_name: Wang
- first_name: Chong
full_name: Liu, Chong
last_name: Liu
citation:
ama: Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially
dictate the susceptibility of cells within glioma development hierarchy to IGF1R
targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724
apa: Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020).
Oncogenic state and cell identity combinatorially dictate the susceptibility of
cells within glioma development hierarchy to IGF1R targeting. Advanced Science.
Wiley. https://doi.org/10.1002/advs.202001724
chicago: Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao,
Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate
the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.”
Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.
ieee: A. Tian et al., “Oncogenic state and cell identity combinatorially
dictate the susceptibility of cells within glioma development hierarchy to IGF1R
targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.
ista: Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R,
Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang
J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell
identity combinatorially dictate the susceptibility of cells within glioma development
hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.
mla: Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate
the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.”
Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.
short: A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai,
R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M.
Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced
Science 7 (2020).
date_created: 2020-10-01T09:44:13Z
date_published: 2020-11-04T00:00:00Z
date_updated: 2023-08-22T09:53:01Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1002/advs.202001724
ec_funded: 1
external_id:
isi:
- '000573860700001'
file:
- access_level: open_access
checksum: 92818c23ecc70e35acfa671f3cfb9909
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:07:24Z
date_updated: 2020-12-10T14:07:24Z
file_id: '8938'
file_name: 2020_AdvScience_Tian.pdf
file_size: 7835833
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:07:24Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '21'
keyword:
- General Engineering
- General Physics and Astronomy
- General Materials Science
- Medicine (miscellaneous)
- General Chemical Engineering
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Advanced Science
publication_identifier:
issn:
- 2198-3844
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Oncogenic state and cell identity combinatorially dictate the susceptibility
of cells within glioma development hierarchy to IGF1R targeting
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: 7
year: '2020'
...
---
_id: '8568'
abstract:
- lang: eng
text: Aqueous iodine based electrochemical energy storage is considered a potential
candidate to improve sustainability and performance of current battery and supercapacitor
technology. It harnesses the redox activity of iodide, iodine, and polyiodide
species in the confined geometry of nanoporous carbon electrodes. However, current
descriptions of the electrochemical reaction mechanism to interconvert these species
are elusive. Here we show that electrochemical oxidation of iodide in nanoporous
carbons forms persistent solid iodine deposits. Confinement slows down dissolution
into triiodide and pentaiodide, responsible for otherwise significant self-discharge
via shuttling. The main tools for these insights are in situ Raman spectroscopy
and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ
Raman confirms the reversible formation of triiodide and pentaiodide. In situ
SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon
nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying
the solid iodine volume fraction and visualizing the iodine structure on 3D lattice
models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate
strategies for improved iodine pore filling capacity and prevention of self-discharge,
applicable to hybrid supercapacitors and batteries.
article_number: '4838'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Harald
full_name: Fitzek, Harald
last_name: Fitzek
- first_name: Gerald
full_name: Kothleitner, Gerald
last_name: Kothleitner
- first_name: Volker
full_name: Presser, Volker
last_name: Presser
- first_name: Bernhard
full_name: Gollas, Bernhard
last_name: Gollas
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Qamar
full_name: Abbas, Qamar
last_name: Abbas
citation:
ama: Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine
electrodeposition in nanoporous carbons. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18610-6
apa: Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger,
S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition
in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6
chicago: Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard
Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible
Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.
ieee: C. Prehal et al., “Persistent and reversible solid iodine electrodeposition
in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature,
2020.
ista: Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas
Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous
carbons. Nature Communications. 11, 4838.
mla: Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition
in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer
Nature, 2020, doi:10.1038/s41467-020-18610-6.
short: C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger,
Q. Abbas, Nature Communications 11 (2020).
date_created: 2020-09-25T07:23:13Z
date_published: 2020-09-24T00:00:00Z
date_updated: 2023-08-22T09:37:24Z
day: '24'
ddc:
- '530'
department:
- _id: StFr
doi: 10.1038/s41467-020-18610-6
external_id:
isi:
- '000573756600004'
file:
- access_level: open_access
checksum: eada7bc8dd16a49390137cff882ef328
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:16:15Z
date_updated: 2020-09-28T13:16:15Z
file_id: '8585'
file_name: 2020_NatureComm_Prehal.pdf
file_size: 1822469
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:16:15Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
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/s41467-020-19720-x
status: public
title: Persistent and reversible solid iodine electrodeposition in nanoporous carbons
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: '8643'
abstract:
- lang: eng
text: The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic
complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing
and escape in mice, a result thought to be caused by a PBG projection to the central
nucleus of the amygdala. However, the isthmic complex, including the PBG, has
been classically considered satellite nuclei of the Superior Colliculus (SC),
which upon stimulation of its medial part also triggers fear and avoidance reactions.
As the PBG-SC connectivity is not well characterized, we investigated whether
the topology of the PBG projection to the SC could be related to the behavioral
consequences of PBG stimulation. To that end, we performed immunohistochemistry,
in situ hybridization and neural tracer injections in the SC and PBG in a diurnal
rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic
and cholinergic markers and were distributed in clearly defined anterior (aPBG)
and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically
to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral
SC and projected exclusively to the contralateral SC. This contralateral projection
forms a dense field of terminals that is restricted to the medial SC, in correspondence
with the SC representation of the aerial binocular field which, we also found,
in O. degus prompted escape reactions upon looming stimulation. Therefore, this
specialized topography allows binocular interactions in the SC region controlling
responses to aerial predators, suggesting a link between the mechanisms by which
the SC and PBG produce defensive behaviors.
acknowledgement: 'We thank Elisa Sentis and Solano Henriquez for their expert technical
assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package.
Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane
Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her
helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing
us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the
confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to
G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).'
article_number: '16220'
article_processing_charge: No
article_type: original
author:
- first_name: Alfonso
full_name: Deichler, Alfonso
last_name: Deichler
- first_name: Denisse
full_name: Carrasco, Denisse
last_name: Carrasco
- first_name: Luciana
full_name: Lopez-Jury, Luciana
last_name: Lopez-Jury
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Natalia
full_name: Marquez, Natalia
last_name: Marquez
- first_name: Jorge
full_name: Mpodozis, Jorge
last_name: Mpodozis
- first_name: Gonzalo
full_name: Marin, Gonzalo
last_name: Marin
citation:
ama: Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity
suggests a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10.
doi:10.1038/s41598-020-72848-0
apa: Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N.,
Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. Springer
Nature. https://doi.org/10.1038/s41598-020-72848-0
chicago: Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga,
Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal
Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus
and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific
Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.
ieee: A. Deichler et al., “A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents,” Scientific Reports, vol.
10. Springer Nature, 2020.
ista: Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis
J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between
the mechanisms by which the superior colliculus and parabigeminal nucleus produce
defensive behaviors in rodents. Scientific Reports. 10, 16220.
mla: Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a
Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal
Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol.
10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.
short: A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J.
Mpodozis, G. Marin, Scientific Reports 10 (2020).
date_created: 2020-10-11T22:01:14Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T09:58:21Z
day: '01'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-020-72848-0
external_id:
isi:
- '000577142600032'
file:
- access_level: open_access
checksum: f6dd99954f1c0ffb4da5a1d2d739bf31
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:39:10Z
date_updated: 2020-10-12T12:39:10Z
file_id: '8651'
file_name: 2020_ScientificReport_Deichler.pdf
file_size: 3906744
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:39:10Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '10'
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 specialized reciprocal connectivity suggests a link between the mechanisms
by which the superior colliculus and parabigeminal nucleus produce defensive behaviors
in rodents
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: '8645'
abstract:
- lang: eng
text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution
to fitness, is common in evolution. To detect epistasis, fitness must be measured
for at least four genotypes: the reference genotype, two different single mutants
and a double mutant with both of the single mutations. For higher-order epistasis
of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional
hypercube in genotype space forming a ‘combinatorially complete dataset’. So far,
only a handful of such datasets have been produced by manual curation. Concurrently,
random mutagenesis experiments have produced measurements of fitness and other
phenotypes in a high-throughput manner, potentially containing a number of combinatorially
complete datasets. We present an effective recursive algorithm for finding all
hypercube structures in random mutagenesis experimental data. To test the algorithm,
we applied it to the data from a recent HIS3 protein dataset and found all 199
847 053 unique combinatorially complete genotype combinations of dimensionality
ranging from 2 to 12. The algorithm may be useful for researchers looking for
higher-order epistasis in their high-throughput experimental data.'
acknowledgement: 'This work was supported by the European Research Council under the
European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement
335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute
of Science and Technology. The work was started at the School of Molecular and Theoretical
Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman
Scientists Support Grant in Centre for Genomic Regulation (CRG). '
article_processing_charge: No
article_type: original
author:
- first_name: Laura A
full_name: Esteban, Laura A
last_name: Esteban
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Daniil M
full_name: Bobrovskiy, Daniil M
last_name: Bobrovskiy
- first_name: Gregory
full_name: Leleytner, Gregory
last_name: Leleytner
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: 'Dmitry N '
full_name: 'Ivankov, Dmitry N '
last_name: Ivankov
citation:
ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841'
apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva,
N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841'
chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner,
Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME:
Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.”
Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.'
ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially
complete datasets from a single experiment,” Bioinformatics, vol. 36, no.
6. Oxford Academic, pp. 1960–1962, 2020.'
ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov
F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete
datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.'
mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially
Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no.
