---
_id: '11637'
abstract:
- lang: eng
text: The ability to detect and respond to acute oxygen (O2) shortages is indispensable
to aerobic life. The molecular mechanisms and circuits underlying this capacity
are poorly understood. Here, we characterize the behavioral responses of feeding
Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of
turning maneuvers followed by a persistent switch to rapid forward movement as
animals seek to avoid and escape hypoxia. While the behavioral responses to 1%
O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit
underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome
function inhibits escape from 1% O2 due to increased cGMP signaling. A primary
source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP)
receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine
secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically
in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits
escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+
decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial
complex I (MCIII), which lead to persistently high reactive oxygen species (ROS),
abrogate acute hypoxia responses. In particular, repressing the expression of
isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1%
O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation
of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia
responses. Our results implicate ROS and precise regulation of intracellular cGMP
in the modulation of acute responses to hypoxia by C. elegans.
acknowledgement: ' This work was funded by H2020 European Research Council (ERC Advanced
grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome
Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0)
to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN
SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR
starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.'
article_number: e3001684
article_processing_charge: No
article_type: original
author:
- first_name: Lina
full_name: Zhao, Lina
last_name: Zhao
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Lars
full_name: Nilsson, Lars
last_name: Nilsson
- first_name: Niko Paresh
full_name: Amin-Wetzel, Niko Paresh
id: E95D3014-9D8C-11E9-9C80-D2F8E5697425
last_name: Amin-Wetzel
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
citation:
ama: Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent
escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 2022;20(6).
doi:10.1371/journal.pbio.3001684
apa: Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono,
M., & Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from
hypoxia in Caenorhabditis elegans. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.3001684
chicago: Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson
Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent
Escape from Hypoxia in Caenorhabditis Elegans.” PLoS Biology. Public Library
of Science, 2022. https://doi.org/10.1371/journal.pbio.3001684.
ieee: L. Zhao et al., “ROS and cGMP signaling modulate persistent escape
from hypoxia in Caenorhabditis elegans,” PLoS Biology, vol. 20, no. 6.
Public Library of Science, 2022.
ista: Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C.
2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis
elegans. PLoS Biology. 20(6), e3001684.
mla: Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from
Hypoxia in Caenorhabditis Elegans.” PLoS Biology, vol. 20, no. 6, e3001684,
Public Library of Science, 2022, doi:10.1371/journal.pbio.3001684.
short: L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono,
C. Chen, PLoS Biology 20 (2022).
date_created: 2022-07-24T22:01:42Z
date_published: 2022-06-21T00:00:00Z
date_updated: 2023-08-03T12:11:44Z
day: '21'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1371/journal.pbio.3001684
external_id:
isi:
- '000828679600001'
pmid:
- '35727855'
file:
- access_level: open_access
checksum: df4902f854ad76769d3203bfdc69f16c
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:38:49Z
date_updated: 2022-07-25T07:38:49Z
file_id: '11643'
file_name: 2022_PLoSBiology_Zhao.pdf
file_size: 3721585
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:38:49Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis
elegans
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: 20
year: '2022'
...
---
_id: '11638'
abstract:
- lang: eng
text: 'Statistical inference is central to many scientific endeavors, yet how it
works remains unresolved. Answering this requires a quantitative understanding
of the intrinsic interplay between statistical models, inference methods, and
the structure in the data. To this end, we characterize the efficacy of direct
coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence
data—in inferring pairwise interactions from samples of ferromagnetic Ising models
on random graphs. Our approach allows for physically motivated exploration of
qualitatively distinct data regimes separated by phase transitions. We show that
inference quality depends strongly on the nature of data-generating distributions:
optimal accuracy occurs at an intermediate temperature where the detrimental effects
from macroscopic order and thermal noise are minimal. Importantly our results
indicate that DCA does not always outperform its local-statistics-based predecessors;
while DCA excels at low temperatures, it becomes inferior to simple correlation
thresholding at virtually all temperatures when data are limited. Our findings
offer insights into the regime in which DCA operates so successfully, and more
broadly, how inference interacts with the structure in the data.'
acknowledgement: This work was supported in part by the Alfred P. Sloan Foundation,
the Simons Foundation, the National Institutes of Health under Award No. R01EB026943,
and the National Science Foundation, through the Center for the Physics of Biological
Function (PHY-1734030).
article_number: '023240'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Vudtiwat
full_name: Ngampruetikorn, Vudtiwat
last_name: Ngampruetikorn
- first_name: Vedant
full_name: Sachdeva, Vedant
last_name: Sachdeva
- first_name: Johanna
full_name: Torrence, Johanna
last_name: Torrence
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: David J.
full_name: Schwab, David J.
last_name: Schwab
- first_name: Stephanie E.
full_name: Palmer, Stephanie E.
last_name: Palmer
citation:
ama: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
Inferring couplings in networks across order-disorder phase transitions. Physical
Review Research. 2022;4(2). doi:10.1103/PhysRevResearch.4.023240
apa: Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J.,
& Palmer, S. E. (2022). Inferring couplings in networks across order-disorder
phase transitions. Physical Review Research. American Physical Society.
https://doi.org/10.1103/PhysRevResearch.4.023240
chicago: Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik,
David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across
Order-Disorder Phase Transitions.” Physical Review Research. American Physical
Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.023240.
ieee: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and
S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,”
Physical Review Research, vol. 4, no. 2. American Physical Society, 2022.
ista: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
2022. Inferring couplings in networks across order-disorder phase transitions.
Physical Review Research. 4(2), 023240.
mla: Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder
Phase Transitions.” Physical Review Research, vol. 4, no. 2, 023240, American
Physical Society, 2022, doi:10.1103/PhysRevResearch.4.023240.
short: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E.
Palmer, Physical Review Research 4 (2022).
date_created: 2022-07-24T22:01:42Z
date_published: 2022-06-24T00:00:00Z
date_updated: 2022-07-25T07:52:35Z
day: '24'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevResearch.4.023240
external_id:
arxiv:
- '2106.02349'
file:
- access_level: open_access
checksum: ed6fdc2a3a096df785fa5f7b17b716c6
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:47:23Z
date_updated: 2022-07-25T07:47:23Z
file_id: '11644'
file_name: 2022_PhysicalReviewResearch_Ngampruetikorn.pdf
file_size: 1379683
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:47:23Z
funded_apc: '1'
has_accepted_license: '1'
intvolume: ' 4'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring couplings in networks across order-disorder phase transitions
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: 4
year: '2022'
...
