---
_id: '10736'
abstract:
- lang: eng
text: Predicting function from sequence is a central problem of biology. Currently,
this is possible only locally in a narrow mutational neighborhood around a wildtype
sequence rather than globally from any sequence. Using random mutant libraries,
we developed a biophysical model that accounts for multiple features of σ70 binding
bacterial promoters to predict constitutive gene expression levels from any sequence.
We experimentally and theoretically estimated that 10–20% of random sequences
lead to expression and ~80% of non-expressing sequences are one mutation away
from a functional promoter. The potential for generating expression from random
sequences is so pervasive that selection acts against σ70-RNA polymerase binding
sites even within inter-genic, promoter-containing regions. This pervasiveness
of σ70-binding sites implies that emergence of promoters is not the limiting step
in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter
function into a mechanistic model enabled not only more accurate predictions of
gene expression levels, but also identified that promoters evolve more rapidly
than previously thought.
acknowledgement: 'We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao,
Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on
the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML;
IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme
7 (2007–2013, grant agreement number 648440) to JPB.'
article_number: e64543
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
- first_name: David
full_name: Toledo-Aparicio, David
last_name: Toledo-Aparicio
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function
and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
apa: Lagator, M., Sarikas, S., Steinrück, M., Toledo-Aparicio, D., Bollback, J.
P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function
and evolution from random sequences. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.64543
chicago: Lagator, Mato, Srdjan Sarikas, Magdalena Steinrück, David Toledo-Aparicio,
Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter
Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications,
2022. https://doi.org/10.7554/eLife.64543.
ieee: M. Lagator et al., “Predicting bacterial promoter function and evolution
from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Lagator M, Sarikas S, Steinrück M, Toledo-Aparicio D, Bollback JP, Guet CC,
Tkačik G. 2022. Predicting bacterial promoter function and evolution from random
sequences. eLife. 11, e64543.
mla: Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution
from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications,
2022, doi:10.7554/eLife.64543.
short: M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
corr_author: '1'
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2025-03-31T16:00:23Z
day: '26'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
- _id: NiBa
doi: 10.7554/eLife.64543
ec_funded: 1
external_id:
isi:
- '000751104400001'
pmid:
- '35080492'
file:
- access_level: open_access
checksum: decdcdf600ff51e9a9703b49ca114170
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T07:14:09Z
date_updated: 2022-02-07T07:14:09Z
file_id: '10739'
file_name: 2022_ELife_Lagator.pdf
file_size: 5604343
relation: main_file
success: 1
file_date_updated: 2022-02-07T07:14:09Z
fulldoi: https://doi.org/10.7554/eLife.64543
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting bacterial promoter function and evolution from random sequences
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2022'
...
---
_id: '10737'
abstract:
- lang: eng
text: We consider two models for the sequence labeling (tagging) problem. The first
one is a Pattern-Based Conditional Random Field (PB), in which the energy of a
string (chain labeling) x=x1…xn∈Dn is a sum of terms over intervals [i,j] where
each term is non-zero only if the substring xi…xj equals a prespecified word
w∈Λ. The second model is a Weighted Context-Free Grammar (WCFG) frequently used
for natural language processing. PB and WCFG encode local and non-local interactions
respectively, and thus can be viewed as complementary. We propose a Grammatical
Pattern-Based CRF model (GPB) that combines the two in a natural way. We argue
that it has certain advantages over existing approaches such as the Hybrid model
of Benedí and Sanchez that combines N-grams and WCFGs. The focus of this paper
is to analyze the complexity of inference tasks in a GPB such as computing MAP.
We present a polynomial-time algorithm for general GPBs and a faster version for
a special case that we call Interaction Grammars.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rustem
full_name: Takhanov, Rustem
id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87
last_name: Takhanov
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free
grammars. Intelligent Data Analysis. 2022;26(1):257-272. doi:10.3233/IDA-205623
apa: Takhanov, R., & Kolmogorov, V. (2022). Combining pattern-based CRFs and
weighted context-free grammars. Intelligent Data Analysis. IOS Press. https://doi.org/10.3233/IDA-205623
chicago: Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs
and Weighted Context-Free Grammars.” Intelligent Data Analysis. IOS Press,
2022. https://doi.org/10.3233/IDA-205623.
ieee: R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted
context-free grammars,” Intelligent Data Analysis, vol. 26, no. 1. IOS
Press, pp. 257–272, 2022.
ista: Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted
context-free grammars. Intelligent Data Analysis. 26(1), 257–272.
mla: Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and
Weighted Context-Free Grammars.” Intelligent Data Analysis, vol. 26, no.
1, IOS Press, 2022, pp. 257–72, doi:10.3233/IDA-205623.
short: R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.
corr_author: '1'
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-14T00:00:00Z
date_updated: 2024-10-09T21:01:33Z
day: '14'
department:
- _id: VlKo
doi: 10.3233/IDA-205623
external_id:
arxiv:
- '1404.5475'
isi:
- '000749997700015'
fulldoi: https://doi.org/10.3233/IDA-205623
intvolume: ' 26'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1404.5475
month: '01'
oa: 1
oa_version: Preprint
page: 257-272
publication: Intelligent Data Analysis
publication_identifier:
eissn:
- 1571-4128
issn:
- 1088-467X
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining pattern-based CRFs and weighted context-free grammars
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2022'
...
---
_id: '10752'
abstract:
- lang: eng
text: 'The digitalization of almost all aspects of our everyday lives has led to
unprecedented amounts of data being freely available on the Internet. In particular
social media platforms provide rich sources of user-generated data, though typically
in unstructured form, and with high diversity, such as written in many different
languages. Automatically identifying meaningful information in such big data resources
and extracting it efficiently is one of the ongoing challenges of our time. A
common step for this is sentiment analysis, which forms the foundation for tasks
such as opinion mining or trend prediction. Unfortunately, publicly available
tools for this task are almost exclusively available for English-language texts.
Consequently, a large fraction of the Internet users, who do not communicate in
English, are ignored in automatized studies, a phenomenon called rare-language
discrimination.In this work we propose a technique to overcome this problem by
a truly multi-lingual model, which can be trained automatically without linguistic
knowledge or even the ability to read the many target languages. The main step
is to combine self-annotation, specifically the use of emoticons as a proxy for
labels, with multi-lingual sentence representations.To evaluate our method we
curated several large datasets from data obtained via the free Twitter streaming
API. The results show that our proposed multi-lingual training is able to achieve
sentiment predictions at the same quality level for rare languages as for frequent
ones, and in particular clearly better than what mono-lingual training achieves
on the same data. '
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This research was funded in parts by the FORTE program of the Austrian
Research Promotion Agency (FFG) and the Federal Ministry of Agriculture, Regions
and Tourism (BMLRT) as part of the AMMONIS project (grant no. 879705). The research
was also supported by the Scientific Service Units (SSU) of IST Austria through
resources provided by Scientific Computing (SciComp).
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Lampert, Jasmin
last_name: Lampert
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0002-4561-241X
citation:
ama: 'Lampert J, Lampert C. Overcoming rare-language discrimination in multi-lingual
sentiment analysis. In: 2021 IEEE International Conference on Big Data.