6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.'
short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva,
F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
date_created: 2020-10-11T22:01:14Z
date_published: 2020-03-15T00:00:00Z
date_updated: 2023-08-22T09:57:29Z
day: '15'
ddc:
- '000'
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btz841
ec_funded: 1
external_id:
isi:
- '000538696800054'
pmid:
- '31742320'
file:
- access_level: open_access
checksum: 21d6f71839deb3b83e4a356193f72767
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:02:09Z
date_updated: 2020-10-12T12:02:09Z
file_id: '8649'
file_name: 2020_Bioinformatics_Esteban.pdf
file_size: 308341
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:02:09Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1960-1962
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
eissn:
- 1460-2059
issn:
- 1367-4803
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HypercubeME: Two hundred million combinatorially complete datasets from a
single experiment'
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2020'
...
---
_id: '8597'
abstract:
- lang: eng
text: Error analysis and data visualization of positive COVID-19 cases in 27 countries
have been performed up to August 8, 2020. This survey generally observes a progression
from early exponential growth transitioning to an intermediate power-law growth
phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth
after the power-law phase with lockdowns or social distancing may be described
as an effect of avoidance. A visualization of the power-law growth exponent over
short time windows is qualitatively similar to the Bhatia visualization for pandemic
progression. Visualizations like these can indicate the onset of second waves
and may influence social policy.
acknowledgement: I would especially like to thank Michael Sixt for encouraging me
to think about these problems while working at home due to restrictions in place.
I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico
Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.
article_number: '065005'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
citation:
ama: Merrin J. Differences in power law growth over time and indicators of COVID-19
pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db
apa: Merrin, J. (2020). Differences in power law growth over time and indicators
of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing.
https://doi.org/10.1088/1478-3975/abb2db
chicago: Merrin, Jack. “Differences in Power Law Growth over Time and Indicators
of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing,
2020. https://doi.org/10.1088/1478-3975/abb2db.
ieee: J. Merrin, “Differences in power law growth over time and indicators of COVID-19
pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP
Publishing, 2020.
ista: Merrin J. 2020. Differences in power law growth over time and indicators of
COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.
mla: Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of
COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no.
6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.
short: J. Merrin, Physical Biology 17 (2020).
date_created: 2020-10-04T22:01:35Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2023-08-22T09:53:29Z
day: '23'
ddc:
- '510'
- '570'
department:
- _id: NanoFab
doi: 10.1088/1478-3975/abb2db
external_id:
isi:
- '000575539700001'
file:
- access_level: open_access
checksum: fec9bdd355ed349f09990faab20838a7
content_type: application/pdf
creator: dernst
date_created: 2020-10-05T13:53:59Z
date_updated: 2020-10-05T13:53:59Z
file_id: '8609'
file_name: 2020_PhysBio_Merrin.pdf
file_size: 1667111
relation: main_file
success: 1
file_date_updated: 2020-10-05T13:53:59Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Physical Biology
publication_identifier:
eissn:
- '14783975'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differences in power law growth over time and indicators of COVID-19 pandemic
progression worldwide
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: 17
year: '2020'
...
---
_id: '8674'
abstract:
- lang: eng
text: 'Extrasynaptic actions of glutamate are limited by high-affinity transporters
expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point
transmission in excitatory circuits. Memory formation in the brain is associated
with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic
glutamate actions is poorly understood. Here, we used advanced imaging methods,
in situ and in vivo, to find that a classical synaptic memory mechanism, long-term
potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical
glutamate sensors combined with patch-clamp and 3D molecular localization reveal
that LTP induction thus prompts spatial retreat of astroglial glutamate transporters,
boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk.
The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling
protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes.
We have therefore uncovered a mechanism by which a memory trace at one synapse
could alter signal handling by multiple neighboring connections.'
acknowledgement: We thank J. Angibaud for organotypic cultures and R. Chereau and
J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre
Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping.
This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251,
ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950,
and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German
Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program
(C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995
(A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine
R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01,
Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O.,
and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and
FP7 MemStick Project No. 201600 (M.G.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Lucie
full_name: Bard, Lucie
last_name: Bard
- first_name: Aude
full_name: Panatier, Aude
last_name: Panatier
- first_name: James P.
full_name: Reynolds, James P.
last_name: Reynolds
- first_name: Olga
full_name: Kopach, Olga
last_name: Kopach
- first_name: Nikolay I.
full_name: Medvedev, Nikolay I.
last_name: Medvedev
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Michel K.
full_name: Herde, Michel K.
last_name: Herde
- first_name: Stefanie
full_name: Anders, Stefanie
last_name: Anders
- first_name: Igor
full_name: Kraev, Igor
last_name: Kraev
- first_name: Janosch P.
full_name: Heller, Janosch P.
last_name: Heller
- first_name: Sylvain
full_name: Rama, Sylvain
last_name: Rama
- first_name: Kaiyu
full_name: Zheng, Kaiyu
last_name: Zheng
- first_name: Thomas P.
full_name: Jensen, Thomas P.
last_name: Jensen
- first_name: Inmaculada
full_name: Sanchez-Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez-Romero
- first_name: Colin J.
full_name: Jackson, Colin J.
last_name: Jackson
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Ole Petter
full_name: Ottersen, Ole Petter
last_name: Ottersen
- first_name: Erlend Arnulf
full_name: Nagelhus, Erlend Arnulf
last_name: Nagelhus
- first_name: Stephane H.R.
full_name: Oliet, Stephane H.R.
last_name: Oliet
- first_name: Michael G.
full_name: Stewart, Michael G.
last_name: Stewart
- first_name: U. VAlentin
full_name: Nägerl, U. VAlentin
last_name: Nägerl
- first_name: 'Dmitri A. '
full_name: 'Rusakov, Dmitri A. '
last_name: Rusakov
citation:
ama: Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover
by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11.
doi:10.1016/j.neuron.2020.08.030
apa: Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev,
N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving
withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030
chicago: Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga
Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate
Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier,
2020. https://doi.org/10.1016/j.neuron.2020.08.030.
ieee: C. Henneberger et al., “LTP induction boosts glutamate spillover by
driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5.
Elsevier, p. P919–936.E11, 2020.
ista: Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge
D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero
I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl
UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal
of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.
mla: Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by
Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5,
Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.
short: C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev,
D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P.
Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus,
S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.
date_created: 2020-10-18T22:01:38Z
date_published: 2020-12-09T00:00:00Z
date_updated: 2023-08-22T09:59:29Z
day: '09'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1016/j.neuron.2020.08.030
external_id:
isi:
- '000603428000010'
pmid:
- '32976770'
file:
- access_level: open_access
checksum: 054562bb50165ef9a1f46631c1c5e36b
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:42:09Z
date_updated: 2020-12-10T14:42:09Z
file_id: '8939'
file_name: 2020_Neuron_Henneberger.pdf
file_size: 7518960
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:42:09Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '5'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: P919-936.E11
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- '10974199'
issn:
- '08966273'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic
astroglia
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: 108
year: '2020'
...
---
_id: '8652'
abstract:
- lang: eng
text: Nature creates electrons with two values of the spin projection quantum number.
In certain applications, it is important to filter electrons with one spin projection
from the rest. Such filtering is not trivial, since spin-dependent interactions
are often weak, and cannot lead to any substantial effect. Here we propose an
efficient spin filter based upon scattering from a two-dimensional crystal, which
is made of aligned point magnets. The polarization of the outgoing electron flux
is controlled by the crystal, and reaches maximum at specific values of the parameters.
In our scheme, polarization increase is accompanied by higher reflectivity of
the crystal. High transmission is feasible in scattering from a quantum cavity
made of two crystals. Our findings can be used for studies of low-energy spin-dependent
scattering from two-dimensional ordered structures made of magnetic atoms or aligned
chiral molecules.
acknowledgement: "This work has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science
Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC)
Starting\r\nGrant No. 801770 (ANGULON)."
article_number: '178'
article_processing_charge: Yes
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a
lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8
apa: Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by
scattering from a lattice of point magnets. Communications Physics. Springer
Nature. https://doi.org/10.1038/s42005-020-00445-8
chicago: Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins
by Scattering from a Lattice of Point Magnets.” Communications Physics.
Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.
ieee: A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering
from a lattice of point magnets,” Communications Physics, vol. 3. Springer
Nature, 2020.
ista: Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering
from a lattice of point magnets. Communications Physics. 3, 178.
mla: Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point
Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.
short: A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).
date_created: 2020-10-13T09:48:59Z
date_published: 2020-10-09T00:00:00Z
date_updated: 2023-08-22T09:58:46Z
day: '09'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1038/s42005-020-00445-8
ec_funded: 1
external_id:
isi:
- '000581681000001'
file:
- access_level: open_access
checksum: 60cd35b99f0780acffc7b6060e49ec8b
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T15:16:28Z
date_updated: 2020-10-14T15:16:28Z
file_id: '8662'
file_name: 2020_CommPhysics_Ghazaryan.pdf
file_size: 1462934
relation: main_file
success: 1
file_date_updated: 2020-10-14T15:16:28Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _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: Communications Physics
publication_identifier:
issn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Filtering spins by scattering from a lattice of point magnets
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: '8669'
abstract:
- lang: eng
text: Pancreatic islets play an essential role in regulating blood glucose level.