---
_id: '11639'
abstract:
- lang: eng
text: We study the list decodability of different ensembles of codes over the real
alphabet under the assumption of an omniscient adversary. It is a well-known result
that when the source and the adversary have power constraints P and N respectively,
the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve
constant list sizes, and the goal of the present paper is to obtain a better understanding
of the smallest achievable list size as a function of the gap to capacity. We
show a reduction from arbitrary codes to spherical codes, and derive a lower bound
on the list size of typical random spherical codes. We also give an upper bound
on the list size achievable using nested Construction-A lattices and infinite
Construction-A lattices. We then define and study a class of infinite constellations
that generalize Construction-A lattices and prove upper and lower bounds for the
same. Other goodness properties such as packing goodness and AWGN goodness of
infinite constellations are proved along the way. Finally, we consider random
lattices sampled from the Haar distribution and show that if a certain conjecture
that originates in analytic number theory is true, then the list size grows as
a polynomial function of the gap-to-capacity.
acknowledgement: "This work was done when Shashank Vatedka was at the Chinese University
of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077.
He would like to acknowledge funding from a seed grant offered by IIT Hyderabad
and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering
Board, India. Yihan Zhang has received funding from the European Union’s Horizon
2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
citation:
ama: Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations.
IEEE Transactions on Information Theory. 2022;68(12):7753-7786. doi:10.1109/TIT.2022.3189542
apa: Zhang, Y., & Vatedka, S. (2022). List decoding random Euclidean codes and
Infinite constellations. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/TIT.2022.3189542
chicago: Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes
and Infinite Constellations.” IEEE Transactions on Information Theory.
IEEE, 2022. https://doi.org/10.1109/TIT.2022.3189542.
ieee: Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite
constellations,” IEEE Transactions on Information Theory, vol. 68, no.
12. IEEE, pp. 7753–7786, 2022.
ista: Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite
constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.
mla: Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and
Infinite Constellations.” IEEE Transactions on Information Theory, vol.
68, no. 12, IEEE, 2022, pp. 7753–86, doi:10.1109/TIT.2022.3189542.
short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.
date_created: 2022-07-24T22:01:42Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-03T12:12:19Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2022.3189542
external_id:
arxiv:
- '1901.03790'
isi:
- '000891796100007'
intvolume: ' 68'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1901.03790
month: '12'
oa: 1
oa_version: Preprint
page: 7753-7786
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: List decoding random Euclidean codes and Infinite constellations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '11640'
abstract:
- lang: eng
text: Spatially explicit population genetic models have long been developed, yet
have rarely been used to test hypotheses about the spatial distribution of genetic
diversity or the genetic divergence between populations. Here, we use spatially
explicit coalescence simulations to explore the properties of the island and the
two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal
variation in deme size. We avoid the simulation of genetic data, using the fact
that under the studied models, summary statistics of genetic diversity and divergence
can be approximated from coalescence times. We perform the simulations using gridCoal,
a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical
Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change
arbitrarily across space and time, as well as migration rates between individual
demes. We identify different factors that can cause a deviation from theoretical
expectations, such as the simulation time in comparison to the effective deme
size and the spatio-temporal autocorrelation across the grid. Our results highlight
that FST, a measure of the strength of population structure, principally depends
on recent demography, which makes it robust to temporal variation in deme size.
In contrast, the amount of genetic diversity is dependent on the distant past
when Ne is large, therefore longer run times are needed to estimate Ne than FST.
Finally, we illustrate the use of gridCoal on a real-world example, the range
expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using
different degrees of spatio-temporal variation in deme size.
acknowledgement: ES was supported by an IST studentship provided by IST Austria. BT
was funded by the European Union's Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project
received further funding awarded to KC from the Swiss National Science Foundation
(SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick
Barton for many invaluable discussions and his comments on the thesis chapter and
this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions
and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for
providing us with the raw data from the LPX-Bern model for silver fir, and Willy
Tinner for helpful insights about the demographic history of silver fir. We also
thank the editor Alana Alexander for useful comments and advice on the manuscript.
Open access funding provided by Eidgenossische Technische Hochschule Zurich.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Katalin
full_name: Csilléry, Katalin
last_name: Csilléry
citation:
ama: Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 2022;22(8):2941-2955.
doi:10.1111/1755-0998.13676
apa: Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess
whether standard population genetic theory holds in the presence of spatio-temporal
heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676
chicago: Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to
Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal
Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley,
2022. https://doi.org/10.1111/1755-0998.13676.
ieee: E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether
standard population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley,
pp. 2941–2955, 2022.
ista: Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 22(8), 2941–2955.
mla: Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic
Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.”
Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55,
doi:10.1111/1755-0998.13676.
short: E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022)
2941–2955.
date_created: 2022-07-24T22:01:43Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-03T12:11:01Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13676
ec_funded: 1
external_id:
isi:
- '000825873600001'
file:
- access_level: open_access
checksum: 3102e203e77b884bffffdbe8e548da88
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:11:23Z
date_updated: 2023-02-02T08:11:23Z
file_id: '12477'
file_name: 2022_MolecularEcologyRes_Szep.pdf
file_size: 6431779
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:11:23Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2941-2955
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
issn:
- 1755-098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using gridCoal to assess whether standard population genetic theory holds in
the presence of spatio-temporal heterogeneity in population size
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2022'
...
---
_id: '11648'
abstract:
- lang: eng
text: 'Progress in structural membrane biology has been significantly accelerated
by the ongoing ''Resolution Revolution'' in cryo electron microscopy (cryo-EM).
In particular, structure determination by single particle analysis has evolved
into the most powerful method for atomic model building of multisubunit membrane
protein complexes. This has created an ever increasing demand in cryo-EM machine
time, which to satisfy is in need of new and affordable cryo electron microscopes.
Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the
structure determination by single particle analysis of three different multisubunit
membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus
elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella
enterica.'
acknowledgement: "Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan
Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project
for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative
Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266
to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and
C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows
(20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from
Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer
project and also would like to thank Hideki Shigematsu for critical reading of the
manuscript. And we are indebted to the two anonymous reviewers who helped us to
improve our manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Jun-ichi
full_name: Kishikawa, Jun-ichi
last_name: Kishikawa
- first_name: Tomoko
full_name: Yamaguchi, Tomoko
last_name: Yamaguchi
- first_name: Atsuko
full_name: Nakanishi, Atsuko
last_name: Nakanishi
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Fumiaki
full_name: Makino, Fumiaki
last_name: Makino
- first_name: Tomoko
full_name: Miyata, Tomoko
last_name: Miyata
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Ken
full_name: Yokoyama, Ken
last_name: Yokoyama
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
citation:
ama: Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane
complexes with the CRYO ARM 200. Microscopy. 2022;71(5):249-261. doi:10.1093/jmicro/dfac037
apa: Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino,
F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the
CRYO ARM 200. Microscopy. Oxford University Press. https://doi.org/10.1093/jmicro/dfac037
chicago: Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi,
Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit
Membrane Complexes with the CRYO ARM 200.” Microscopy. Oxford University
Press, 2022. https://doi.org/10.1093/jmicro/dfac037.
ieee: C. Gerle et al., “Structures of multisubunit membrane complexes with
the CRYO ARM 200,” Microscopy, vol. 71, no. 5. Oxford University Press,
pp. 249–261, 2022.
ista: Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata
T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit
membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.
mla: Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with
the CRYO ARM 200.” Microscopy, vol. 71, no. 5, Oxford University Press,
2022, pp. 249–61, doi:10.1093/jmicro/dfac037.
short: C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino,
T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy
71 (2022) 249–261.
date_created: 2022-07-25T10:04:58Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:13:37Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1093/jmicro/dfac037
external_id:
isi:
- '000837950900001'
pmid:
- '35861182'
file:
- access_level: open_access
checksum: 23b51c163636bf9313f7f0818312e67e
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T08:34:48Z
date_updated: 2023-02-03T08:34:48Z
file_id: '12498'
file_name: 2022_Microscopy_Gerle.pdf
file_size: 7812696
relation: main_file
success: 1
file_date_updated: 2023-02-03T08:34:48Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '5'
keyword:
- Radiology
- Nuclear Medicine and imaging
- Instrumentation
- Structural Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 249-261
pmid: 1
publication: Microscopy
publication_identifier:
eissn:
- 2050-5701
issn:
- 2050-5698
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structures of multisubunit membrane complexes with the CRYO ARM 200
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: 71
year: '2022'
...
---
_id: '11653'
abstract:
- lang: eng
text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual
lineages of parthenogenetic females, which produce rare males at low frequencies.
Although they are known to have ZW chromosomes, these are not well characterized,
and it is unclear whether they are shared across the clade. Furthermore, the underlying
genetic architecture of the transmission of asexuality, which can occur when rare
males mate with closely related sexual females, is not well understood. We produced
a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized
in detail the pair of sex chromosomes of this species. We combined this new assembly
with short-read genomic data for the sexual species A. sp. Kazakhstan and several
asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization
of sex-chromosome evolution across the genus. We identified a small differentiated
region of the ZW pair that is shared by all sexual and asexual lineages, supporting
the shared ancestry of the sex chromosomes. We also inferred that recombination
suppression has spread to larger sections of the chromosome independently in the
American and Eurasian lineages. Finally, we took advantage of a rare male, which
we backcrossed to sexual females, to explore the genetic basis of asexuality.
Our results suggest that parthenogenesis is likely partly controlled by a locus
on the Z chromosome, highlighting the interplay between sex determination and
asexuality.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653
apa: Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022,
“ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653
chicago: Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022,
‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.
ieee: M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute
of Science and Technology Austria, 2022.
ista: Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW
sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.
mla: Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW
Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”
Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.
short: M.N. Elkrewi, (2022).
contributor:
- first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
last_name: Khauratovich
- first_name: Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
- first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
last_name: Sax
- first_name: Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
- first_name: Francisco
last_name: 'Hontoria '
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2022-07-26T11:01:47Z
date_published: 2022-08-05T00:00:00Z
date_updated: 2024-02-21T12:35:53Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:11653
file:
- access_level: open_access
checksum: 5f1d7c6d7ab5375ed2564521432bed0c
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2022-07-26T12:37:52Z
date_updated: 2022-08-08T22:30:04Z
description: |
The folder contains the following datasets (fasta files, and text files):
Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan
male draft assembly
Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana
Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and
A. parthenogenetica females and rare male.
Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window
Sup. Dataset 5: FASTA file with candidate W scaffolds
Sup. Dataset 6: Candidate W-derived transcripts and alignments
Sup. Dataset 7: Gene expression with genomic location
Sup. Dataset 8: VCF for asexual female and rare male
Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)
Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using
A. sp. Kazakhstan as the reference), and inferred ancestry
Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their
locations in the Artemia sinica male genome.
embargo: 2022-08-07
file_id: '11655'
file_name: Data.zip
file_size: 2209382998
relation: main_file
title: Supplementary Datasets
file_date_updated: 2022-08-08T22:30:04Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: used_in_publication
status: public
status: public
title: Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution
and contagious parthenogenesis in Artemia brine shrimp"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11658'
abstract:
- lang: eng
text: The depth of a cell in an arrangement of n (non-vertical) great-spheres in
Sd is the number of great-spheres that pass above the cell. We prove Euler-type
relations, which imply extensions of the classic Dehn–Sommerville relations for
convex polytopes to sublevel sets of the depth function, and we use the relations
to extend the expressions for the number of faces of neighborly polytopes to the
number of cells of levels in neighborly arrangements.
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.
article_processing_charge: No
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
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements:
Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings
on Mathematics.'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications.
Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz
Zentrum für Informatik.'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics. Schloss
Dagstuhl - Leibniz Zentrum für Informatik, n.d.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth
in arrangements: Dehn–Sommerville–Euler relations with applications,” Leibniz
International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz Zentrum
für Informatik.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in
arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International
Proceedings on Mathematics.'
mla: 'Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics, Schloss
Dagstuhl - Leibniz Zentrum für Informatik.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz
International Proceedings on Mathematics (n.d.).
date_created: 2022-07-27T09:27:34Z
date_published: 2022-07-27T00:00:00Z
date_updated: 2022-07-28T07:57:48Z
day: '27'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: b2f511e8b1cae5f1892b0cdec341acac
content_type: application/pdf
creator: scultrer
date_created: 2022-07-27T09:25:53Z
date_updated: 2022-07-27T09:25:53Z
file_id: '11659'
file_name: D-S-E.pdf
file_size: 639266
relation: main_file
file_date_updated: 2022-07-27T09:25:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Leibniz International Proceedings on Mathematics
publication_status: submitted
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
status: public
title: 'Depth in arrangements: Dehn–Sommerville–Euler relations with applications'
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
year: '2022'
...