IEEE; 2022:5185-5192. doi:10.1109/bigdata52589.2021.9672003'
apa: 'Lampert, J., & Lampert, C. (2022). Overcoming rare-language discrimination
in multi-lingual sentiment analysis. In 2021 IEEE International Conference
on Big Data (pp. 5185–5192). Orlando, FL, United States: IEEE. https://doi.org/10.1109/bigdata52589.2021.9672003'
chicago: Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination
in Multi-Lingual Sentiment Analysis.” In 2021 IEEE International Conference
on Big Data, 5185–92. IEEE, 2022. https://doi.org/10.1109/bigdata52589.2021.9672003.
ieee: J. Lampert and C. Lampert, “Overcoming rare-language discrimination in multi-lingual
sentiment analysis,” in 2021 IEEE International Conference on Big Data,
Orlando, FL, United States, 2022, pp. 5185–5192.
ista: 'Lampert J, Lampert C. 2022. Overcoming rare-language discrimination in multi-lingual
sentiment analysis. 2021 IEEE International Conference on Big Data. Big Data:
International Conference on Big Data, 5185–5192.'
mla: Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination
in Multi-Lingual Sentiment Analysis.” 2021 IEEE International Conference on
Big Data, IEEE, 2022, pp. 5185–92, doi:10.1109/bigdata52589.2021.9672003.
short: J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data,
IEEE, 2022, pp. 5185–5192.
conference:
end_date: 2021-12-18
location: Orlando, FL, United States
name: 'Big Data: International Conference on Big Data'
start_date: 2021-12-15
corr_author: '1'
date_created: 2022-02-10T14:08:23Z
date_published: 2022-01-13T00:00:00Z
date_updated: 2024-10-21T06:01:53Z
day: '13'
department:
- _id: ChLa
doi: 10.1109/bigdata52589.2021.9672003
external_id:
isi:
- '000800559505036'
fulldoi: https://doi.org/10.1109/bigdata52589.2021.9672003
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 5185-5192
publication: 2021 IEEE International Conference on Big Data
publication_identifier:
isbn:
- '9781665439022'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming rare-language discrimination in multi-lingual sentiment analysis
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2022'
...
---
_id: '10753'
abstract:
- lang: eng
text: This is a comment on "Meta-learning synaptic plasticity and memory addressing
for continual familiarity detection." Neuron. 2022 Feb 2;110(3):544-557.e8.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- 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: 'Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron.
2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014'
apa: 'Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines
that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014'
chicago: 'Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines
That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.'
ieee: 'B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace
us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.'
ista: 'Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace
us? Neuron. 110(3), 361–362.'
mla: 'Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That
Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014.'
short: B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.
corr_author: '1'
date_created: 2022-02-13T23:01:34Z
date_published: 2022-02-02T00:00:00Z
date_updated: 2026-06-18T08:47:45Z
day: '02'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.neuron.2022.01.014
external_id:
isi:
- '000751819100005'
pmid:
- '35114107'
fulldoi: https://doi.org/10.1016/j.neuron.2022.01.014
intvolume: ' 110'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2022.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 361-362
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A familiar thought: Machines that replace us?'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2022'
...
---
_id: '10754'
abstract:
- lang: eng
text: Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy
approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers,
such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine
kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted
therapy for patients with EGFR mutation-positive cancers. While preclinical studies
and clinical trials have shown that afatinib has benefits for esophageal cancer
patients, it is not known whether a combination of afatinib and RP4010 could achieve
better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through
EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect
of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human
esophageal squamous cell carcinoma cell line, using both experimental and mathematical
simulations. Our mathematical simulation of Ca2+ oscillations could fit well with
experimental data responding to afatinib or RP4010, both separately or in combination.
Guided by simulation, we were able to identify a proper ratio of afatinib and
RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect
evidence by experimental measurement of intracellular Ca2+ and cell proliferation.
This intracellular Ca2+ dynamic-based mathematical simulation approach could be
useful for a rapid and cost-effective evaluation of combined targeting therapy
drugs.
acknowledgement: "This work was partially supported by grants from National Institutes
of Health (NIH) (R01 CA185055, S10OD0252300) and The University of Texas System
STARs Award (to Z.P.),\r\nThe University of Texas at Arlington Interdisciplinary
Research Program (to B.C., H.V.K. and Z.P.). "
article_number: '1763'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yan
full_name: Chang, Yan
last_name: Chang
- first_name: Marah
full_name: Funk, Marah
last_name: Funk
- first_name: Souvik
full_name: Roy, Souvik
last_name: Roy
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Sangyong
full_name: Choi, Sangyong
last_name: Choi
- first_name: Hristo V.
full_name: Kojouharov, Hristo V.
last_name: Kojouharov
- first_name: Benito
full_name: Chen, Benito
last_name: Chen
- first_name: Zui
full_name: Pan, Zui
last_name: Pan
citation:
ama: Chang Y, Funk M, Roy S, et al. Developing a mathematical model of intracellular
Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010
in esophageal cancer. International Journal of Molecular Sciences. 2022;23(3).
doi:10.3390/ijms23031763
apa: Chang, Y., Funk, M., Roy, S., Stephenson, E. R., Choi, S., Kojouharov, H. V.,
… Pan, Z. (2022). Developing a mathematical model of intracellular Calcium dynamics
for evaluating combined anticancer effects of afatinib and RP4010 in esophageal
cancer. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23031763
chicago: Chang, Yan, Marah Funk, Souvik Roy, Elizabeth R Stephenson, Sangyong Choi,
Hristo V. Kojouharov, Benito Chen, and Zui Pan. “Developing a Mathematical Model
of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of
Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular
Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23031763.
ieee: Y. Chang et al., “Developing a mathematical model of intracellular
Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010
in esophageal cancer,” International Journal of Molecular Sciences, vol.
23, no. 3. MDPI, 2022.
ista: Chang Y, Funk M, Roy S, Stephenson ER, Choi S, Kojouharov HV, Chen B, Pan
Z. 2022. Developing a mathematical model of intracellular Calcium dynamics for
evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer.
International Journal of Molecular Sciences. 23(3), 1763.
mla: Chang, Yan, et al. “Developing a Mathematical Model of Intracellular Calcium
Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in
Esophageal Cancer.” International Journal of Molecular Sciences, vol. 23,
no. 3, 1763, MDPI, 2022, doi:10.3390/ijms23031763.
short: Y. Chang, M. Funk, S. Roy, E.R. Stephenson, S. Choi, H.V. Kojouharov, B.
Chen, Z. Pan, International Journal of Molecular Sciences 23 (2022).
date_created: 2022-02-13T23:01:35Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2025-06-11T13:46:46Z
day: '01'
ddc:
- '510'
- '576'
department:
- _id: HeEd
doi: 10.3390/ijms23031763
external_id:
isi:
- '000754773500001'
pmid:
- '35163685'
file:
- access_level: open_access
checksum: 8890ad20c54e90dc58ad5ea97c902998
content_type: application/pdf
creator: dernst
date_created: 2022-02-14T07:46:30Z
date_updated: 2022-02-14T07:46:30Z
file_id: '10756'
file_name: 2022_IJMS_Chang.pdf
file_size: 24416183
relation: main_file
success: 1
file_date_updated: 2022-02-14T07:46:30Z
fulldoi: https://doi.org/10.3390/ijms23031763
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developing a mathematical model of intracellular Calcium dynamics for evaluating
combined anticancer effects of afatinib and RP4010 in esophageal cancer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '10755'
abstract:
- lang: eng
text: We provide a definition of the effective mass for the classical polaron described
by the Landau–Pekar (LP) equations. It is based on a novel variational principle,
minimizing the energy functional over states with given (initial) velocity. The
resulting formula for the polaron's effective mass agrees with the prediction
by LP (1948 J. Exp. Theor. Phys. 18 419–423).
acknowledgement: "We thank Herbert Spohn for helpful comments. Funding from the European
Union’s Horizon\r\n2020 research and innovation programme under the ERC Grant Agreement
No. 694227\r\n(DF and RS) and under the Marie Skłodowska-Curie Grant Agreement No.
754411 (SR) is\r\ngratefully acknowledged."
article_number: '015201'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for
the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical.
2022;55(1). doi:10.1088/1751-8121/ac3947'
apa: 'Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (2022). The effective
mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/ac3947'
chicago: 'Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer.