Although the molecular pathways underlying islet cell differentiation are beginning
to be resolved, the cellular basis of islet morphogenesis and fate allocation
remain unclear. By combining unbiased and targeted lineage tracing, we address
the events leading to islet formation in the mouse. From the statistical analysis
of clones induced at multiple embryonic timepoints, here we show that, during
the secondary transition, islet formation involves the aggregation of multiple
equipotent endocrine progenitors that transition from a phase of stochastic amplification
by cell division into a phase of sublineage restriction and limited islet fission.
Together, these results explain quantitatively the heterogeneous size distribution
and degree of polyclonality of maturing islets, as well as dispersion of progenitors
within and between islets. Further, our results show that, during the secondary
transition, α- and β-cells are generated in a contemporary manner. Together, these
findings provide insight into the cellular basis of islet development.
article_number: '5037'
article_processing_charge: No
article_type: original
author:
- first_name: Magdalena K.
full_name: Sznurkowska, Magdalena K.
last_name: Sznurkowska
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Roberta
full_name: Azzarelli, Roberta
last_name: Azzarelli
- first_name: Lemonia
full_name: Chatzeli, Lemonia
last_name: Chatzeli
- first_name: Tatsuro
full_name: Ikeda, Tatsuro
last_name: Ikeda
- first_name: Shosei
full_name: Yoshida, Shosei
last_name: Yoshida
- first_name: Anna
full_name: Philpott, Anna
last_name: Philpott
- first_name: Benjamin D
full_name: Simons, Benjamin D
last_name: Simons
citation:
ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis
of islet specification in mouse pancreas. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18837-3
apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T.,
Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification
in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3
chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia
Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons.
“Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.
ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification
in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott
A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse
pancreas. Nature Communications. 11, 5037.
mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification
in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature,
2020, doi:10.1038/s41467-020-18837-3.
short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida,
A. Philpott, B.D. Simons, Nature Communications 11 (2020).
date_created: 2020-10-18T22:01:35Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2023-08-22T10:18:17Z
day: '07'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-020-18837-3
external_id:
isi:
- '000577244600003'
pmid:
- '33028844'
file:
- access_level: open_access
checksum: 0ecc0eab72d2d50694852579611a6624
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:27:46Z
date_updated: 2020-10-19T11:27:46Z
file_id: '8677'
file_name: 2020_NatureComm_Sznurkowska.pdf
file_size: 5540540
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:27:46Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the cellular basis of islet specification in mouse pancreas
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: '8672'
abstract:
- lang: eng
text: Cell fate transitions are key to development and homeostasis. It is thus essential
to understand the cellular mechanisms controlling fate transitions. Cell division
has been implicated in fate decisions in many stem cell types, including neuronal
and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells,
the role of division remains unclear. Here, we show that exit from naive pluripotency
in mouse ES cells generally occurs after a division. We further show that exit
timing is strongly correlated between sister cells, which remain connected by
cytoplasmic bridges long after division, and that bridge abscission progressively
accelerates as cells exit naive pluripotency. Finally, interfering with abscission
impairs naive pluripotency exit, and artificially inducing abscission accelerates
it. Altogether, our data indicate that a switch in the division machinery leading
to faster abscission regulates pluripotency exit. Our study identifies abscission
as a key cellular process coupling cell division to fate transitions.
acknowledgement: This work was supported by the Medical Research Council UK (MRC Program
award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv
and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust
(Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support
from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support
from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation
Bettencourt-Schueller (Prix Jeune Chercheur, 2015).
article_processing_charge: No
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Céline
full_name: Labouesse, Céline
last_name: Labouesse
- first_name: Ian J.
full_name: White, Ian J.
last_name: White
- first_name: Meghan
full_name: Agnew, Meghan
last_name: Agnew
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to
embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001
apa: Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut,
K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic
stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001
chicago: Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard
B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division
to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.
ieee: A. Chaigne et al., “Abscission couples cell division to embryonic stem
cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208,
2020.
ista: Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK.
2020. Abscission couples cell division to embryonic stem cell fate. Developmental
Cell. 55(2), 195–208.
mla: Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem
Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208,
doi:10.1016/j.devcel.2020.09.001.
short: A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut,
E.K. Paluch, Developmental Cell 55 (2020) 195–208.
date_created: 2020-10-18T22:01:37Z
date_published: 2020-10-26T00:00:00Z
date_updated: 2023-08-22T10:16:58Z
day: '26'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2020.09.001
external_id:
isi:
- '000582501100012'
pmid:
- '32979313'
file:
- access_level: open_access
checksum: 88e1a031a61689165d19a19c2f16d795
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T10:20:02Z
date_updated: 2021-02-04T10:20:02Z
file_id: '9086'
file_name: 2020_DevelopmCell_Chaigne.pdf
file_size: 6929686
relation: main_file
success: 1
file_date_updated: 2021-02-04T10:20:02Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 195-208
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abscission couples cell division to embryonic stem cell fate
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: 55
year: '2020'
...
---
_id: '8697'
abstract:
- lang: eng
text: In the computation of the material properties of random alloys, the method
of 'special quasirandom structures' attempts to approximate the properties of
the alloy on a finite volume with higher accuracy by replicating certain statistics
of the random atomic lattice in the finite volume as accurately as possible. In
the present work, we provide a rigorous justification for a variant of this method
in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach
is based on a recent analysis of a related variance reduction method in stochastic
homogenization of linear elliptic PDEs and the locality properties of the TFW
model. Concerning the latter, we extend an exponential locality result by Nazar
and Ortner to include point charges, a result that may be of independent interest.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Fischer JL, Kniely M. Variance reduction for effective energies of random lattices
in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772.
doi:10.1088/1361-6544/ab9728
apa: Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies
of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity.
IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728
chicago: Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective
Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity.
IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.
ieee: J. L. Fischer and M. Kniely, “Variance reduction for effective energies of
random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity,
vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.
ista: Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random
lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.
mla: Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies
of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity,
vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.
short: J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.
date_created: 2020-10-25T23:01:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T10:38:38Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1088/1361-6544/ab9728
external_id:
arxiv:
- '1906.12245'
isi:
- '000576492700001'
file:
- access_level: open_access
checksum: ed90bc6eb5f32ee6157fef7f3aabc057
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T12:09:57Z
date_updated: 2020-10-27T12:09:57Z
file_id: '8710'
file_name: 2020_Nonlinearity_Fischer.pdf
file_size: 1223899
relation: main_file
success: 1
file_date_updated: 2020-10-27T12:09:57Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '11'
oa: 1
oa_version: Published Version
page: 5733-5772
publication: Nonlinearity
publication_identifier:
eissn:
- '13616544'
issn:
- '09517715'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variance reduction for effective energies of random lattices in the Thomas-Fermi-von
Weizsäcker model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2020'
...
---
_id: '8680'
abstract:
- lang: eng
text: Animal development entails the organization of specific cell types in space
and time, and spatial patterns must form in a robust manner. In the zebrafish
spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen
signaling and large-scale cellular rearrangements during morphogenesis and growth.
By directly measuring adhesion forces and preferences for three types of endogenous
neural progenitors, we provide evidence for the differential adhesion model in
which differences in intercellular adhesion mediate cell sorting. Cell type–specific
combinatorial expression of different classes of cadherins (N-cadherin, cadherin
11, and protocadherin 19) results in homotypic preference ex vivo and patterning
robustness in vivo. Furthermore, the differential adhesion code is regulated by
the sonic hedgehog morphogen gradient. We propose that robust patterning during
tissue morphogenesis results from interplay between adhesion-based self-organization
and morphogen-directed patterning.
acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical
discussions of and technical assistance during the work and B. Appel, S. Holley,
J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon
Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship
of the Company of Biologists, a Collaborative Research grant from the Burroughs
Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH
grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Tony Y.-C.
full_name: Tsai, Tony Y.-C.
last_name: Tsai
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Tugba
full_name: Colak-Champollion, Tugba
last_name: Colak-Champollion
- first_name: Holger
full_name: Knaut, Holger
last_name: Knaut
- 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
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. 2020;370(6512):113-116.
doi:10.1126/science.aba6637
apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg,
C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aba6637
chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion,
Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code
Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.
ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation
during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association
for the Advancement of Science, pp. 113–116, 2020.
ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ,
Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue
morphogenesis. Science. 370(6512), 113–116.
mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation
during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association
for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.
short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J.
Heisenberg, S.G. Megason, Science 370 (2020) 113–116.
date_created: 2020-10-19T14:09:38Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2023-08-22T10:36:35Z
day: '02'
department:
- _id: CaHe
doi: 10.1126/science.aba6637
ec_funded: 1
external_id:
isi:
- '000579169000053'
intvolume: ' 370'
isi: 1
issue: '6512'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/803635v1
month: '10'
oa: 1
oa_version: Preprint
page: 113-116
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
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/sticking-together/
scopus_import: '1'
status: public
title: An adhesion code ensures robust pattern formation during tissue morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 370
year: '2020'
...
---
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2023-08-22T10:37:10Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- '15461718'
issn:
- '10614036'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...
---
_id: '8679'
abstract:
- lang: eng
text: A central goal of artificial intelligence in high-stakes decision-making applications
is to design a single algorithm that simultaneously expresses generalizability
by learning coherent representations of their world and interpretable explanations
of its dynamics. Here, we combine brain-inspired neural computation principles
and scalable deep learning architectures to design compact neural controllers
for task-specific compartments of a full-stack autonomous vehicle control system.