---
_id: '11660'
abstract:
- lang: eng
text: 'We characterize critical points of 1-dimensional maps paired in persistent
homology geometrically and this way get elementary proofs of theorems about the
symmetry of persistence diagrams and the variation of such maps. In particular,
we identify branching points and endpoints of networks as the sole source of asymmetry
and relate the cycle basis in persistent homology with a version of the stable
marriage problem. Our analysis provides the foundations of fast algorithms for
maintaining collections of interrelated sorted lists together with their persistence
diagrams. '
acknowledgement: 'This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. '
alternative_title:
- LIPIcs
article_processing_charge: No
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. A window to
the persistence of 1D maps. I: Geometric characterization of critical point pairs.
LIPIcs.'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization
of critical point pairs. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik.'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization
of Critical Point Pairs.” LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, n.d.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A
window to the persistence of 1D maps. I: Geometric characterization of critical
point pairs,” LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window
to the persistence of 1D maps. I: Geometric characterization of critical point
pairs. LIPIcs.'
mla: 'Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric
Characterization of Critical Point Pairs.” LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs
(n.d.).
date_created: 2022-07-27T09:31:15Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2022-07-28T08:05:34Z
day: '25'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: 95903f9d1649e8e437a967b6f2f64730
content_type: application/pdf
creator: scultrer
date_created: 2022-07-27T09:30:30Z
date_updated: 2022-07-27T09:30:30Z
file_id: '11661'
file_name: window 1.pdf
file_size: 564836
relation: main_file
file_date_updated: 2022-07-27T09:30:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: LIPIcs
publication_status: submitted
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
status: public
title: 'A window to the persistence of 1D maps. I: Geometric characterization of critical
point pairs'
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
year: '2022'
...
---
_id: '11686'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After
nearly six years during which wMel was observed only at low frequencies in PE,
corresponding to an apparent equilibrium between immigration and selection, wMel
rose to fixation by 2018. Using analytic approximations and statistical analyses,
we demonstrate that the observed fixation of wMel at PE is consistent with both
stochastic transition past an unstable threshold frequency and deterministic transformation
produced by steady immigration at a rate just above the threshold required for
deterministic invasion. The indeterminacy results from a delicate balance of parameters
needed to produce the delayed transition observed. Our analyses suggest that once
Wolbachia transinfections are established locally through systematic introductions,
stochastic “threshold crossing” is likely to only minimally enhance spatial spread,
providing a local ratchet that slightly – but systematically – aids area-wide
transformation of disease-vector populations in heterogeneous landscapes.
acknowledgement: 'Bill and Melinda Gates Foundation, Award: OPP1180815'
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control.
2022. doi:10.25338/B81931'
apa: 'Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why
did the Wolbachia transinfection cross the road? Drift, deterministic dynamics
and disease control. Dryad. https://doi.org/10.25338/B81931'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.'
ieee: 'M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the
Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease
control.” Dryad, 2022.'
ista: 'Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control,
Dryad, 10.25338/B81931.'
mla: 'Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control. Dryad, 2022, doi:10.25338/B81931.'
short: M. Turelli, N.H. Barton, (2022).
date_created: 2022-07-29T06:45:41Z
date_published: 2022-01-06T00:00:00Z
date_updated: 2023-08-02T13:50:08Z
day: '06'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.25338/B81931
keyword:
- Biological sciences
main_file_link:
- open_access: '1'
url: https://doi.org/10.25338/B81931
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '10604'
relation: used_in_publication
status: public
status: public
title: 'Wolbachia frequency data from: Why did the Wolbachia transinfection cross
the road? Drift, deterministic dynamics and disease control'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '11695'
abstract:
- lang: eng
text: 'Data underlying the figures in the publication "The chemistry of Cu3N and
Cu3PdN nanocrystals" '
article_processing_charge: No
author:
- first_name: Mahsa
full_name: Parvizian, Mahsa
last_name: Parvizian
- first_name: Alejandra
full_name: Duran Balsa, Alejandra
last_name: Duran Balsa
- first_name: Rohan
full_name: Pokratath, Rohan
last_name: Pokratath
- first_name: Curran
full_name: Kalha, Curran
last_name: Kalha
- first_name: Seungho
full_name: Lee, Seungho
last_name: Lee
- first_name: Dietger
full_name: Van den Eynden, Dietger
last_name: Van den Eynden
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Anna
full_name: Regoutz, Anna
last_name: Regoutz
- first_name: Jonathan
full_name: De Roo, Jonathan
last_name: De Roo
citation:
ama: Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of
Cu3N and Cu3PdN nanocrystals.” 2022. doi:10.5281/ZENODO.6542908
apa: Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den
Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.”
Zenodo. https://doi.org/10.5281/ZENODO.6542908
chicago: Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha,
Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan
De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022.
https://doi.org/10.5281/ZENODO.6542908.
ieee: M. Parvizian et al., “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’”
Zenodo, 2022.
ista: Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D,
Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN
nanocrystals’, Zenodo, 10.5281/ZENODO.6542908.
mla: Parvizian, Mahsa, et al. Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”
Zenodo, 2022, doi:10.5281/ZENODO.6542908.
short: M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den
Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).
date_created: 2022-07-29T09:31:13Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2023-08-03T07:19:12Z
day: '12'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.5281/ZENODO.6542908
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.6542908
month: '05'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '11451'
relation: used_in_publication
status: public
status: public
title: Data for "The chemistry of Cu3N and Cu3PdN nanocrystals"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '11700'
abstract:
- lang: eng
text: This paper contains two contributions in the study of optimal transport on
metric graphs. Firstly, we prove a Benamou–Brenier formula for the Wasserstein
distance, which establishes the equivalence of static and dynamical optimal transport.
Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov
equations can be formulated as gradient flow of the free energy in the Wasserstein
space of probability measures. The proofs of these results are based on careful
regularisation arguments to circumvent some of the difficulties arising in metric
graphs, namely, branching of geodesics and the failure of semi-convexity of entropy
functionals in the Wasserstein space.
acknowledgement: "ME acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG),
Grant SFB 1283/2 2021 – 317210226. DF and JM were supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 716117). JM also acknowledges support by the Austrian Science
Fund (FWF), Project SFB F65. The work of DM was partially supported by the Deutsche
Forschungsgemeinschaft\r\n(DFG), Grant 397230547. This article is based upon work
from COST Action\r\n18232 MAT-DYN-NET, supported by COST (European Cooperation in
Science\r\nand Technology), www.cost.eu. We wish to thank Martin Burger and Jan-Frederik\r\nPietschmann
for useful discussions. We are grateful to the anonymous referees for\r\ntheir careful
reading and useful suggestions."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthias
full_name: Erbar, Matthias
last_name: Erbar
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Delio
full_name: Mugnolo, Delio
last_name: Mugnolo
citation:
ama: Erbar M, Forkert DL, Maas J, Mugnolo D. Gradient flow formulation of diffusion
equations in the Wasserstein space over a metric graph. Networks and Heterogeneous
Media. 2022;17(5):687-717. doi:10.3934/nhm.2022023
apa: Erbar, M., Forkert, D. L., Maas, J., & Mugnolo, D. (2022). Gradient flow
formulation of diffusion equations in the Wasserstein space over a metric graph.
Networks and Heterogeneous Media. American Institute of Mathematical Sciences.
https://doi.org/10.3934/nhm.2022023
chicago: Erbar, Matthias, Dominik L Forkert, Jan Maas, and Delio Mugnolo. “Gradient
Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric
Graph.” Networks and Heterogeneous Media. American Institute of Mathematical
Sciences, 2022. https://doi.org/10.3934/nhm.2022023.
ieee: M. Erbar, D. L. Forkert, J. Maas, and D. Mugnolo, “Gradient flow formulation
of diffusion equations in the Wasserstein space over a metric graph,” Networks
and Heterogeneous Media, vol. 17, no. 5. American Institute of Mathematical
Sciences, pp. 687–717, 2022.
ista: Erbar M, Forkert DL, Maas J, Mugnolo D. 2022. Gradient flow formulation of
diffusion equations in the Wasserstein space over a metric graph. Networks and
Heterogeneous Media. 17(5), 687–717.
mla: Erbar, Matthias, et al. “Gradient Flow Formulation of Diffusion Equations in
the Wasserstein Space over a Metric Graph.” Networks and Heterogeneous Media,
vol. 17, no. 5, American Institute of Mathematical Sciences, 2022, pp. 687–717,
doi:10.3934/nhm.2022023.
short: M. Erbar, D.L. Forkert, J. Maas, D. Mugnolo, Networks and Heterogeneous Media
17 (2022) 687–717.
date_created: 2022-07-31T22:01:46Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:25:49Z
day: '01'
department:
- _id: JaMa
doi: 10.3934/nhm.2022023
ec_funded: 1
external_id:
arxiv:
- '2105.05677'
isi:
- '000812422100001'
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2105.05677
month: '10'
oa: 1
oa_version: Preprint
page: 687-717
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Networks and Heterogeneous Media
publication_identifier:
eissn:
- 1556-181X
issn:
- 1556-1801
publication_status: published
publisher: American Institute of Mathematical Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow formulation of diffusion equations in the Wasserstein space over
a metric graph
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2022'
...
---
_id: '11701'
abstract:
- lang: eng
text: In this paper we develop a new approach to nonlinear stochastic partial differential
equations with Gaussian noise. Our aim is to provide an abstract framework which
is applicable to a large class of SPDEs and includes many important cases of nonlinear
parabolic problems which are of quasi- or semilinear type. This first part is
on local existence and well-posedness. A second part in preparation is on blow-up
criteria and regularization. Our theory is formulated in an Lp-setting, and because
of this we can deal with nonlinearities in a very efficient way. Applications
to several concrete problems and their quasilinear variants are given. This includes
Burgers' equation, the Allen–Cahn equation, the Cahn–Hilliard equation, reaction–diffusion
equations, and the porous media equation. The interplay of the nonlinearities
and the critical spaces of initial data leads to new results and insights for
these SPDEs. The proofs are based on recent developments in maximal regularity
theory for the linearized problem for deterministic and stochastic evolution equations.
In particular, our theory can be seen as a stochastic version of the theory of
critical spaces due to Prüss–Simonett–Wilke (2018). Sharp weighted time-regularity
allow us to deal with rough initial values and obtain instantaneous regularization
results. The abstract well-posedness results are obtained by a combination of
several sophisticated splitting and truncation arguments.
acknowledgement: The second author is supported by the VIDI subsidy 639.032.427 of
the Netherlands Organisation for Scientific Research (NWO).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in
critical spaces Part I. Stochastic maximal regularity and local existence. Nonlinearity.
2022;35(8):4100-4210. doi:10.1088/1361-6544/abd613
apa: Agresti, A., & Veraar, M. (2022). Nonlinear parabolic stochastic evolution
equations in critical spaces Part I. Stochastic maximal regularity and local existence.
Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/abd613
chicago: Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution
Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.”
Nonlinearity. IOP Publishing, 2022. https://doi.org/10.1088/1361-6544/abd613.
ieee: A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations
in critical spaces Part I. Stochastic maximal regularity and local existence,”
Nonlinearity, vol. 35, no. 8. IOP Publishing, pp. 4100–4210, 2022.
ista: Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations
in critical spaces Part I. Stochastic maximal regularity and local existence.
Nonlinearity. 35(8), 4100–4210.
mla: Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution
Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.”
Nonlinearity, vol. 35, no. 8, IOP Publishing, 2022, pp. 4100–210, doi:10.1088/1361-6544/abd613.
short: A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.
date_created: 2022-07-31T22:01:47Z
date_published: 2022-08-04T00:00:00Z
date_updated: 2023-08-03T12:25:08Z
day: '04'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1088/1361-6544/abd613
external_id:
arxiv:
- '2001.00512'
isi:
- '000826695900001'
file:
- access_level: open_access
checksum: 997a4bff2dfbee3321d081328c2f1e1a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T10:39:36Z
date_updated: 2022-08-01T10:39:36Z
file_id: '11715'
file_name: 2022_Nonlinearity_Agresti.pdf
file_size: 2122096
relation: main_file
success: 1
file_date_updated: 2022-08-01T10:39:36Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '08'
oa: 1
oa_version: Published Version
page: 4100-4210
publication: Nonlinearity
publication_identifier:
eissn:
- 1361-6544
issn:
- 0951-7715
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonlinear parabolic stochastic evolution equations in critical spaces Part
I. Stochastic maximal regularity and local existence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '11702'
abstract:
- lang: eng
text: When Mendel’s work was rediscovered in 1900, and extended to establish classical
genetics, it was initially seen in opposition to Darwin’s theory of evolution
by natural selection on continuous variation, as represented by the biometric
research program that was the foundation of quantitative genetics. As Fisher,
Haldane, and Wright established a century ago, Mendelian inheritance is exactly
what is needed for natural selection to work efficiently. Yet, the synthesis remains
unfinished. We do not understand why sexual reproduction and a fair meiosis predominate
in eukaryotes, or how far these are responsible for their diversity and complexity.