“The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics
A: Mathematical and Theoretical. IOP Publishing, 2022. https://doi.org/10.1088/1751-8121/ac3947.'
ieee: 'D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass
problem for the Landau-Pekar equations,” Journal of Physics A: Mathematical
and Theoretical, vol. 55, no. 1. IOP Publishing, 2022.'
ista: 'Feliciangeli D, Rademacher SAE, Seiringer R. 2022. The effective mass problem
for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical.
55(1), 015201.'
mla: 'Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar
Equations.” Journal of Physics A: Mathematical and Theoretical, vol. 55,
no. 1, 015201, IOP Publishing, 2022, doi:10.1088/1751-8121/ac3947.'
short: 'D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Journal of Physics A:
Mathematical and Theoretical 55 (2022).'
corr_author: '1'
date_created: 2022-02-13T23:01:35Z
date_published: 2022-01-19T00:00:00Z
date_updated: 2025-04-15T06:54:54Z
day: '19'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1088/1751-8121/ac3947
ec_funded: 1
external_id:
arxiv:
- '2107.03720'
file:
- access_level: open_access
checksum: 0875e562705563053d6dd98fba4d8578
content_type: application/pdf
creator: dernst
date_created: 2022-02-14T08:20:19Z
date_updated: 2022-02-14T08:20:19Z
file_id: '10757'
file_name: 2022_JournalPhysicsA_Feliciangeli.pdf
file_size: 1132380
relation: main_file
success: 1
file_date_updated: 2022-02-14T08:20:19Z
fulldoi: https://doi.org/10.1088/1751-8121/ac3947
has_accepted_license: '1'
intvolume: ' 55'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_identifier:
eissn:
- 1751-8121
issn:
- 1751-8113
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '9791'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The effective mass problem for the Landau-Pekar equations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2022'
...
---
_id: '10758'
abstract:
- lang: eng
text: 5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic
acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed
to play essential regulatory roles in transcription, maintenance and base-excision
processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy
to address the effects of 5caC incorporation into canonical DNA strands at multiple
pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent
global destabilizing and a base-pair mobility enhancing local impact on dsDNA,
albeit without any detectable influence on the ground-state B-DNA structure. Measurement
of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted
how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure
by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation
of 5caC results in a lower activation energy for the dissociation process and
a higher barrier for annealing. Studies on conformational exchange on the microsecond
time scale regime revealed a sharply localized base-pair motion involving exclusively
the modified site and its immediate surroundings. By direct comparison with canonical
and 5-formylcytosine (5fC)-edited strands, we were able to address the impact
of the two most oxidized naturally occurring cytosine derivatives in the genome.
These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing
questions of its capacity as a substrate in base excision repair processes and
its purpose as an independent, stable epigenetic mark.
acknowledgement: "We thank Markus Müller for valued discussions and Felix Xu for assistance
in the measurement of UV/vis melting profiles. This work was supported in part by
the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075,
EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for
NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie.
Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Romeo C. A.
full_name: Dubini, Romeo C. A.
last_name: Dubini
- first_name: Eva
full_name: Korytiaková, Eva
last_name: Korytiaková
- first_name: Thea
full_name: Schinkel, Thea
last_name: Schinkel
- first_name: Pia
full_name: Heinrichs, Pia
last_name: Heinrichs
- first_name: Thomas
full_name: Carell, Thomas
last_name: Carell
- first_name: Petra
full_name: Rovo, Petra
id: c316e53f-b965-11eb-b128-bb26acc59c00
last_name: Rovo
orcid: 0000-0001-8729-7326
citation:
ama: Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR
chemical exchange techniques reveal local and global effects of oxidized cytosine
derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050
apa: Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T.,
& Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global
effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American
Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050
chicago: Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas
Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and
Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au.
American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.
ieee: R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and
P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects
of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no.
3. American Chemical Society, pp. 237–246, 2022.
ista: Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022.
1H NMR chemical exchange techniques reveal local and global effects of oxidized
cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.
mla: Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local
and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry
Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050.
short: R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo,
ACS Physical Chemistry Au 2 (2022) 237–246.
corr_author: '1'
date_created: 2022-02-16T11:18:21Z
date_published: 2022-02-11T00:00:00Z
date_updated: 2025-04-15T06:53:09Z
day: '11'
ddc:
- '540'
department:
- _id: NMR
doi: 10.1021/acsphyschemau.1c00050
external_id:
pmid:
- '35637781'
file:
- access_level: open_access
checksum: 5ce3f907848f5c7caf77f1adfe5826c6
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T07:53:20Z
date_updated: 2022-07-29T07:53:20Z
file_id: '11692'
file_name: 2022_ACSPhysChemAU_Dubini.pdf
file_size: 2351220
relation: main_file
success: 1
file_date_updated: 2022-07-29T07:53:20Z
fulldoi: https://doi.org/10.1021/acsphyschemau.1c00050
has_accepted_license: '1'
intvolume: ' 2'
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 237-246
pmid: 1
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: ACS Physical Chemistry Au
publication_identifier:
eissn:
- 2694-2445
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2021.12.14.472563
scopus_import: '1'
status: public
title: 1H NMR chemical exchange techniques reveal local and global effects of oxidized
cytosine derivatives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2022'
...
---
OA_place: publisher
_id: '10759'
abstract:
- lang: eng
text: In this Thesis, I study composite quantum impurities with variational techniques,
both inspired by machine learning as well as fully analytic. I supplement this
with exploration of other applications of machine learning, in particular artificial
neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle
systems with variational approach. I derive a Hamiltonian describing the angulon
quasiparticle in the presence of a magnetic field. I apply analytic variational
treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive
systems, based on artificial neural networks. I exemplify this approach on the
example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue
using artificial neural networks, albeit in a different setting. I apply artificial
neural networks to detect phases from snapshots of two types physical systems.
Namely, I study Monte Carlo snapshots of multilayer classical spin models as well
as molecular dynamics maps of colloidal systems. The main type of networks that
I use here are convolutional neural networks, known for their applicability to
image data.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
citation:
ama: Rzadkowski W. Analytic and machine learning approaches to composite quantum
impurities. 2022. doi:10.15479/at:ista:10759
apa: Rzadkowski, W. (2022). Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759
chicago: Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite
Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.
ieee: W. Rzadkowski, “Analytic and machine learning approaches to composite quantum
impurities,” Institute of Science and Technology Austria, 2022.
ista: Rzadkowski W. 2022. Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria.
mla: Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite
Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.
short: W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum
Impurities, Institute of Science and Technology Austria, 2022.
corr_author: '1'
date_created: 2022-02-16T13:27:37Z
date_published: 2022-02-21T00:00:00Z
date_updated: 2026-06-18T19:29:09Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiLe
doi: 10.15479/at:ista:10759
ec_funded: 1
file:
- access_level: closed
checksum: 0fc54ad1eaede879c665ac9b53c93e22
content_type: application/zip
creator: wrzadkow
date_created: 2022-02-21T13:58:16Z
date_updated: 2022-02-22T07:20:12Z
file_id: '10785'
file_name: Rzadkowski_thesis_final_source.zip
file_size: 17668233
relation: source_file
- access_level: open_access
checksum: 22d2d7af37ca31f6b1730c26cac7bced
content_type: application/pdf
creator: wrzadkow
date_created: 2022-02-21T14:02:54Z
date_updated: 2022-02-21T14:02:54Z
file_id: '10786'
file_name: Rzadkowski_thesis_final.pdf
file_size: 13307331
relation: main_file
success: 1
file_date_updated: 2022-02-22T07:20:12Z
fulldoi: https://doi.org/10.15479/at:ista:10759
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '120'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10762'
relation: part_of_dissertation
status: public
- id: '415'
relation: part_of_dissertation
status: public
- id: '8644'
relation: part_of_dissertation
status: public
- id: '7956'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Analytic and machine learning approaches to composite quantum impurities
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '10763'
abstract:
- lang: eng
text: "AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission
at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding
domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating
kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane
AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms.
Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in
both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement
of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes
specific gating states. We further show how TARPs alter\r\nchannel rectification,
by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal
that the Q/R-editing site couples the channel constriction at the filter entrance
to the\r\ngate, and forms the major cation binding site in the conduction path.
Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating
and conductance."
acknowledgement: "We thank Ondrej Cais for critical reading of the manuscript. We
are grateful to LMB\r\nscientific computing and the EM facility for support, Paul
Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments
with Relion 3.1. This work was\r\nsupported by grants from the Medical Research
Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the
MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00
and RYC2018-025720-I)."
article_number: '734'
article_processing_charge: No
article_type: original
author:
- first_name: Beatriz
full_name: Herguedas, Beatriz
last_name: Herguedas
- first_name: Bianka K.
full_name: Kohegyi, Bianka K.
last_name: Kohegyi
- first_name: Jan Niklas
full_name: Dohrke, Jan Niklas
last_name: Dohrke
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Hinze
full_name: Ho, Hinze
last_name: Ho
- first_name: Saher A.
full_name: Shaikh, Saher A.
last_name: Shaikh
- first_name: Remigijus
full_name: Lape, Remigijus
last_name: Lape
- first_name: James M.
full_name: Krieger, James M.
last_name: Krieger
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation
of the GluA1/2-γ8 AMPA receptor. Nature Communications. 2022;13. doi:10.1038/s41467-022-28404-7
apa: Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H.,
… Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8
AMPA receptor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28404-7
chicago: Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson,
Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and
Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA
Receptor.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28404-7.
ieee: B. Herguedas et al., “Mechanisms underlying TARP modulation of the
GluA1/2-γ8 AMPA receptor,” Nature Communications, vol. 13. Springer Nature,
2022.
ista: Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape
R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8
AMPA receptor. Nature Communications. 13, 734.
mla: Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8
AMPA Receptor.” Nature Communications, vol. 13, 734, Springer Nature, 2022,
doi:10.1038/s41467-022-28404-7.
short: B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A.
Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).
date_created: 2022-02-20T23:01:30Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:14:43Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-022-28404-7
external_id:
isi:
- '000757297200008'
pmid:
- '35136046'
file:
- access_level: open_access
checksum: d86ee8eabe8b794730729ffbb1a8832e
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T07:59:32Z
date_updated: 2022-02-21T07:59:32Z
file_id: '10778'
file_name: 2022_NatureCommunications_Herguedas.pdf
file_size: 2625540
relation: main_file
success: 1
file_date_updated: 2022-02-21T07:59:32Z
fulldoi: https://doi.org/10.1038/s41467-022-28404-7
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 13
year: '2022'
...
---
_id: '10764'
abstract:
- lang: eng
text: Presynaptic glutamate replenishment is fundamental to brain function. In high
activity regimes, such as epileptic episodes, this process is thought to rely
on the glutamate-glutamine cycle between neurons and astrocytes. However the presence
of an astroglial glutamine supply, as well as its functional relevance in vivo
in the healthy brain remain controversial, partly due to a lack of tools that
can directly examine glutamine transfer. Here, we generated a fluorescent probe
that tracks glutamine in live cells, which provides direct visual evidence of
an activity-dependent glutamine supply from astroglial networks to presynaptic
structures under physiological conditions. This mobilization is mediated by connexin43,
an astroglial protein with both gap-junction and hemichannel functions, and is
essential for synaptic transmission and object recognition memory. Our findings
uncover an indispensable recruitment of astroglial glutamine in physiological
synaptic activity and memory via an unconventional pathway, thus providing an
astrocyte basis for cognitive processes.
acknowledgement: 'We thank D. Mazaud and. J. Cazères for technical assistance. This
work was supported by grants from the European Research Council (Consolidator grant
#683154) and European Union’s Horizon 2020 research and innovation program (Marie
Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R.
and from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development
(grant #622289) to G.C.'
article_number: '753'
article_processing_charge: No
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Danijela
full_name: Bataveljic, Danijela
last_name: Bataveljic
- first_name: Josien
full_name: Visser, Josien
last_name: Visser
- first_name: Naresh
full_name: Kumar, Naresh
last_name: Kumar
- first_name: Julien
full_name: Moulard, Julien
last_name: Moulard
- first_name: Glenn
full_name: Dallérac, Glenn
last_name: Dallérac
- first_name: Daria
full_name: Mozheiko, Daria
last_name: Mozheiko
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
- first_name: Pascal
full_name: Ezan, Pascal
last_name: Ezan
- first_name: Cédric
full_name: Mongin, Cédric
last_name: Mongin
- first_name: Oana
full_name: Chever, Oana
last_name: Chever
- first_name: Alexis Pierre
full_name: Bemelmans, Alexis Pierre
last_name: Bemelmans
- first_name: Joachim
full_name: Lübke, Joachim
last_name: Lübke
- first_name: Isabelle
full_name: Leray, Isabelle
last_name: Leray
- first_name: Nathalie
full_name: Rouach, Nathalie
last_name: Rouach
citation:
ama: Cheung GT, Bataveljic D, Visser J, et al. Physiological synaptic activity and
recognition memory require astroglial glutamine. Nature Communications.
2022;13. doi:10.1038/s41467-022-28331-7
apa: Cheung, G. T., Bataveljic, D., Visser, J., Kumar, N., Moulard, J., Dallérac,
G., … Rouach, N. (2022). Physiological synaptic activity and recognition memory
require astroglial glutamine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28331-7
chicago: Cheung, Giselle T, Danijela Bataveljic, Josien Visser, Naresh Kumar, Julien
Moulard, Glenn Dallérac, Daria Mozheiko, et al. “Physiological Synaptic Activity
and Recognition Memory Require Astroglial Glutamine.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28331-7.
ieee: G. T. Cheung et al., “Physiological synaptic activity and recognition
memory require astroglial glutamine,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Cheung GT, Bataveljic D, Visser J, Kumar N, Moulard J, Dallérac G, Mozheiko
D, Rollenhagen A, Ezan P, Mongin C, Chever O, Bemelmans AP, Lübke J, Leray I,
Rouach N. 2022. Physiological synaptic activity and recognition memory require
astroglial glutamine. Nature Communications. 13, 753.
mla: Cheung, Giselle T., et al. “Physiological Synaptic Activity and Recognition
Memory Require Astroglial Glutamine.” Nature Communications, vol. 13, 753,
Springer Nature, 2022, doi:10.1038/s41467-022-28331-7.
short: G.T. Cheung, D. Bataveljic, J. Visser, N. Kumar, J. Moulard, G. Dallérac,
D. Mozheiko, A. Rollenhagen, P. Ezan, C. Mongin, O. Chever, A.P. Bemelmans, J.
Lübke, I. Leray, N. Rouach, Nature Communications 13 (2022).
date_created: 2022-02-20T23:01:30Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:22:38Z
day: '08'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1038/s41467-022-28331-7
external_id:
isi:
- '000757297200017'
pmid:
- '35136061'
file:
- access_level: open_access
checksum: 51d580aff2327dd957946208a9749e1a
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T07:51:33Z
date_updated: 2022-02-21T07:51:33Z
file_id: '10777'
file_name: 2022_NatureCommunications_Cheung.pdf
file_size: 7910519
relation: main_file
success: 1
file_date_updated: 2022-02-21T07:51:33Z
fulldoi: https://doi.org/10.1038/s41467-022-28331-7
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physiological synaptic activity and recognition memory require astroglial glutamine
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 13
year: '2022'
...