We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated
input features to outputs by 253 synapses, learns to map high-dimensional inputs
into steering commands. This system shows superior generalizability, interpretability
and robustness compared with orders-of-magnitude larger black-box learning systems.
The obtained neural agents enable high-fidelity autonomy for task-specific parts
of a complex autonomous system.
article_processing_charge: No
article_type: original
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652.
doi:10.1038/s42256-020-00237-3
apa: Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu,
R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine
Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3
chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela
Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature
Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.
ieee: M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural
circuit policies enabling auditable autonomy,” Nature Machine Intelligence,
vol. 2. Springer Nature, pp. 642–652, 2020.
ista: Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit
policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.
mla: Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.”
Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52,
doi:10.1038/s42256-020-00237-3.
short: M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature
Machine Intelligence 2 (2020) 642–652.
date_created: 2020-10-19T13:46:06Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:36:06Z
day: '01'
department:
- _id: ToHe
doi: 10.1038/s42256-020-00237-3
external_id:
isi:
- '000583337200011'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 642-652
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Machine Intelligence
publication_identifier:
eissn:
- 2522-5839
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-deep-learning-models/
scopus_import: '1'
status: public
title: Neural circuit policies enabling auditable autonomy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2
year: '2020'
...
---
_id: '8670'
abstract:
- lang: eng
text: The α–z Rényi relative entropies are a two-parameter family of Rényi relative
entropies that are quantum generalizations of the classical α-Rényi relative entropies.
In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α,
z) for which the data processing inequality (DPI) is valid. In this paper, we
give algebraic conditions for the equality in DPI. For the full range of parameters
(α, z), we give necessary conditions and sufficient conditions. For most parameters,
we give equivalent conditions. This generalizes and strengthens the results of
Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].
acknowledgement: This research was supported by the European Union’s Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for
their helpful comments.
article_number: '102201'
article_processing_charge: No
article_type: original
author:
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Zhang H. Equality conditions of data processing inequality for α-z Rényi relative
entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787
apa: Zhang, H. (2020). Equality conditions of data processing inequality for α-z
Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing.
https://doi.org/10.1063/5.0022787
chicago: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z
Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing,
2020. https://doi.org/10.1063/5.0022787.
ieee: H. Zhang, “Equality conditions of data processing inequality for α-z Rényi
relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10.
AIP Publishing, 2020.
ista: Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi
relative entropies. Journal of Mathematical Physics. 61(10), 102201.
mla: Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi
Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10,
102201, AIP Publishing, 2020, doi:10.1063/5.0022787.
short: H. Zhang, Journal of Mathematical Physics 61 (2020).
date_created: 2020-10-18T22:01:36Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T10:32:29Z
day: '01'
department:
- _id: JaMa
doi: 10.1063/5.0022787
ec_funded: 1
external_id:
arxiv:
- '2007.06644'
isi:
- '000578529200001'
intvolume: ' 61'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.06644
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equality conditions of data processing inequality for α-z Rényi relative entropies
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2020'
...
---
_id: '8698'
abstract:
- lang: eng
text: The brain represents and reasons probabilistically about complex stimuli and
motor actions using a noisy, spike-based neural code. A key building block for
such neural computations, as well as the basis for supervised and unsupervised
learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional
neural activity patterns. Despite progress in statistical modeling of neural responses
and deep learning, current approaches either do not scale to large neural populations
or cannot be implemented using biologically realistic mechanisms. Inspired by
the sparse and random connectivity of real neuronal circuits, we present a model
for neural codes that accurately estimates the likelihood of individual spiking
patterns and has a straightforward, scalable, efficient, learnable, and realistic
neural implementation. This model’s performance on simultaneously recorded spiking
activity of >100 neurons in the monkey visual and prefrontal cortices is comparable
with or better than that of state-of-the-art models. Importantly, the model can
be learned using a small number of samples and using a local learning rule that
utilizes noise intrinsic to neural circuits. Slower, structural changes in random
connectivity, consistent with rewiring and pruning processes, further improve
the efficiency and sparseness of the resulting neural representations. Our results
merge insights from neuroanatomy, machine learning, and theoretical neuroscience
to suggest random sparse connectivity as a key design principle for neuronal computation.
acknowledgement: We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir
Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn
for invaluable discussions of the learning rule. This work was supported by European
Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12
(to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs.
Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to
R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration
on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative
Research in Computational Neuroscience) grant (to R.K. and E.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Ori
full_name: Maoz, Ori
last_name: Maoz
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mohamad Saleh
full_name: Esteki, Mohamad Saleh
last_name: Esteki
- first_name: Roozbeh
full_name: Kiani, Roozbeh
last_name: Kiani
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the
National Academy of Sciences of the United States of America. 2020;117(40):25066-25073.
doi:10.1073/pnas.1912804117
apa: Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020).
Learning probabilistic neural representations with randomly connected circuits.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117
chicago: Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad
Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected
Circuits.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.
ieee: O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic
neural representations with randomly connected circuits,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 117, no.
40. National Academy of Sciences, pp. 25066–25073, 2020.
ista: Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic
neural representations with randomly connected circuits. Proceedings of the National
Academy of Sciences of the United States of America. 117(40), 25066–25073.
mla: Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly
Connected Circuits.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 117, no. 40, National Academy of Sciences,
2020, pp. 25066–73, doi:10.1073/pnas.1912804117.
short: O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of
the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.
date_created: 2020-10-25T23:01:16Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2023-08-22T12:11:23Z
day: '06'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.1912804117
external_id:
isi:
- '000579045200012'
pmid:
- '32948691'
file:
- access_level: open_access
checksum: c6a24fdecf3f28faf447078e7a274a88
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T14:57:50Z
date_updated: 2020-10-27T14:57:50Z
file_id: '8713'
file_name: 2020_PNAS_Maoz.pdf
file_size: 1755359
relation: main_file
success: 1
file_date_updated: 2020-10-27T14:57:50Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 25066-25073
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning probabilistic neural representations with randomly connected circuits
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: 117
year: '2020'
...
---
_id: '8704'
abstract:
- lang: eng
text: Traditional robotic control suits require profound task-specific knowledge
for designing, building and testing control software. The rise of Deep Learning
has enabled end-to-end solutions to be learned entirely from data, requiring minimal
knowledge about the application area. We design a learning scheme to train end-to-end
linear dynamical systems (LDS)s by gradient descent in imitation learning robotic
domains. We introduce a new regularization loss component together with a learning
algorithm that improves the stability of the learned autonomous system, by forcing
the eigenvalues of the internal state updates of an LDS to be negative reals.
We evaluate our approach on a series of real-life and simulated robotic experiments,
in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures.
Our results show that our stabilizing method significantly improves test performance
of LDS, enabling such linear models to match the performance of contemporary nonlinear
RNN architectures. A video of the obstacle avoidance performance of our method
on a mobile robot, in unseen environments, compared to other methods can be viewed
at https://youtu.be/mhEsCoNao5E.
acknowledgement: M.L. is supported in parts by the Austrian Science Fund (FWF) under
grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the
Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion
Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing
Company.
alternative_title:
- ICRA
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent
neural network compartment of an end-to-end robot learning scheme. In: Proceedings
- IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452.
doi:10.1109/ICRA40945.2020.9196608'
apa: 'Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss
stabilizes the recurrent neural network compartment of an end-to-end robot learning
scheme. In Proceedings - IEEE International Conference on Robotics and Automation
(pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608'
chicago: Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin
Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot
Learning Scheme.” In Proceedings - IEEE International Conference on Robotics
and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.
ieee: M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the
recurrent neural network compartment of an end-to-end robot learning scheme,”
in Proceedings - IEEE International Conference on Robotics and Automation,
Paris, France, 2020, pp. 5446–5452.
ista: 'Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the
recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings
- IEEE International Conference on Robotics and Automation. ICRA: International
Conference on Robotics and Automation, ICRA, , 5446–5452.'
mla: Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network
Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International
Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.
short: M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International
Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.
conference:
end_date: 2020-08-31
location: Paris, France
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2020-05-31
date_created: 2020-10-25T23:01:19Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2023-08-22T10:40:15Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/ICRA40945.2020.9196608
external_id:
isi:
- '000712319503110'
file:
- access_level: open_access
checksum: fccf7b986ac78046918a298cc6849a50
content_type: application/pdf
creator: dernst
date_created: 2020-11-06T10:58:49Z
date_updated: 2020-11-06T10:58:49Z
file_id: '8733'
file_name: 2020_ICRA_Lechner.pdf
file_size: 1070010
relation: main_file
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language:
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oa_version: Submitted Version
page: 5446-5452
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings - IEEE International Conference on Robotics and Automation
publication_identifier:
isbn:
- '9781728173955'
issn:
- '10504729'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end
robot learning scheme
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8700'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
acknowledgement: We would like to thank the staff of CCU Genome for sequencing, Tat’yana
Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided,
as well as the laboratory staff for productive discussion of the results. We also
thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna
Kryuchkova for the exceptional contribution to the present work.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molecular Biology. Springer Nature.
https://doi.org/10.1134/S0026893320050088
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation
Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature,
2020. https://doi.org/10.1134/S0026893320050088.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer
Nature, pp. 739–748, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 54(5), 739–748.
mla: Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon
Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology,
vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular
Biology 54 (2020) 739–748.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:38Z
day: '01'
department:
- _id: FyKo
doi: 10.1134/S0026893320050088
external_id:
isi:
- '000579441200009'
intvolume: ' 54'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 739-748
publication: Molecular Biology
publication_identifier:
eissn:
- '16083245'
issn:
- '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8701'
relation: original
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8701'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian
Academy of Sciences. https://doi.org/10.31857/S0026898420050080
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian
Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian
Academy of Sciences, pp. 837–848, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.
mla: Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon
contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia
biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48,
doi:10.31857/S0026898420050080.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia
biologiia 54 (2020) 837–848.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T10:39:37Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420050080
external_id:
pmid:
- '33009793'
intvolume: ' 54'
issue: '5'
language:
- iso: rus
month: '09'
oa_version: None
page: 837-848
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8700'
relation: translation
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_id: '14096'
abstract:
- lang: eng
text: A binary neutron star merger has been observed in a multi-messenger detection
of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron
stars that merge within a Hubble time, as well as many other compact binaries,
are expected to form via common envelope evolution. Yet five decades of research
on common envelope evolution have not yet resulted in a satisfactory understanding
of the multi-spatial multi-timescale evolution for the systems that lead to compact
binaries. In this paper, we report on the first successful simulations of common
envelope ejection leading to binary neutron star formation in 3D hydrodynamics.