Moreover, although quantitative geneticists have long known that adaptive variation
is highly polygenic, and that this is essential for efficient selection, this
is only now becoming appreciated by molecular biologists—and we still do not have
a good framework for understanding polygenic variation or diffuse function.
acknowledgement: I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions
and comments.
article_number: e2122147119
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
citation:
ama: Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119
apa: Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy
of Sciences of the United States of America. Proceedings of the National Academy
of Sciences. https://doi.org/10.1073/pnas.2122147119
chicago: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.
ieee: N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30. Proceedings
of the National Academy of Sciences, 2022.
ista: Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy
of Sciences of the United States of America. 119(30), e2122147119.
mla: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30, e2122147119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.
short: N.H. Barton, Proceedings of the National Academy of Sciences of the United
States of America 119 (2022).
date_created: 2022-07-31T22:01:47Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2022-08-01T11:00:25Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2122147119
external_id:
pmid:
- '35858408'
file:
- access_level: open_access
checksum: 06c866196a8957f0c37b8a121771c885
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T10:58:28Z
date_updated: 2022-08-01T10:58:28Z
file_id: '11716'
file_name: 2022_PNAS_Barton.pdf
file_size: 848511
relation: main_file
success: 1
file_date_updated: 2022-08-01T10:58:28Z
has_accepted_license: '1'
intvolume: ' 119'
issue: '30'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The "New Synthesis"
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: 119
year: '2022'
...
---
_id: '11703'
abstract:
- lang: eng
text: Polyploidization may precipitate dramatic changes to the genome, including
chromosome rearrangements, gene loss, and changes in gene expression. In dioecious
plants, the sex-determining mechanism may also be disrupted by polyploidization,
with the potential evolution of hermaphroditism. However, while dioecy appears
to have persisted through a ploidy transition in some species, it is unknown whether
the newly formed polyploid maintained its sex-determining system uninterrupted,
or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop
a bioinformatic pipeline using RNA-sequencing data from natural populations to
demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited
its sex-determining region from one of its diploid progenitor species, M. annua,
and likely remained dioecious through the transition. The sex-determining region
of M. canariensis is smaller than that of its diploid progenitor, suggesting that
the non-recombining region of M. annua expanded subsequent to the polyploid origin
of M. canariensis. Homeologous pairs show partial sexual subfunctionalization.
We discuss the possibility that gene duplicates created by polyploidization might
contribute to resolving sexual antagonism.
acknowledgement: "JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en),
Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/)
under the European Union’s Horizon 2020 research and innovation program, grant number
715257. The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by
Aline Revel, and RNA extraction and library preparation were performed by Dessislava
Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center
for Integrative Genomics at the University of Lausanne. All other computational
analyses were performed on the server at IST Austria."
article_number: e1010226
article_processing_charge: No
article_type: original
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: John R.
full_name: Pannell, John R.
last_name: Pannell
citation:
ama: Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are
maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS
Genetics. 2022;18(7). doi:10.1371/journal.pgen.1010226
apa: Toups, M. A., Vicoso, B., & Pannell, J. R. (2022). Dioecy and chromosomal
sex determination are maintained through allopolyploid speciation in the plant
genus Mercurialis. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1010226
chicago: Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal
Sex Determination Are Maintained through Allopolyploid Speciation in the Plant
Genus Mercurialis.” PLoS Genetics. Public Library of Science, 2022. https://doi.org/10.1371/journal.pgen.1010226.
ieee: M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination
are maintained through allopolyploid speciation in the plant genus Mercurialis,”
PLoS Genetics, vol. 18, no. 7. Public Library of Science, 2022.
ista: Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination
are maintained through allopolyploid speciation in the plant genus Mercurialis.
PLoS Genetics. 18(7), e1010226.
mla: Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained
through Allopolyploid Speciation in the Plant Genus Mercurialis.” PLoS Genetics,
vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:10.1371/journal.pgen.1010226.
short: M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).
date_created: 2022-07-31T22:01:48Z
date_published: 2022-07-06T00:00:00Z
date_updated: 2023-08-03T12:17:12Z
day: '06'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1371/journal.pgen.1010226
ec_funded: 1
external_id:
isi:
- '000886643100006'
pmid:
- '35793353'
file:
- access_level: open_access
checksum: aa4c137f82635e700856c359dccfaa0a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T07:49:25Z
date_updated: 2022-08-01T07:49:25Z
file_id: '11708'
file_name: 2022_PLoSGenetics_Toups.pdf
file_size: 1620272
relation: main_file
success: 1
file_date_updated: 2022-08-01T07:49:25Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dioecy and chromosomal sex determination are maintained through allopolyploid
speciation in the plant genus Mercurialis
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: 18
year: '2022'
...
---
_id: '11704'
abstract:
- lang: eng
text: In Fall 2020, several European countries reported rapid increases in COVID-19
cases along with growing estimates of the effective reproduction rates. Such an
acceleration in epidemic spread is usually attributed to time-dependent effects,
e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc.
In this case however the acceleration occurred when counter measures such as testing
and contact tracing exceeded their capacity limit. Considering Austria as an example,
here we show that this dynamics can be captured by a time-independent, i.e. autonomous,
compartmental model that incorporates these capacity limits. In this model, the
epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting
in an increasing fraction of undetected cases that drive the effective reproduction
rate progressively higher. We demonstrate that standard models which does not
include this effect necessarily result in a systematic underestimation of the
effective reproduction rate.
article_number: e0269975
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics.