---
_id: '10768'
abstract:
- lang: eng
text: Among the most fascinated properties of the plant hormone auxin is its ability
to promote formation of its own directional transport routes. These gradually
narrowing auxin channels form from the auxin source toward the sink and involve
coordinated, collective polarization of individual cells. Once established, the
channels provide positional information, along which new vascular strands form,
for example, during organogenesis, regeneration, or leave venation. The main prerequisite
of this still mysterious auxin canalization mechanism is a feedback between auxin
signaling and its directional transport. This is manifested by auxin-induced re-arrangements
of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent
open questions relate to how position of auxin source and sink as well as tissue
context are sensed and translated into tissue polarization and how cells communicate
to polarize coordinately. Recently, identification of the first molecular players
opens new avenues into molecular studies of this intriguing example of self-organizing
plant development.
acknowledgement: The authors apologize to those researchers whose work was not cited.
In addition, exciting topics such as PIN polarization in context of phyllotaxis,
shoot branching and termination of gravitropic bending, or role of additional auxin
transporters could not have been included owing to lack of space. This work was
supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge
the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021).
article_number: '102174'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward
molecular players. Current Opinion in Plant Biology. 2022;65(2). doi:10.1016/j.pbi.2022.102174'
apa: 'Hajny, J., Tan, S., & Friml, J. (2022). Auxin canalization: From speculative
models toward molecular players. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2022.102174'
chicago: 'Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative
Models toward Molecular Players.” Current Opinion in Plant Biology. Elsevier,
2022. https://doi.org/10.1016/j.pbi.2022.102174.'
ieee: 'J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models
toward molecular players,” Current Opinion in Plant Biology, vol. 65, no.
2. Elsevier, 2022.'
ista: 'Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models
toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.'
mla: 'Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular
Players.” Current Opinion in Plant Biology, vol. 65, no. 2, 102174, Elsevier,
2022, doi:10.1016/j.pbi.2022.102174.'
short: J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).
corr_author: '1'
date_created: 2022-02-20T23:01:32Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2024-10-09T21:01:37Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2022.102174
external_id:
isi:
- '000758724700004'
pmid:
- '35123880'
file:
- access_level: open_access
checksum: f1ee02b6fb4200934eeb31fa69120885
content_type: application/pdf
creator: dernst
date_created: 2022-03-10T13:34:09Z
date_updated: 2022-03-10T13:34:09Z
file_id: '10844'
file_name: 2022_CurrentOpPlantBiology_Hajny.pdf
file_size: 820322
relation: main_file
success: 1
file_date_updated: 2022-03-10T13:34:09Z
fulldoi: https://doi.org/10.1016/j.pbi.2022.102174
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Auxin canalization: From speculative models toward molecular players'
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: 65
year: '2022'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '10769'
abstract:
- lang: eng
text: studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas
y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos
con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía
de entrelazamiento en un intervalo, construimos la función c entrópica que es
finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo
alcance proveniente de la superficie de Fermi. Motivados por trabajos previos
de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos
oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una
medida de correlación entre diferentes regiones. Usando una expansión de distancia
grande desarrollada por Cardy, argumentamos que la información mutua detecta las
correlaciones inducidas por la superficie de Fermi todavía al orden dominante
en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones
de Renyi para distinguir estados con diferente carga. Encontramos que estados
en diferentes sectores de superselección dan origen a un comportamiento super-extensivo
en la entropía relativa.
acknowledgement: "Se agradece a Horacio Casini por distintas discusiones y comentarios
a lo largo del trabajo. LD cuenta con el apoyo de CNEA y UNCuyo, Inst. GT cuenta
con el apoyo de CONICET,\r\nANPCyT, CNEA, y UNCuyo, Inst. Balseiro. RM cuenta con
el apoyo de IST Austria. MS cuenta con el apoyode CONICET y UNCuyo, Inst. Balseiro.
También se agradece a la Asociación Argentina de Física por la posibilidad de presentar
este artículo en el marco de una Mención Especial por el Premio Luis Másperi 2020."
article_processing_charge: No
article_type: original
author:
- first_name: L.
full_name: Daguerre, L.
last_name: Daguerre
- first_name: G.
full_name: Torroba, G.
last_name: Torroba
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: M.
full_name: Solís, M.
last_name: Solís
citation:
ama: 'Daguerre L, Torroba G, Medina Ramos RA, Solís M. Non relativistic quantum
field theory: Dynamics and irreversibility. Anales de la Asociacion Fisica
Argentina. 2022;32(4):93-98. doi:10.31527/analesafa.2021.32.4.93'
apa: 'Daguerre, L., Torroba, G., Medina Ramos, R. A., & Solís, M. (2022). Non
relativistic quantum field theory: Dynamics and irreversibility. Anales de
la Asociacion Fisica Argentina. Asociación Física Argentina. https://doi.org/10.31527/analesafa.2021.32.4.93'
chicago: 'Daguerre, L., G. Torroba, Raimel A Medina Ramos, and M. Solís. “Non relativistic
quantum field theory: Dynamics and irreversibility.” Anales de la Asociacion
Fisica Argentina. Asociación Física Argentina, 2022. https://doi.org/10.31527/analesafa.2021.32.4.93.'
ieee: 'L. Daguerre, G. Torroba, R. A. Medina Ramos, and M. Solís, “Non relativistic
quantum field theory: Dynamics and irreversibility,” Anales de la Asociacion
Fisica Argentina, vol. 32, no. 4. Asociación Física Argentina, pp. 93–98,
2022.'
ista: 'Daguerre L, Torroba G, Medina Ramos RA, Solís M. 2022. Non relativistic quantum
field theory: Dynamics and irreversibility. Anales de la Asociacion Fisica Argentina.
32(4), 93–98.'
mla: 'Daguerre, L., et al. “Non relativistic quantum field theory: Dynamics and
irreversibility.” Anales de la Asociacion Fisica Argentina, vol. 32, no.
4, Asociación Física Argentina, 2022, pp. 93–98, doi:10.31527/analesafa.2021.32.4.93.'
short: L. Daguerre, G. Torroba, R.A. Medina Ramos, M. Solís, Anales de la Asociacion
Fisica Argentina 32 (2022) 93–98.
date_created: 2022-02-20T23:01:32Z
date_published: 2022-01-13T00:00:00Z
date_updated: 2026-04-02T12:30:12Z
day: '13'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.31527/analesafa.2021.32.4.93
file:
- access_level: open_access
checksum: ca66a3017205677c5b4d22b3bb74fb0b
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T09:32:44Z
date_updated: 2022-02-21T09:32:44Z
file_id: '10782'
file_name: 2022_AnalesAFA_Daguerre.pdf
file_size: 4505751
relation: main_file
success: 1
file_date_updated: 2022-02-21T09:32:44Z
fulldoi: https://doi.org/10.31527/analesafa.2021.32.4.93
has_accepted_license: '1'
intvolume: ' 32'
issue: '4'
language:
- iso: spa
month: '01'
oa: 1
oa_version: Published Version
page: 93-98
publication: Anales de la Asociacion Fisica Argentina
publication_identifier:
eissn:
- 1850-1168
publication_status: published
publisher: Asociación Física Argentina
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Non relativistic quantum field theory: Dynamics and irreversibility'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 32
year: '2022'
...
---
_id: '10771'
abstract:
- lang: eng
text: A critical overview of the theory of the chirality-induced spin selectivity
(CISS) effect, that is, phenomena in which the chirality of molecular species
imparts significant spin selectivity to various electron processes, is provided.