We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red
supergiant and a 1.4M⊙ neutron star for different initial separations and initial
conditions. For all of our simulations, we find complete envelope ejection and
final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion,
leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent
efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may
be specific for these extended progenitors. We fully resolve the core of the star
to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D
analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive
computational cost of simulating these systems. The framework we develop in this
paper can be used to simulate a wide variety of interactions between stars, from
stellar mergers to common envelope episodes leading to GW sources.
article_number: '2011.06630'
article_processing_charge: No
author:
- first_name: Jamie A. P. Law-Smith
full_name: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith
last_name: Jamie A. P. Law-Smith
- first_name: Rosa Wallace
full_name: Everson, Rosa Wallace
last_name: Everson
- first_name: Enrico Ramirez-Ruiz
full_name: Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz
last_name: Enrico Ramirez-Ruiz
- first_name: Selma E. de
full_name: Mink, Selma E. de
last_name: Mink
- first_name: Lieke A. C. van
full_name: Son, Lieke A. C. van
last_name: Son
- 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: Stefan
full_name: Zellmann, Stefan
last_name: Zellmann
- first_name: Alejandro Vigna-Gómez
full_name: Alejandro Vigna-Gómez, Alejandro Vigna-Gómez
last_name: Alejandro Vigna-Gómez
- first_name: Mathieu
full_name: Renzo, Mathieu
last_name: Renzo
- first_name: Samantha
full_name: Wu, Samantha
last_name: Wu
- first_name: Sophie L.
full_name: Schrøder, Sophie L.
last_name: Schrøder
- first_name: Ryan J.
full_name: Foley, Ryan J.
last_name: Foley
- first_name: Tenley Hutchinson-Smith
full_name: Tenley Hutchinson-Smith, Tenley Hutchinson-Smith
last_name: Tenley Hutchinson-Smith
citation:
ama: Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al.
Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics.
arXiv. doi:10.48550/arXiv.2011.06630
apa: Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz,
E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith,
T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation
in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630
chicago: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico
Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva
Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope
Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2011.06630.
ieee: J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope
ejection and binary neutron star formation in 3D hydrodynamics,” arXiv.
.
ista: Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE
de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M,
Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope
ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630.
mla: Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope
Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv,
2011.06630, doi:10.48550/arXiv.2011.06630.
short: J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz,
S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez,
M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv
(n.d.).
date_created: 2023-08-21T10:10:41Z
date_published: 2020-11-12T00:00:00Z
date_updated: 2023-08-22T11:03:00Z
day: '12'
doi: 10.48550/arXiv.2011.06630
external_id:
arxiv:
- '2011.06630'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2011.06630
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Successful common envelope ejection and binary neutron star formation in 3D
hydrodynamics
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8699'
abstract:
- lang: eng
text: In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground
state to the details of the local lattice structure shows a large potential for
the manipulation of the functional properties by inducing local lattice distortions.
We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform
momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and
at the ligand sites to unveil the response of the low-energy elementary excitations.
We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films
displays large softening along the [h,0] direction, while along the [h,h] direction
it shows hardening. This evolution reveals a renormalization of the magnetic interactions
caused by a strain-driven cross-over from anisotropic to isotropic interactions
between the magnetic moments. Moreover, we detect dispersive electron–hole pair
excitations which shift to lower (higher) energies upon compressive (tensile)
strain, manifesting a reduction (increase) in the size of the charge gap. This
behavior shows an intimate coupling between charge excitations and lattice distortions
in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals.
Our work highlights the central role played by the lattice degrees of freedom
in determining both the pseudospin and charge excitations of Sr2IrO4 and provides
valuable information toward the control of the ground state of complex oxides
in the presence of high spin–orbit coupling.
acknowledgement: 'We gratefully acknowledge C. Sahle for experimental support at the
ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS
beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S.
thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported
by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the
NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution:
Computational Design and Discovery of Novel Materials) and the Sinergia network
Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1
and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects
2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was
supported by the Swiss National Science Foundation under Project 200021 – 182695.
This research used resources of the APS, a U.S. Department of Energy (DOE) Office
of Science User Facility operated for the DOE Office of Science by Argonne National
Laboratory under Contract DE-AC02-06CH11357.'
article_processing_charge: No
article_type: original
author:
- first_name: Eugenio
full_name: Paris, Eugenio
last_name: Paris
- first_name: Yi
full_name: Tseng, Yi
last_name: Tseng
- first_name: Ekaterina
full_name: Paerschke, Ekaterina
id: 8275014E-6063-11E9-9B7F-6338E6697425
last_name: Paerschke
orcid: 0000-0003-0853-8182
- first_name: Wenliang
full_name: Zhang, Wenliang
last_name: Zhang
- first_name: Mary H
full_name: Upton, Mary H
last_name: Upton
- first_name: Anna
full_name: Efimenko, Anna
last_name: Efimenko
- first_name: Katharina
full_name: Rolfs, Katharina
last_name: Rolfs
- first_name: Daniel E
full_name: McNally, Daniel E
last_name: McNally
- first_name: Laura
full_name: Maurel, Laura
last_name: Maurel
- first_name: Muntaser
full_name: Naamneh, Muntaser
last_name: Naamneh
- first_name: Marco
full_name: Caputo, Marco
last_name: Caputo
- first_name: Vladimir N
full_name: Strocov, Vladimir N
last_name: Strocov
- first_name: Zhiming
full_name: Wang, Zhiming
last_name: Wang
- first_name: Diego
full_name: Casa, Diego
last_name: Casa
- first_name: Christof W
full_name: Schneider, Christof W
last_name: Schneider
- first_name: Ekaterina
full_name: Pomjakushina, Ekaterina
last_name: Pomjakushina
- first_name: Krzysztof
full_name: Wohlfeld, Krzysztof
last_name: Wohlfeld
- first_name: Milan
full_name: Radovic, Milan
last_name: Radovic
- first_name: Thorsten
full_name: Schmitt, Thorsten
last_name: Schmitt
citation:
ama: Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and
spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of
Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117
apa: Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A.,
… Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions
in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117
chicago: Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton,
Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital
Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.
ieee: E. Paris et al., “Strain engineering of the charge and spin-orbital
interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 117, no. 40. National Academy of Sciences,
pp. 24764–24770, 2020.
ista: Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally
DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina
E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and
spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences
of the United States of America. 117(40), 24764–24770.
mla: Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions
in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp.
24764–70, doi:10.1073/pnas.2012043117.
short: E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs,
D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa,
C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings
of the National Academy of Sciences of the United States of America 117 (2020)
24764–24770.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-10-06T00:00:00Z
date_updated: 2023-08-22T12:11:52Z
day: '06'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2012043117
ec_funded: 1
external_id:
arxiv:
- '2009.12262'
isi:
- '000579059100029'
pmid:
- '32958669'
file:
- access_level: open_access
checksum: 1638fa36b442e2868576c6dd7d6dc505
content_type: application/pdf
creator: cziletti
date_created: 2020-10-28T11:53:12Z
date_updated: 2020-10-28T11:53:12Z
file_id: '8715'
file_name: 2020_PNAS_Paris.pdf
file_size: 1176522
relation: main_file
success: 1
file_date_updated: 2020-10-28T11:53:12Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 24764-24770
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strain engineering of the charge and spin-orbital interactions in Sr2IrO4
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: 117
year: '2020'
...