PLoS ONE. 2022;17(7). doi:10.1371/journal.pone.0269975
apa: Budanur, N. B., & Hof, B. (2022). An autonomous compartmental model for
accelerating epidemics. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0269975
chicago: Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for
Accelerating Epidemics.” PLoS ONE. Public Library of Science, 2022. https://doi.org/10.1371/journal.pone.0269975.
ieee: N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating
epidemics,” PLoS ONE, vol. 17, no. 7. Public Library of Science, 2022.
ista: Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating
epidemics. PLoS ONE. 17(7), e0269975.
mla: Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating
Epidemics.” PLoS ONE, vol. 17, no. 7, e0269975, Public Library of Science,
2022, doi:10.1371/journal.pone.0269975.
short: N.B. Budanur, B. Hof, PLoS ONE 17 (2022).
date_created: 2022-07-31T22:01:48Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2023-08-03T12:24:22Z
day: '18'
ddc:
- '510'
department:
- _id: BjHo
doi: 10.1371/journal.pone.0269975
external_id:
isi:
- '000911392100055'
file:
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checksum: 1ddd9b91e6dec31ab0e7a8433ca2d452
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creator: dernst
date_created: 2022-08-01T08:02:38Z
date_updated: 2022-08-01T08:02:38Z
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file_size: 1421256
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success: 1
file_date_updated: 2022-08-01T08:02:38Z
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intvolume: ' 17'
isi: 1
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language:
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month: '07'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
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- id: '11711'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An autonomous compartmental model for accelerating epidemics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2022'
...
---
_id: '11705'
abstract:
- lang: eng
text: 'The broad implementation of thermoelectricity requires high-performance and
low-cost materials. One possibility is employing surfactant-free solution synthesis
to produce nanopowders. We propose the strategy of functionalizing “naked” particles’
surface by inorganic molecules to control the nanostructure and, consequently,
thermoelectric performance. In particular, we use bismuth thiolates to functionalize
surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates
decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1)
carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement
and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity
reduction by small grain domains, grain boundaries and nanostructuration. Overall,
the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average
z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed
SnTe.'
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by Electron Microscopy Facility (EMF)
and the Nanofabrication Facility (NNF). This work was financially supported by IST
Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF
“Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N).
Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation
program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks
the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO
Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S.
and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is
supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706)
and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported
by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat
de Catalunya.
article_number: e202207002
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Spadaro, Maria
last_name: Spadaro
- first_name: Kristopher M.
full_name: Koskela, Kristopher M.
last_name: Koskela
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Richard L.
full_name: Brutchey, Richard L.
last_name: Brutchey
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free
particles: A strategy to tailor the properties of nanocomposites for enhanced
thermoelectric performance. Angewandte Chemie - International Edition.
2022;61(35). doi:10.1002/anie.202207002'
apa: 'Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T.,
… Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A
strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207002'
chicago: 'Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela,
Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria
Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to
Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.”
Angewandte Chemie - International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207002.'
ieee: 'C. Chang et al., “Surface functionalization of surfactant-free particles:
A strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance,” Angewandte Chemie - International Edition, vol. 61, no. 35.
Wiley, 2022.'
ista: 'Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol
J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles:
A strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance. Angewandte Chemie - International Edition. 61(35), e202207002.'
mla: 'Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles:
A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric
Performance.” Angewandte Chemie - International Edition, vol. 61, no. 35,
e202207002, Wiley, 2022, doi:10.1002/anie.202207002.'
short: C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo,
J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition
61 (2022).
date_created: 2022-07-31T22:01:48Z
date_published: 2022-08-26T00:00:00Z
date_updated: 2023-08-03T12:23:52Z
day: '26'
ddc:
- '540'
department:
- _id: MaIb
- _id: EM-Fac
doi: 10.1002/anie.202207002
ec_funded: 1
external_id:
isi:
- '000828274200001'
file:
- access_level: open_access
checksum: ad601f2b9e26e46ab4785162be58b5ed
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:01:00Z
date_updated: 2023-02-02T08:01:00Z
file_id: '12476'
file_name: 2022_AngewandteChemieInternat_Chang.pdf
file_size: 4072650
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:01:00Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '35'
language:
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month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surface functionalization of surfactant-free particles: A strategy to tailor
the properties of nanocomposites for enhanced thermoelectric performance'
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: 61
year: '2022'
...
---
_id: '11707'
abstract:
- lang: eng
text: 'In this work we introduce the graph-theoretic notion of mendability: for
each locally checkable graph problem we can define its mending radius, which captures
the idea of how far one needs to modify a partial solution in order to “patch
a hole.” We explore how mendability is connected to the existence of efficient
algorithms, especially in distributed, parallel, and fault-tolerant settings.
It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds
in the LOCAL model of distributed computing. One of the surprises is that in paths
and cycles, a converse also holds in the following sense: if a problem Π can be
solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently
solvable but that is also O(1)-mendable. We also explore the structure of the
landscape of mendability. For example, we show that in trees, the mending radius
of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs
the structure is much more diverse.'
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No 840605. This work was supported in part by the Academy of Finland, Grants 314888
and 333837. The authors would also like to thank David Harris, Neven Villani, and
the anonymous reviewers for their very helpful comments and feedback on previous
versions of this work.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alkida
full_name: Balliu, Alkida
last_name: Balliu
- first_name: Juho
full_name: Hirvonen, Juho
last_name: Hirvonen
- first_name: Darya
full_name: Melnyk, Darya
last_name: Melnyk
- first_name: Dennis
full_name: Olivetti, Dennis
last_name: Olivetti
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
citation:
ama: 'Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending.
In: Parter M, ed. International Colloquium on Structural Information and Communication
Complexity. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:10.1007/978-3-031-09993-9_1'
apa: 'Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., & Suomela,
J. (2022). Local mending. In M. Parter (Ed.), International Colloquium on Structural
Information and Communication Complexity (Vol. 13298, pp. 1–20). Paderborn,
Germany: Springer Nature. https://doi.org/10.1007/978-3-031-09993-9_1'
chicago: Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki,
and Jukka Suomela. “Local Mending.” In International Colloquium on Structural
Information and Communication Complexity, edited by Merav Parter, 13298:1–20.
LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-09993-9_1.
ieee: A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela,
“Local mending,” in International Colloquium on Structural Information and
Communication Complexity, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.
ista: 'Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local
mending. International Colloquium on Structural Information and Communication
Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol.