Based on discussions in a recently held workshop, and further work published since,
the status of CISS effects—in electron transmission, electron transport, and chemical
reactions—is reviewed. For each, a detailed discussion of the state-of-the-art
in theoretical understanding is provided and remaining challenges and research
opportunities are identified.
article_number: '2106629'
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Ferdinand
full_name: Evers, Ferdinand
last_name: Evers
- first_name: Amnon
full_name: Aharony, Amnon
last_name: Aharony
- first_name: Nir
full_name: Bar-Gill, Nir
last_name: Bar-Gill
- first_name: Ora
full_name: Entin-Wohlman, Ora
last_name: Entin-Wohlman
- first_name: Per
full_name: Hedegård, Per
last_name: Hedegård
- first_name: Oded
full_name: Hod, Oded
last_name: Hod
- first_name: Pavel
full_name: Jelinek, Pavel
last_name: Jelinek
- first_name: Grzegorz
full_name: Kamieniarz, Grzegorz
last_name: Kamieniarz
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Karen
full_name: Michaeli, Karen
last_name: Michaeli
- first_name: Vladimiro
full_name: Mujica, Vladimiro
last_name: Mujica
- first_name: Ron
full_name: Naaman, Ron
last_name: Naaman
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Sivan
full_name: Refaely-Abramson, Sivan
last_name: Refaely-Abramson
- first_name: Oren
full_name: Tal, Oren
last_name: Tal
- first_name: Jos
full_name: Thijssen, Jos
last_name: Thijssen
- first_name: Michael
full_name: Thoss, Michael
last_name: Thoss
- first_name: Jan M.
full_name: Van Ruitenbeek, Jan M.
last_name: Van Ruitenbeek
- first_name: Latha
full_name: Venkataraman, Latha
last_name: Venkataraman
- first_name: David H.
full_name: Waldeck, David H.
last_name: Waldeck
- first_name: Binghai
full_name: Yan, Binghai
last_name: Yan
- first_name: Leeor
full_name: Kronik, Leeor
last_name: Kronik
citation:
ama: 'Evers F, Aharony A, Bar-Gill N, et al. Theory of chirality induced spin selectivity:
Progress and challenges. Advanced Materials. 2022;34(13). doi:10.1002/adma.202106629'
apa: 'Evers, F., Aharony, A., Bar-Gill, N., Entin-Wohlman, O., Hedegård, P., Hod,
O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress
and challenges. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106629'
chicago: 'Evers, Ferdinand, Amnon Aharony, Nir Bar-Gill, Ora Entin-Wohlman, Per
Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity:
Progress and Challenges.” Advanced Materials. Wiley, 2022. https://doi.org/10.1002/adma.202106629.'
ieee: 'F. Evers et al., “Theory of chirality induced spin selectivity: Progress
and challenges,” Advanced Materials, vol. 34, no. 13. Wiley, 2022.'
ista: 'Evers F, Aharony A, Bar-Gill N, Entin-Wohlman O, Hedegård P, Hod O, Jelinek
P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely-Abramson
S, Tal O, Thijssen J, Thoss M, Van Ruitenbeek JM, Venkataraman L, Waldeck DH,
Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress
and challenges. Advanced Materials. 34(13), 2106629.'
mla: 'Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress
and Challenges.” Advanced Materials, vol. 34, no. 13, 2106629, Wiley, 2022,
doi:10.1002/adma.202106629.'
short: F. Evers, A. Aharony, N. Bar-Gill, O. Entin-Wohlman, P. Hedegård, O. Hod,
P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y.
Paltiel, S. Refaely-Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. Van Ruitenbeek,
L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022).
date_created: 2022-02-20T23:01:33Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2026-04-02T12:45:15Z
day: '01'
department:
- _id: MiLe
doi: 10.1002/adma.202106629
external_id:
arxiv:
- '2108.09998'
isi:
- '000753795900001'
pmid:
- '35064943'
fulldoi: https://doi.org/10.1002/adma.202106629
intvolume: ' 34'
isi: 1
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.09998
month: '04'
oa: 1
oa_version: Preprint
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theory of chirality induced spin selectivity: Progress and challenges'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 34
year: '2022'
...
---
_id: '10772'
abstract:
- lang: eng
text: We introduce tropical corals, balanced trees in a half-space, and show that
they correspond to holomorphic polygons capturing the product rule in Lagrangian
Floer theory for the elliptic curve. We then prove a correspondence theorem equating
counts of tropical corals to punctured log Gromov–Witten invariants of the Tate
curve. This implies that the homogeneous coordinate ring of the mirror to the
Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming
a prediction of homological mirror symmetry.
acknowledgement: 'This paper is based on my PhD thesis, which would not be possible
without the support of my advisor Bernd Siebert. I also thank Dan Abramovich, Mohammed
Abouzaid, Mark Gross, Tom Coates and Dimitri Zvonkine for many useful conversations.
Finally, I thank the anonymous referees for their many insightful comments and valuable
suggestions which have resulted in major improvements to this article. This project
has received funding from the EuropeanResearch Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement Number:
682603), and from Fondation Mathématique Jacques Hadamard. '
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Nuroemuer Huelya
full_name: Arguez, Nuroemuer Huelya
id: 3c26b22e-c843-11eb-aa56-d38ffa0bdd08
last_name: Arguez
citation:
ama: Arguez NH. Mirror symmetry for the Tate curve via tropical and log corals.
Journal of the London Mathematical Society. 2022;105(1):343-411. doi:10.1112/jlms.12515
apa: Arguez, N. H. (2022). Mirror symmetry for the Tate curve via tropical and log
corals. Journal of the London Mathematical Society. London Mathematical
Society. https://doi.org/10.1112/jlms.12515
chicago: Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical
and Log Corals.” Journal of the London Mathematical Society. London Mathematical
Society, 2022. https://doi.org/10.1112/jlms.12515.
ieee: N. H. Arguez, “Mirror symmetry for the Tate curve via tropical and log corals,”
Journal of the London Mathematical Society, vol. 105, no. 1. London Mathematical
Society, pp. 343–411, 2022.
ista: Arguez NH. 2022. Mirror symmetry for the Tate curve via tropical and log corals.
Journal of the London Mathematical Society. 105(1), 343–411.
mla: Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical
and Log Corals.” Journal of the London Mathematical Society, vol. 105,
no. 1, London Mathematical Society, 2022, pp. 343–411, doi:10.1112/jlms.12515.
short: N.H. Arguez, Journal of the London Mathematical Society 105 (2022) 343–411.
corr_author: '1'
date_created: 2022-02-20T23:01:33Z
date_published: 2022-02-05T00:00:00Z
date_updated: 2024-10-09T21:01:37Z
day: '05'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/jlms.12515
external_id:
arxiv:
- '1712.10260'
isi:
- '000751600600001'
file:
- access_level: open_access
checksum: 8bd0fd9694be894a191857ddf27678f0
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T11:22:58Z
date_updated: 2022-02-21T11:22:58Z
file_id: '10783'
file_name: 2022_JournLondonMathSociety_Arguez.pdf
file_size: 936873
relation: main_file
success: 1
file_date_updated: 2022-02-21T11:22:58Z
fulldoi: https://doi.org/10.1112/jlms.12515
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 343-411
publication: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mirror symmetry for the Tate curve via tropical and log corals
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: 105
year: '2022'
...
---
_id: '10773'
abstract:
- lang: eng
text: The Voronoi tessellation in Rd is defined by locally minimizing the power
distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined
by locally maximizing the negative power distance to other such points. We prove
that the average of the two piecewise quadratic functions is piecewise linear,
and that all three functions have the same critical points and values. Discretizing
the two piecewise quadratic functions, we get the alpha shapes as sublevel sets
of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel
sets of the discrete function on the Voronoi tessellation. For the same non-critical
value, the corresponding shapes are disjoint, separated by a narrow channel that
contains no critical points but the entire level set of the piecewise linear function.
acknowledgement: Open access funding provided by the Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera Di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera Di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
last_name: Saghafian
citation:
ama: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete
and Computational Geometry. 2022;67:811-842. doi:10.1007/s00454-022-00371-2
apa: Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian, M.