---
_id: '8737'
abstract:
- lang: eng
text: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping
by an unknown mechanism. Here, we present cryo-electron microscopy structures
of ovine complex I in five different conditions, including turnover, at resolutions
up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally
define the proton translocation pathways. Quinone binds at three positions along
the quinone cavity, as does the inhibitor rotenone that also binds within subunit
ND4. Dramatic conformational changes around the quinone cavity couple the redox
reaction to proton translocation during open-to-closed state transitions of the
enzyme. In the induced deactive state, the open conformation is arrested by the
ND6 subunit. We propose a detailed molecular coupling mechanism of complex I,
which is an unexpected combination of conformational changes and electrostatic
interactions.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
acknowledgement: We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria)
for their help with collecting cryo-EM datasets. We thank the IST Life Science and
Electron Microscopy Facilities for providing equipment. This work has been supported
by iNEXT,project number 653706, funded by the Horizon 2020 program of the European
Union. This article reflects only the authors’view,and the European Commission is
not responsible for any use that may be made of the information it contains. CIISB
research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged
for the financial support of the measurements at the CF Cryo-electron Microscopy
and Tomography CEITEC MU.This project has received funding from the European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant
Agreement no. 665385
article_number: eabc4209
article_processing_charge: No
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex
I. Science. 2020;370(6516). doi:10.1126/science.abc4209
apa: Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian
respiratory complex I. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.abc4209
chicago: Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian
Respiratory Complex I.” Science. American Association for the Advancement
of Science, 2020. https://doi.org/10.1126/science.abc4209.
ieee: D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory
complex I,” Science, vol. 370, no. 6516. American Association for the Advancement
of Science, 2020.
ista: Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory
complex I. Science. 370(6516), eabc4209.
mla: Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian
Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American
Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209.
short: D. Kampjut, L.A. Sazanov, Science 370 (2020).
date_created: 2020-11-08T23:01:23Z
date_published: 2020-10-30T00:00:00Z
date_updated: 2023-08-22T12:35:38Z
day: '30'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1126/science.abc4209
ec_funded: 1
external_id:
isi:
- '000583031800004'
pmid:
- '32972993'
file:
- access_level: open_access
checksum: 658ba90979ca9528a2efdfac8547047a
content_type: application/pdf
creator: lsazanov
date_created: 2020-11-26T18:47:58Z
date_updated: 2020-11-26T18:47:58Z
file_id: '8820'
file_name: Full_manuscript_with_SI_opt_red.pdf
file_size: 7618987
relation: main_file
success: 1
file_date_updated: 2020-11-26T18:47:58Z
has_accepted_license: '1'
intvolume: ' 370'
isi: 1
issue: '6516'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Science
publication_identifier:
eissn:
- '10959203'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The coupling mechanism of mammalian respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 370
year: '2020'
...
---
_id: '8722'
abstract:
- lang: eng
text: "Load imbalance pervasively exists in distributed deep learning training systems,
either caused by the inherent imbalance in learned tasks or by the system itself.
Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy
for a wide variety of tasks, but relies on global synchronization to accumulate
the gradients at every training step. In this paper, we propose eager-SGD, which
relaxes the global synchronization for\r\ndecentralized accumulation. To implement
eager-SGD, we propose to use two partial collectives: solo and majority. With
solo allreduce, the faster processes contribute their gradients eagerly without
waiting for the slower processes, whereas with majority allreduce, at least half
of the participants must contribute gradients before continuing, all without using
a central parameter server. We theoretically prove the convergence of the algorithms
and describe the partial collectives in detail. Experimental results on load-imbalanced
environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD
achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing
accuracy."
article_processing_charge: No
author:
- first_name: Shigang
full_name: Li, Shigang
last_name: Li
- first_name: Tal Ben-Nun
full_name: Tal Ben-Nun, Tal Ben-Nun
last_name: Tal Ben-Nun
- first_name: Salvatore Di
full_name: Girolamo, Salvatore Di
last_name: Girolamo
- 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: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
citation:
ama: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced
training workloads in deep learning with partial collective operations. In: Proceedings
of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming.
Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528'
apa: 'Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler,
T. (2020). Taming unbalanced training workloads in deep learning with partial
collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on
Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA,
United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528'
chicago: Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian
Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning
with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, 45–61. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528.
ieee: S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler,
“Taming unbalanced training workloads in deep learning with partial collective
operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, San Diego, CA, United States, 2020,
pp. 45–61.
ista: 'Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming
unbalanced training workloads in deep learning with partial collective operations.
Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel
Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming,
45–61.'
mla: Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning
with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, Association for Computing
Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.
short: S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:,
Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel
Programming, Association for Computing Machinery, 2020, pp. 45–61.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-11-05T15:25:30Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-22T12:13:48Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3332466.3374528
ec_funded: 1
external_id:
arxiv:
- '1908.04207'
isi:
- '000564476500004'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.04207
month: '02'
oa: 1
oa_version: Preprint
page: 45-61
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Taming unbalanced training workloads in deep learning with partial collective
operations
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '8744'
abstract:
- lang: eng
text: Understanding the conformational sampling of translation-arrested ribosome
nascent chain complexes is key to understand co-translational folding. Up to now,
coupling of cysteine oxidation, disulfide bond formation and structure formation
in nascent chains has remained elusive. Here, we investigate the eye-lens protein
γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical
simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic
resonance and cryo-electron microscopy, we show that thiol groups of cysteine
residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide
bonds. Thus, covalent modification chemistry occurs already prior to nascent chain
release as the ribosome exit tunnel provides sufficient space even for disulfide
bond formation which can guide protein folding.
acknowledgement: 'We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe,
Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche
Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular
Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at
BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG
graduate college: CLiC.'
article_number: '5569'
article_processing_charge: No
article_type: original
author:
- first_name: Linda
full_name: Schulte, Linda
last_name: Schulte
- first_name: Jiafei
full_name: Mao, Jiafei
last_name: Mao
- first_name: Julian
full_name: Reitz, Julian
last_name: Reitz
- first_name: Sridhar
full_name: Sreeramulu, Sridhar
last_name: Sreeramulu
- first_name: Denis
full_name: Kudlinzki, Denis
last_name: Kudlinzki
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jakob
full_name: Meier-Credo, Jakob
last_name: Meier-Credo
- first_name: Krishna
full_name: Saxena, Krishna
last_name: Saxena
- first_name: Florian
full_name: Buhr, Florian
last_name: Buhr
- first_name: Julian D.
full_name: Langer, Julian D.
last_name: Langer
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
- first_name: Clemens
full_name: Glaubitz, Clemens
last_name: Glaubitz
- first_name: Harald
full_name: Schwalbe, Harald
last_name: Schwalbe
citation:
ama: Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation
in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x
apa: Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V.,
… Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal
exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x
chicago: Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki,
Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide
Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.
ieee: L. Schulte et al., “Cysteine oxidation and disulfide formation in the
ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature,
2020.
ista: Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo
J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe
H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Nature Communications. 11, 5569.
mla: Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal
Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020,
doi:10.1038/s41467-020-19372-x.
short: L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau,
J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis,
C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).
date_created: 2020-11-09T07:49:36Z
date_published: 2020-11-04T00:00:00Z
date_updated: 2023-08-22T12:36:07Z
day: '04'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-020-19372-x
external_id:
isi:
- '000592028600001'
file:
- access_level: open_access
checksum: b2688f0347e69e6629bba582077278c5
content_type: application/pdf
creator: dernst
date_created: 2020-11-09T07:56:24Z
date_updated: 2020-11-09T07:56:24Z
file_id: '8745'
file_name: 2020_NatureComm_Schulte.pdf
file_size: 1670898
relation: main_file
success: 1
file_date_updated: 2020-11-09T07:56:24Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
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: '8747'
abstract:
- lang: eng
text: "Appropriately designed nanocomposites allow improving the thermoelectric
performance by several mechanisms, including phonon scattering, modulation doping
and energy filtering, while additionally promoting better mechanical properties
than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe
nanocomposites based on the consolidation of heterostructured nanoparticles is
described and the thermoelectric properties of the obtained materials are investigated.
We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures,
based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires.
We characterize the structural and chemical properties of the synthesized nanostructures
and of the nanocomposites\r\nproduced by hot-pressing the particles at moderate
temperatures. Besides, the transport properties of the nanocomposites are investigated
as a function of the amount of Cu introduced. Overall, the presence of Cu decreases
the material thermal conductivity through promotion of phonon scattering, modulates
the charge carrier concentration through electron spillover, and increases the
Seebeck coefficient through filtering of charge carriers at energy barriers. These
effects result in an improvement of over 50% of the thermoelectric figure of merit
of Bi2Te3."
acknowledgement: "This work was supported by the European Regional Development Funds
and by the Spanish Ministerio de Economı´a y\r\nCompetitividad through the project
SEHTOP (ENE2016-77798-C4-3-R). Y. Z. and X. H., thank the China Scholarship Council
for scholarship support. M. C. has received funding from the European Union’s Horizon
2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385. M. I. acknowledges financial support from IST Austria. Y. L. acknowledges
funding from the European Union’s Horizon 2020 Research and Innovation Programme
under the Marie Sklodowska-Curie grant agreement no. 754411. ICN2 acknowledges funding
from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project ENE2017-85087-C3.
ICN2 is supported by the Severo Ochoa program from the Spanish MINECO (grant no.
SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part
of the present work has been performed in the framework of Universitat \r\nAuto`noma
de Barcelona Materials Science PhD program."
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mariano
full_name: Calcabrini, Mariano
last_name: Calcabrini
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Xu
full_name: Han, Xu
last_name: Han
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Zhang Y, Liu Y, Calcabrini M, et al. Bismuth telluride-copper telluride nanocomposites
from heterostructured building blocks. Journal of Materials Chemistry C.
2020;8(40):14092-14099. doi:10.1039/D0TC02182B
apa: Zhang, Y., Liu, Y., Calcabrini, M., Xing, C., Han, X., Arbiol, J., … Cabot,
A. (2020). Bismuth telluride-copper telluride nanocomposites from heterostructured
building blocks. Journal of Materials Chemistry C. Royal Society of Chemistry.
https://doi.org/10.1039/D0TC02182B
chicago: Zhang, Yu, Yu Liu, Mariano Calcabrini, Congcong Xing, Xu Han, Jordi Arbiol,
Doris Cadavid, Maria Ibáñez, and Andreu Cabot. “Bismuth Telluride-Copper Telluride
Nanocomposites from Heterostructured Building Blocks.” Journal of Materials
Chemistry C. Royal Society of Chemistry, 2020. https://doi.org/10.1039/D0TC02182B.
ieee: Y. Zhang et al., “Bismuth telluride-copper telluride nanocomposites
from heterostructured building blocks,” Journal of Materials Chemistry C,
vol. 8, no. 40. Royal Society of Chemistry, pp. 14092–14099, 2020.
ista: Zhang Y, Liu Y, Calcabrini M, Xing C, Han X, Arbiol J, Cadavid D, Ibáñez M,
Cabot A. 2020. Bismuth telluride-copper telluride nanocomposites from heterostructured
building blocks. Journal of Materials Chemistry C. 8(40), 14092–14099.
mla: Zhang, Yu, et al. “Bismuth Telluride-Copper Telluride Nanocomposites from Heterostructured
Building Blocks.” Journal of Materials Chemistry C, vol. 8, no. 40, Royal
Society of Chemistry, 2020, pp. 14092–99, doi:10.1039/D0TC02182B.
short: Y. Zhang, Y. Liu, M. Calcabrini, C. Xing, X. Han, J. Arbiol, D. Cadavid,
M. Ibáñez, A. Cabot, Journal of Materials Chemistry C 8 (2020) 14092–14099.
date_created: 2020-11-09T08:37:51Z
date_published: 2020-10-28T00:00:00Z
date_updated: 2023-08-22T12:41:05Z
day: '28'
department:
- _id: MaIb
doi: 10.1039/D0TC02182B
ec_funded: 1
external_id:
isi:
- '000581559100015'
intvolume: ' 8'
isi: 1
issue: '40'
language:
- iso: eng
month: '10'
oa_version: None
page: 14092-14099
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Materials Chemistry C
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bismuth telluride-copper telluride nanocomposites from heterostructured building
blocks
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2020'
...
---
_id: '14095'
abstract:
- lang: eng
text: 'The Habitable Exoplanet Observatory, or HabEx, has been designed to be the
Great Observatory of the 2030s. For the first time in human history, technologies
have matured sufficiently to enable an affordable space-based telescope mission
capable of discovering and characterizing Earthlike planets orbiting nearby bright
sunlike stars in order to search for signs of habitability and biosignatures.
Such a mission can also be equipped with instrumentation that will enable broad
and exciting general astrophysics and planetary science not possible from current
or planned facilities. HabEx is a space telescope with unique imaging and multi-object
spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR.
These capabilities allow for a broad suite of compelling science that cuts across
the entire NASA astrophysics portfolio. HabEx has three primary science goals:
(1) Seek out nearby worlds and explore their habitability; (2) Map out nearby
planetary systems and understand the diversity of the worlds they contain; (3)
Enable new explorations of astrophysical systems from our own solar system to
external galaxies by extending our reach in the UV through near-IR. This Great
Observatory science will be selected through a competed GO program, and will account
for about 50% of the HabEx primary mission. The preferred HabEx architecture is
a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns
and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph
and a starshade, each with their own dedicated instrument.'
article_number: '2001.06683'
article_processing_charge: No
author:
- first_name: B. Scott
full_name: Gaudi, B. Scott
last_name: Gaudi
- first_name: Sara
full_name: Seager, Sara
last_name: Seager
- first_name: Bertrand
full_name: Mennesson, Bertrand
last_name: Mennesson
- first_name: Alina
full_name: Kiessling, Alina
last_name: Kiessling
- first_name: Keith
full_name: Warfield, Keith
last_name: Warfield
- first_name: Kerri
full_name: Cahoy, Kerri
last_name: Cahoy
- first_name: John T.
full_name: Clarke, John T.
last_name: Clarke
- first_name: Shawn Domagal-Goldman
full_name: Shawn Domagal-Goldman, Shawn Domagal-Goldman
last_name: Shawn Domagal-Goldman
- first_name: Lee
full_name: Feinberg, Lee
last_name: Feinberg
- first_name: Olivier
full_name: Guyon, Olivier
last_name: Guyon
- first_name: Jeremy
full_name: Kasdin, Jeremy
last_name: Kasdin
- first_name: Dimitri
full_name: Mawet, Dimitri
last_name: Mawet
- first_name: Peter
full_name: Plavchan, Peter
last_name: Plavchan
- first_name: Tyler
full_name: Robinson, Tyler
last_name: Robinson
- first_name: Leslie
full_name: Rogers, Leslie
last_name: Rogers
- first_name: Paul
full_name: Scowen, Paul
last_name: Scowen
- first_name: Rachel
full_name: Somerville, Rachel
last_name: Somerville
- first_name: Karl
full_name: Stapelfeldt, Karl
last_name: Stapelfeldt
- first_name: Christopher
full_name: Stark, Christopher
last_name: Stark
- first_name: Daniel
full_name: Stern, Daniel
last_name: Stern
- first_name: Margaret
full_name: Turnbull, Margaret
last_name: Turnbull
- first_name: Rashied
full_name: Amini, Rashied
last_name: Amini
- first_name: Gary
full_name: Kuan, Gary
last_name: Kuan
- first_name: Stefan
full_name: Martin, Stefan
last_name: Martin
- first_name: Rhonda
full_name: Morgan, Rhonda
last_name: Morgan
- first_name: David
full_name: Redding, David
last_name: Redding
- first_name: H. Philip
full_name: Stahl, H. Philip
last_name: Stahl
- first_name: Ryan
full_name: Webb, Ryan
last_name: Webb
- first_name: Oscar Alvarez-Salazar
full_name: Oscar Alvarez-Salazar, Oscar Alvarez-Salazar
last_name: Oscar Alvarez-Salazar
- first_name: William L.
full_name: Arnold, William L.
last_name: Arnold
- first_name: Manan
full_name: Arya, Manan
last_name: Arya
- first_name: Bala
full_name: Balasubramanian, Bala
last_name: Balasubramanian
- first_name: Mike
full_name: Baysinger, Mike
last_name: Baysinger
- first_name: Ray
full_name: Bell, Ray
last_name: Bell
- first_name: Chris
full_name: Below, Chris
last_name: Below
- first_name: Jonathan
full_name: Benson, Jonathan
last_name: Benson
- first_name: Lindsey
full_name: Blais, Lindsey
last_name: Blais
- first_name: Jeff
full_name: Booth, Jeff
last_name: Booth
- first_name: Robert
full_name: Bourgeois, Robert
last_name: Bourgeois
- first_name: Case
full_name: Bradford, Case
last_name: Bradford
- first_name: Alden
full_name: Brewer, Alden
last_name: Brewer
- first_name: Thomas
full_name: Brooks, Thomas
last_name: Brooks
- first_name: Eric
full_name: Cady, Eric
last_name: Cady
- first_name: Mary
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last_name: Caldwell
- first_name: Rob
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last_name: Calvet
- first_name: Steven
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last_name: Carr
- first_name: Derek
full_name: Chan, Derek
last_name: Chan
- first_name: Velibor
full_name: Cormarkovic, Velibor
last_name: Cormarkovic
- first_name: Keith
full_name: Coste, Keith
last_name: Coste
- first_name: Charlie
full_name: Cox, Charlie
last_name: Cox
- first_name: Rolf
full_name: Danner, Rolf
last_name: Danner
- first_name: Jacqueline
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last_name: Davis
- first_name: Larry
full_name: Dewell, Larry
last_name: Dewell
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last_name: Dorsett
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last_name: Dunn
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last_name: East
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last_name: Effinger
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last_name: Hull
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last_name: Kissil
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last_name: Tang
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last_name: Tseng
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last_name: Valente
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last_name: Buren
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last_name: Westerhoff
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last_name: Wofford
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full_name: Wu, Gordon
last_name: Wu
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full_name: Woo, Jahning
last_name: Woo
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full_name: Wood, Milana
last_name: Wood
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full_name: Ziemer, John
last_name: Ziemer
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full_name: Arney, Giada
last_name: Arney
- first_name: Jay
full_name: Anderson, Jay
last_name: Anderson
- first_name: Jesús Maíz-Apellániz
full_name: Jesús Maíz-Apellániz, Jesús Maíz-Apellániz
last_name: Jesús Maíz-Apellániz
- first_name: James
full_name: Bartlett, James
last_name: Bartlett
- first_name: Ruslan
full_name: Belikov, Ruslan
last_name: Belikov
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full_name: Bendek, Eduardo
last_name: Bendek
- first_name: Brad
full_name: Cenko, Brad
last_name: Cenko
- first_name: Ewan
full_name: Douglas, Ewan
last_name: Douglas
- first_name: Shannon
full_name: Dulz, Shannon
last_name: Dulz
- first_name: Chris
full_name: Evans, Chris
last_name: Evans
- first_name: Virginie
full_name: Faramaz, Virginie
last_name: Faramaz
- first_name: Y. Katherina
full_name: Feng, Y. Katherina
last_name: Feng
- first_name: Harry
full_name: Ferguson, Harry
last_name: Ferguson
- first_name: Kate
full_name: Follette, Kate
last_name: Follette
- first_name: Saavik
full_name: Ford, Saavik
last_name: Ford
- first_name: Miriam
full_name: García, Miriam
last_name: García
- first_name: Marla
full_name: Geha, Marla
last_name: Geha
- first_name: Dawn
full_name: Gelino, Dawn
last_name: Gelino
- 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: Sergi
full_name: Hildebrandt, Sergi
last_name: Hildebrandt
- first_name: Renyu
full_name: Hu, Renyu
last_name: Hu
- first_name: Knud
full_name: Jahnke, Knud
last_name: Jahnke
- first_name: Grant
full_name: Kennedy, Grant
last_name: Kennedy
- first_name: Laura
full_name: Kreidberg, Laura
last_name: Kreidberg
- first_name: Andrea
full_name: Isella, Andrea
last_name: Isella
- first_name: Eric
full_name: Lopez, Eric
last_name: Lopez
- first_name: Franck
full_name: Marchis, Franck
last_name: Marchis
- first_name: Lucas
full_name: Macri, Lucas
last_name: Macri
- first_name: Mark
full_name: Marley, Mark
last_name: Marley
- first_name: William
full_name: Matzko, William
last_name: Matzko
- first_name: Johan
full_name: Mazoyer, Johan
last_name: Mazoyer
- first_name: Stephan
full_name: McCandliss, Stephan
last_name: McCandliss
- first_name: Tiffany
full_name: Meshkat, Tiffany
last_name: Meshkat
- first_name: Christoph
full_name: Mordasini, Christoph
last_name: Mordasini
- first_name: Patrick
full_name: Morris, Patrick
last_name: Morris
- first_name: Eric
full_name: Nielsen, Eric
last_name: Nielsen
- first_name: Patrick
full_name: Newman, Patrick
last_name: Newman
- first_name: Erik
full_name: Petigura, Erik
last_name: Petigura
- first_name: Marc
full_name: Postman, Marc
last_name: Postman
- first_name: Amy
full_name: Reines, Amy
last_name: Reines