(2022). Continuous and discrete radius functions on Voronoi tessellations and
Delaunay mosaics. Discrete and Computational Geometry. Springer Nature.
https://doi.org/10.1007/s00454-022-00371-2
chicago: Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Continuous and Discrete Radius Functions on Voronoi Tessellations
and Delaunay Mosaics.” Discrete and Computational Geometry. Springer Nature,
2022. https://doi.org/10.1007/s00454-022-00371-2.
ieee: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics,”
Discrete and Computational Geometry, vol. 67. Springer Nature, pp. 811–842,
2022.
ista: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2022. Continuous
and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete
and Computational Geometry. 67, 811–842.
mla: Biswas, Ranita, et al. “Continuous and Discrete Radius Functions on Voronoi
Tessellations and Delaunay Mosaics.” Discrete and Computational Geometry,
vol. 67, Springer Nature, 2022, pp. 811–42, doi:10.1007/s00454-022-00371-2.
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Discrete
and Computational Geometry 67 (2022) 811–842.
corr_author: '1'
date_created: 2022-02-20T23:01:34Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2024-10-09T21:01:38Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-022-00371-2
external_id:
isi:
- '000752175300002'
file:
- access_level: open_access
checksum: 9383d3b70561bacee905e335dc922680
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:07:55Z
date_updated: 2022-08-02T06:07:55Z
file_id: '11718'
file_name: 2022_DiscreteCompGeometry_Biswas.pdf
file_size: 2518111
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:07:55Z
fulldoi: https://doi.org/10.1007/s00454-022-00371-2
has_accepted_license: '1'
intvolume: ' 67'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 811-842
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Continuous and discrete radius functions on Voronoi tessellations and Delaunay
mosaics
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: 67
year: '2022'
...
---
_id: '10774'
abstract:
- lang: eng
text: We study the problem of specifying sequential information-flow properties
of systems. Information-flow properties are hyperproperties, as they compare different
traces of a system. Sequential information-flow properties can express changes,
over time, in the information-flow constraints. For example, information-flow
constraints during an initialization phase of a system may be different from information-flow
constraints that are required during the operation phase. We formalize several
variants of interpreting sequential information-flow constraints, which arise
from different assumptions about what can be observed of the system. For this
purpose, we introduce a first-order logic, called Hypertrace Logic, with both
trace and time quantifiers for specifying linear-time hyperproperties. We prove
that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted
quantifier prefixes, cannot specify the majority of the studied variants of sequential
information flow, including all variants in which the transition between sequential
phases (such as initialization and operation) happens asynchronously. Our results
rely on new equivalences between sets of traces that cannot be distinguished by
certain classes of formulas from Hypertrace Logic. This presents a new approach
to proving inexpressiveness results for HyperLTL.
acknowledgement: This work was funded in part by the Wittgenstein Award Z211-N23 of
the Austrian Science Fund (FWF) and by the FWF project W1255-N23.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- 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: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana Oliveira
full_name: Da Costa, Ana Oliveira
last_name: Da Costa
citation:
ama: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential
information flow. In: Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
Vol 13182. Springer Nature; 2022:1-19. doi:10.1007/978-3-030-94583-1_1'
apa: 'Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa,
A. O. (2022). Flavors of sequential information flow. In Lecture Notes in Computer
Science (including subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics) (Vol. 13182, pp. 1–19). Philadelphia, PA, United
States: Springer Nature. https://doi.org/10.1007/978-3-030-94583-1_1'
chicago: Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), 13182:1–19. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-94583-1_1.
ieee: E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa,
“Flavors of sequential information flow,” in Lecture Notes in Computer Science
(including subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), Philadelphia, PA, United States, 2022, vol. 13182, pp.
1–19.
ista: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors
of sequential information flow. Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182,
1–19.'
mla: Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), vol. 13182, Springer Nature, 2022, pp.
1–19, doi:10.1007/978-3-030-94583-1_1.
short: E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:,
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp.
1–19.
conference:
end_date: 2022-01-18
location: Philadelphia, PA, United States
name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation'
start_date: 2022-01-16
date_created: 2022-02-20T23:01:34Z
date_published: 2022-01-14T00:00:00Z
date_updated: 2026-04-16T09:13:43Z
day: '14'
department:
- _id: ToHe
doi: 10.1007/978-3-030-94583-1_1
external_id:
arxiv:
- '2105.02013'
isi:
- '001059208500001'
fulldoi: https://doi.org/10.1007/978-3-030-94583-1_1
intvolume: ' 13182'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.02013'
month: '01'
oa: 1
oa_version: Preprint
page: 1-19
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_identifier:
eisbn:
- '9783030945831'
eissn:
- 1611-3349
isbn:
- '9783030945824'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavors of sequential information flow
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 13182
year: '2022'
...
---
_id: '10775'
abstract:
- lang: eng
text: List-decodability of Reed–Solomon codes has received a lot of attention, but
the best-possible dependence between the parameters is still not well-understood.
In this work, we focus on the case where the list-decoding radius is of the form
r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon
codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any
Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between
rate and list-decoding radius is best-possible for any code with list size less
than exponential in the block length. By achieving this trade-off between rate
and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo,
and Wootters, and resolve the main motivating question of their work. Moreover,
while their result requires the field to be exponentially large in the block length,
we only need the field size to be polynomially large (and in fact, almost-linear
suffices). We deduce our main result from a more general theorem, in which we
prove good list-decodability properties of random puncturings of any given code
with very large distance.
acknowledgement: Research supported by NSF Award DMS-1953990.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
citation:
ama: Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon
codes. IEEE Transactions on Information Theory. 2022;68(6):3823-3828. doi:10.1109/TIT.2022.3148779
apa: Ferber, A., Kwan, M. A., & Sauermann, L. (2022). List-decodability with
large radius for Reed-Solomon codes. IEEE Transactions on Information Theory.
IEEE. https://doi.org/10.1109/TIT.2022.3148779
chicago: Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability
with Large Radius for Reed-Solomon Codes.” IEEE Transactions on Information
Theory. IEEE, 2022. https://doi.org/10.1109/TIT.2022.3148779.
ieee: A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius
for Reed-Solomon codes,” IEEE Transactions on Information Theory, vol.
68, no. 6. IEEE, pp. 3823–3828, 2022.
ista: Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius
for Reed-Solomon codes. IEEE Transactions on Information Theory. 68(6), 3823–3828.
mla: Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon
Codes.” IEEE Transactions on Information Theory, vol. 68, no. 6, IEEE,
2022, pp. 3823–28, doi:10.1109/TIT.2022.3148779.
short: A. Ferber, M.A. Kwan, L. Sauermann, IEEE Transactions on Information Theory
68 (2022) 3823–3828.
corr_author: '1'
date_created: 2022-02-20T23:01:34Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-07-10T11:50:08Z
day: '01'
department:
- _id: MaKw
doi: 10.1109/TIT.2022.3148779
external_id:
arxiv:
- '2012.10584'
isi:
- '000799622500022'
fulldoi: https://doi.org/10.1109/TIT.2022.3148779
intvolume: ' 68'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.10584
month: '06'
oa: 1
oa_version: Preprint
page: 3823-3828
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '11145'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: List-decodability with large radius for Reed-Solomon codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '10776'
abstract:
- lang: eng
text: 'Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior).
Given a point p in the interior of K, a hyperplane h passing through p is called
barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question
whether, for every K, there exists an interior point p through which there are
at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly
resolved affirmatively by showing that this is the case if p=p0 is the point of
maximal depth in K. However, while working on a related question, we noticed that
one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample;
this re-opens Grünbaum’s question. It follows from known results that for n≥2,
there are always at least three distinct barycentric cuts through the point p0∈K
of maximal depth. Using tools related to Morse theory we are able to improve this
bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.'
acknowledgement: The work by Zuzana Patáková has been partially supported by Charles
University Research Center Program No. UNCE/SCI/022, and part of it was done during
her research stay at IST Austria. The work by Martin Tancer is supported by the
GAČR Grant 19-04113Y and by the Charles University Projects PRIMUS/17/SCI/3 and
UNCE/SCI/004.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Patakova Z, Tancer M, Wagner U. Barycentric cuts through a convex body. Discrete
and Computational Geometry. 2022;68:1133-1154. doi:10.1007/s00454-021-00364-7
apa: Patakova, Z., Tancer, M., & Wagner, U. (2022). Barycentric cuts through
a convex body. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-021-00364-7
chicago: Patakova, Zuzana, Martin Tancer, and Uli Wagner. “Barycentric Cuts through
a Convex Body.” Discrete and Computational Geometry. Springer Nature, 2022.
https://doi.org/10.1007/s00454-021-00364-7.
ieee: Z. Patakova, M. Tancer, and U. Wagner, “Barycentric cuts through a convex
body,” Discrete and Computational Geometry, vol. 68. Springer Nature, pp.