- first_name: Aki
full_name: Roberge, Aki
last_name: Roberge
- first_name: Ian
full_name: Roederer, Ian
last_name: Roederer
- first_name: Garreth
full_name: Ruane, Garreth
last_name: Ruane
- first_name: Edouard
full_name: Schwieterman, Edouard
last_name: Schwieterman
- first_name: Dan
full_name: Sirbu, Dan
last_name: Sirbu
- first_name: Christopher
full_name: Spalding, Christopher
last_name: Spalding
- first_name: Harry
full_name: Teplitz, Harry
last_name: Teplitz
- first_name: Jason
full_name: Tumlinson, Jason
last_name: Tumlinson
- first_name: Neal
full_name: Turner, Neal
last_name: Turner
- first_name: Jessica
full_name: Werk, Jessica
last_name: Werk
- first_name: Aida
full_name: Wofford, Aida
last_name: Wofford
- first_name: Mark
full_name: Wyatt, Mark
last_name: Wyatt
- first_name: Amber
full_name: Young, Amber
last_name: Young
- first_name: Rob
full_name: Zellem, Rob
last_name: Zellem
citation:
ama: Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory
(HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683
apa: Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy,
K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept
study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683
chicago: Gaudi, B. Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith
Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory
(HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683.
ieee: B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission
concept study final report,” arXiv. .
ista: Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept
study final report. arXiv, 2001.06683.
mla: Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission
Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683.
short: B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy,
J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin,
D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt,
C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding,
H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian,
M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois,
C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D.
Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett,
D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene,
J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R.
Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist,
M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading,
J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad,
J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi,
M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf,
K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith,
B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras,
J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick,
D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney,
J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek,
B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K.
Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt,
R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L.
Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini,
P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge,
I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J.
Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv
(n.d.).
date_created: 2023-08-21T10:10:21Z
date_published: 2020-01-18T00:00:00Z
date_updated: 2023-08-22T13:13:18Z
day: '18'
doi: 10.48550/arXiv.2001.06683
extern: '1'
external_id:
arxiv:
- '2001.06683'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2001.06683'
month: '01'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: The habitable exoplanet observatory (HabEx) mission concept study final report
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8767'
abstract:
- lang: eng
text: Resources are rarely distributed uniformly within a population. Heterogeneity
in the concentration of a drug, the quality of breeding sites, or wealth can all
affect evolutionary dynamics. In this study, we represent a collection of properties
affecting the fitness at a given location using a color. A green node is rich
in resources while a red node is poorer. More colors can represent a broader spectrum
of resource qualities. For a population evolving according to the birth-death
Moran model, the first question we address is which structures, identified by
graph connectivity and graph coloring, are evolutionarily equivalent. We prove
that all properly two-colored, undirected, regular graphs are evolutionarily equivalent
(where “properly colored” means that no two neighbors have the same color). We
then compare the effects of background heterogeneity on properly two-colored graphs
to those with alternative schemes in which the colors are permuted. Finally, we
discuss dynamic coloring as a model for spatiotemporal resource fluctuations,
and we illustrate that random dynamic colorings often diminish the effects of
background heterogeneity relative to a proper two-coloring.
acknowledgement: 'We thank Igor Erovenko for many helpful comments on an earlier version
of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the
Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation
(A.M.). The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript.'
article_number: e1008402
article_processing_charge: No
article_type: original
author:
- first_name: Kamran
full_name: Kaveh, Kamran
last_name: Kaveh
- first_name: Alex
full_name: McAvoy, Alex
last_name: McAvoy
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic
graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402
apa: Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran
process on 2-chromatic graphs. PLOS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1008402
chicago: Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak.
“The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology.
Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402.
ieee: K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on
2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public
Library of Science, 2020.
ista: Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic
graphs. PLOS Computational Biology. 16(11), e1008402.
mla: Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational
Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.
short: K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology
16 (2020).
date_created: 2020-11-18T07:20:23Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2023-08-22T12:49:18Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1008402
external_id:
isi:
- '000591317200004'
file:
- access_level: open_access
checksum: 555456dd0e47bcf9e0994bcb95577e88
content_type: application/pdf
creator: dernst
date_created: 2020-11-18T07:26:10Z
date_updated: 2020-11-18T07:26:10Z
file_id: '8768'
file_name: 2020_PlosCompBio_Kaveh.pdf
file_size: 2498594
relation: main_file
success: 1
file_date_updated: 2020-11-18T07:26:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '11'
keyword:
- Ecology
- Modelling and Simulation
- Computational Theory and Mathematics
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
- Molecular Biology
- Cellular and Molecular Neuroscience
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: PLOS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Moran process on 2-chromatic graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2020'
...
---
_id: '8750'
abstract:
- lang: eng
text: "Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor
hybrid systems reachability is a challenging task. In this paper we present\r\nan
approach based on conservative set-based enclosure of the dynamics that can\r\nhandle
systems with uncertain parameters and inputs, where the uncertainties\r\nare bound
to given intervals. The method is evaluated on the plant model of an\r\nexperimental
electro-mechanical braking system with periodic controller. In\r\nthis model,
the fast-switching controller dynamics requires simulation time\r\nscales of the
order of nanoseconds. Accurate set-based computations for\r\nrelatively large
time horizons are known to be expensive. However, by\r\nappropriately decoupling
the time variable with respect to the spatial\r\nvariables, and enclosing the
uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show
that the computation time can be lowered to 5000\r\ntimes faster with respect
to previous works. This is a step forward in formal\r\nverification of hybrid
systems because reduced run-times allow engineers to\r\nintroduce more expressiveness
in their models with a relatively inexpensive\r\ncomputational cost."
article_number: '9314994'
article_processing_charge: No
author:
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Daniel
full_name: Freire, Daniel
last_name: Freire
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric
linear hybrid systems with time-triggered transitions. In: 18th ACM-IEEE International
Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994'
apa: 'Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability
analysis of parametric linear hybrid systems with time-triggered transitions.
In 18th ACM-IEEE International Conference on Formal Methods and Models for
System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994'
chicago: Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability
Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.”
In 18th ACM-IEEE International Conference on Formal Methods and Models for
System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994.
ieee: M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of
parametric linear hybrid systems with time-triggered transitions,” in 18th
ACM-IEEE International Conference on Formal Methods and Models for System Design,
Virtual Conference, 2020.
ista: 'Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of
parametric linear hybrid systems with time-triggered transitions. 18th ACM-IEEE
International Conference on Formal Methods and Models for System Design. MEMOCODE:
Conference on Formal Methods and Models for System Design, 9314994.'
mla: Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear
Hybrid Systems with Time-Triggered Transitions.” 18th ACM-IEEE International
Conference on Formal Methods and Models for System Design, 9314994, IEEE,
2020, doi:10.1109/MEMOCODE51338.2020.9314994.
short: M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference
on Formal Methods and Models for System Design, IEEE, 2020.
conference:
end_date: 2020-12-04
location: Virtual Conference
name: 'MEMOCODE: Conference on Formal Methods and Models for System Design'
start_date: 2020-12-02
date_created: 2020-11-10T07:04:57Z
date_published: 2020-12-04T00:00:00Z
date_updated: 2023-08-22T12:48:18Z
day: '04'
department:
- _id: ToHe
doi: 10.1109/MEMOCODE51338.2020.9314994
ec_funded: 1
external_id:
arxiv:
- '2006.12325'
isi:
- '000661920400013'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.12325
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 18th ACM-IEEE International Conference on Formal Methods and Models for
System Design
publication_identifier:
isbn:
- '9781728191485'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient reachability analysis of parametric linear hybrid systems with time-triggered
transitions
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...