1133–1154, 2022.
ista: Patakova Z, Tancer M, Wagner U. 2022. Barycentric cuts through a convex body.
Discrete and Computational Geometry. 68, 1133–1154.
mla: Patakova, Zuzana, et al. “Barycentric Cuts through a Convex Body.” Discrete
and Computational Geometry, vol. 68, Springer Nature, 2022, pp. 1133–54, doi:10.1007/s00454-021-00364-7.
short: Z. Patakova, M. Tancer, U. Wagner, Discrete and Computational Geometry 68
(2022) 1133–1154.
date_created: 2022-02-20T23:01:35Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-02T14:38:58Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-021-00364-7
external_id:
arxiv:
- '2003.13536'
isi:
- '000750681500001'
fulldoi: https://doi.org/10.1007/s00454-021-00364-7
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2003.13536
month: '12'
oa: 1
oa_version: Preprint
page: 1133-1154
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Barycentric cuts through a convex body
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '10787'
abstract:
- lang: eng
text: "A species distributed across diverse environments may adapt to local conditions.
We ask how quickly such a species changes its range in response to changed conditions.
Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in
metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210))
used the infinite island model to find the stationary distribution of allele frequencies
and deme sizes. We extend this to find how a metapopulation responds to changes
in carrying capacity, selection strength, or migration rate when deme sizes are
fixed. We further develop a ‘fixed-state’ approximation. Under this approximation,
polymorphism is only possible for a narrow range of habitat proportions when selection
is weak compared to drift, but for a much wider range otherwise. When rates of
selection or migration relative to drift change in a single deme of the metapopulation,
the population takes a time of order m−1 to reach the new equilibrium. However,
even with many loci, there can be substantial fluctuations in net adaptation,
because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation,
variation may gradually be lost by chance, even if it would persist in an infinite
metapopulation. When conditions change across the whole metapopulation, there
can be rapid change, which is predicted well by the fixed-state approximation.
This work helps towards an understanding of how metapopulations extend their range
across diverse environments.\r\nThis article is part of the theme issue ‘Species’
ranges in the face of changing environments (Part II)’."
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
[FWF P-32896B].
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment.
Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1848). doi:10.1098/rstb.2021.0009'
apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation
to a changing environment. Philosophical Transactions of the Royal Society
B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009'
chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a
Metapopulation to a Changing Environment.” Philosophical Transactions of the
Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.'
ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing
environment,” Philosophical Transactions of the Royal Society B: Biological
Sciences, vol. 377, no. 1848. The Royal Society, 2022.'
ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing
environment. Philosophical Transactions of the Royal Society B: Biological Sciences.
377(1848).'
mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation
to a Changing Environment.” Philosophical Transactions of the Royal Society
B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.'
short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society
B: Biological Sciences 377 (2022).'
corr_author: '1'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2026-04-07T12:54:28Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
- '000758140300001'
pmid:
- '35184588'
file:
- access_level: open_access
checksum: 3b0243738f01bf3c07e0d7e8dc64f71d
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:14:32Z
date_updated: 2022-08-02T06:14:32Z
file_id: '11719'
file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf
file_size: 1349672
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:14:32Z
fulldoi: https://doi.org/10.1098/rstb.2021.0009
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1848'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The response of a metapopulation to a changing environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 377
year: '2022'
...
---
_id: '10791'
abstract:
- lang: eng
text: The mammalian neocortex is composed of diverse neuronal and glial cell classes
that broadly arrange in six distinct laminae. Cortical layers emerge during development
and defects in the developmental programs that orchestrate cortical lamination
are associated with neurodevelopmental diseases. The developmental principle of
cortical layer formation depends on concerted radial projection neuron migration,
from their birthplace to their final target position. Radial migration occurs
in defined sequential steps, regulated by a large array of signaling pathways.
However, based on genetic loss-of-function experiments, most studies have thus
far focused on the role of cell-autonomous gene function. Yet, cortical neuron
migration in situ is a complex process and migrating neurons traverse along diverse
cellular compartments and environments. The role of tissue-wide properties and
genetic state in radial neuron migration is however not clear. Here we utilized
mosaic analysis with double markers (MADM) technology to either sparsely or globally
delete gene function, followed by quantitative single-cell phenotyping. The MADM-based
gene ablation paradigms in combination with computational modeling demonstrated
that global tissue-wide effects predominate cell-autonomous gene function albeit
in a gene-specific manner. Our results thus suggest that the genetic landscape
in a tissue critically affects the overall migration phenotype of individual cortical
projection neurons. In a broader context, our findings imply that global tissue-wide
effects represent an essential component of the underlying etiology associated
with focal malformations of cortical development in particular, and neurological
diseases in general.
acknowledged_ssus:
- _id: LifeSc
- _id: PreCl
- _id: Bio
acknowledgement: "A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian
Academy of Sciences. This work also received support from IST Austria institutional
funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC
funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical
support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer
lab for discussion. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the Imaging and Optics Facility, Lab
Support Facility and Preclinical Facility."
article_number: kvac009
article_processing_charge: No
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Li Huei
full_name: Tsai, Li Huei
last_name: Tsai
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic
gene function in radial neuron migration. Oxford Open Neuroscience. 2022;1(1).
doi:10.1093/oons/kvac009
apa: Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter,
S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration. Oxford Open Neuroscience. Oxford University
Press. https://doi.org/10.1093/oons/kvac009
chicago: Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena
Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override
Cell-Intrinsic Gene Function in Radial Neuron Migration.” Oxford Open Neuroscience.
Oxford University Press, 2022. https://doi.org/10.1093/oons/kvac009.
ieee: A. H. Hansen et al., “Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration,” Oxford Open Neuroscience, vol. 1,
no. 1. Oxford University Press, 2022.
ista: Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM,
Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects
override cell-intrinsic gene function in radial neuron migration. Oxford Open
Neuroscience. 1(1), kvac009.
mla: Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function
in Radial Neuron Migration.” Oxford Open Neuroscience, vol. 1, no. 1, kvac009,
Oxford University Press, 2022, doi:10.1093/oons/kvac009.
short: A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter,
C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford
Open Neuroscience 1 (2022).
corr_author: '1'
date_created: 2022-02-25T07:52:11Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2026-04-07T13:29:13Z
day: '07'
ddc:
- '570'
department:
- _id: SiHi
- _id: BjHo
- _id: LifeSc
- _id: EM-Fac
doi: 10.1093/oons/kvac009
ec_funded: 1
external_id:
pmid:
- '38596707'
file:
- access_level: open_access
checksum: 822e76e056c07099d1fb27d1ece5941b
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:00:30Z
date_updated: 2023-08-16T08:00:30Z
file_id: '14061'
file_name: 2023_OxfordOpenNeuroscience_Hansen.pdf
file_size: 4846551
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:00:30Z
fulldoi: https://doi.org/10.1093/oons/kvac009
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular mechanisms of radial neuronal migration
publication: Oxford Open Neuroscience
publication_identifier:
eissn:
- 2753-149X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '12726'
relation: dissertation_contains
status: public
- id: '14530'
relation: dissertation_contains
status: public
status: public
title: Tissue-wide effects override cell-intrinsic gene function in radial neuron
migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2022'
...