13298, 1–20.'
mla: Balliu, Alkida, et al. “Local Mending.” International Colloquium on Structural
Information and Communication Complexity, edited by Merav Parter, vol. 13298,
Springer Nature, 2022, pp. 1–20, doi:10.1007/978-3-031-09993-9_1.
short: A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:,
M. Parter (Ed.), International Colloquium on Structural Information and Communication
Complexity, Springer Nature, 2022, pp. 1–20.
conference:
end_date: 2022-06-29
location: Paderborn, Germany
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2022-06-27
date_created: 2022-07-31T22:01:49Z
date_published: 2022-06-25T00:00:00Z
date_updated: 2023-08-03T12:16:29Z
day: '25'
department:
- _id: DaAl
doi: 10.1007/978-3-031-09993-9_1
ec_funded: 1
editor:
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
external_id:
arxiv:
- '2102.08703'
isi:
- '000876977400001'
intvolume: ' 13298'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.08703
month: '06'
oa: 1
oa_version: Preprint
page: 1-20
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: International Colloquium on Structural Information and Communication
Complexity
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031099922'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Local mending
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13298
year: '2022'
...
---
_id: '11711'
abstract:
- lang: eng
text: Codes and data for reproducing the results of N. B. Budanur and B. Hof "An
autonomous compartmental model for accelerating epidemics"
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Budanur NB. burakbudanur/autoacc-public. 2022. doi:10.5281/ZENODO.6802720
apa: Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. https://doi.org/10.5281/ZENODO.6802720
chicago: Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6802720.
ieee: N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.
ista: Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, 10.5281/ZENODO.6802720.
mla: Budanur, Nazmi B. Burakbudanur/Autoacc-Public. Zenodo, 2022, doi:10.5281/ZENODO.6802720.
short: N.B. Budanur, (2022).
date_created: 2022-08-01T08:06:33Z
date_published: 2022-07-06T00:00:00Z
date_updated: 2023-08-03T12:24:21Z
day: '06'
ddc:
- '000'
department:
- _id: BjHo
doi: 10.5281/ZENODO.6802720
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.6802720
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '11704'
relation: used_in_publication
status: public
status: public
title: burakbudanur/autoacc-public
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '11713'
abstract:
- lang: eng
text: "Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF
toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions
at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli.
The MazEF system has been used in various biotechnology and synthetic biology
applications. In this study, we infer how ectopic mazF overexpression affects
production of heterologous proteins. To this end, we quantified the levels of
fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing
or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the
5′-untranslated region of these reporter mRNAs under the same conditions by comparing
expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless
mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression,
fluorescent proteins are translated from the canonical as well as leaderless mRNAs.
Our analysis further indicates that longer mazF overexpression generally increases
the concentration of fluorescent proteins translated from ACA-less mRNAs, however
it also substantially increases bacterial population heterogeneity. Finally, our
results suggest that the strength and duration of mazF overexpression should be
optimized for each experimental setup, to maximize the heterologous protein production
and minimize the amount of phenotypic heterogeneity in bacterial populations,
which is unfavorable in biotechnological processes."
acknowledgement: "We acknowledge the Max Perutz Labs FACS Facility together with Thomas
Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded
by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF
Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research
Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207),
to IM. Open access funding provided by the Austrian Science Fund."
article_number: '173'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Martina
full_name: Sauert, Martina
last_name: Sauert
- first_name: Tanino G.
full_name: Albanese, Tanino G.
last_name: Albanese
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression
during ectopic MazF production in Escherichia coli. BMC Research Notes.
2022;15. doi:10.1186/s13104-022-06061-9
apa: Nikolic, N., Sauert, M., Albanese, T. G., & Moll, I. (2022). Quantifying
heterologous gene expression during ectopic MazF production in Escherichia coli.
BMC Research Notes. Springer Nature. https://doi.org/10.1186/s13104-022-06061-9
chicago: Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying
Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”
BMC Research Notes. Springer Nature, 2022. https://doi.org/10.1186/s13104-022-06061-9.
ieee: N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous
gene expression during ectopic MazF production in Escherichia coli,” BMC Research
Notes, vol. 15. Springer Nature, 2022.
ista: Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene
expression during ectopic MazF production in Escherichia coli. BMC Research Notes.
15, 173.
mla: Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic
MazF Production in Escherichia Coli.” BMC Research Notes, vol. 15, 173,
Springer Nature, 2022, doi:10.1186/s13104-022-06061-9.
short: N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).
date_created: 2022-08-01T09:04:27Z
date_published: 2022-05-13T00:00:00Z
date_updated: 2022-08-01T09:27:40Z
day: '13'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1186/s13104-022-06061-9
external_id:
pmid:
- '35562780'
file:
- access_level: open_access
checksum: 008156e5340e9789f0f6d82bde4d347a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T09:24:42Z
date_updated: 2022-08-01T09:24:42Z
file_id: '11714'
file_name: 2022_BMCResearchNotes_Nikolic.pdf
file_size: 1545310
relation: main_file
success: 1
file_date_updated: 2022-08-01T09:24:42Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26956E74-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00738
name: Bacterial toxin-antitoxin systems as antiphage defense mechanisms
publication: BMC Research Notes
publication_identifier:
issn:
- 1756-0500
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13104-022-06152-7
scopus_import: '1'
status: public
title: Quantifying heterologous gene expression during ectopic MazF production in
Escherichia coli
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: 15
year: '2022'
...
---
_id: '11717'
abstract:
- lang: eng
text: "We study rigidity of rational maps that come from Newton's root finding method
for polynomials of arbitrary degrees. We establish dynamical rigidity of these
maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit
can be distinguished in combinatorial terms from all other orbits), or the orbit
of this point eventually lands in the filled-in Julia set of a polynomial-like
restriction of the original map. As a corollary, we show that the Julia sets of
Newton maps in many non-trivial cases are locally connected; in particular, every
cubic Newton map without Siegel points has locally connected Julia set.\r\nIn
the parameter space of Newton maps of arbitrary degree we obtain the following
rigidity result: any two combinatorially equivalent Newton maps are quasiconformally
conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable,
or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized
renormalization concept called “complex box mappings” for which we extend a dynamical
rigidity result by Kozlovski and van Strien so as to include irrationally indifferent
and renormalizable situations."
acknowledgement: 'We are grateful to a number of colleagues for helpful and inspiring
discussions during the time when we worked on this project, in particular Dima Dudko,
Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van
Strien. Finally, we would like to thank our dynamics research group for numerous
helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge,
Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski.
We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of
the European Research Council (ERC), as well as hospitality of Cornell University
in the spring of 2018 while much of this work was prepared. The first-named author
also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).'
article_number: '108591'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Kostiantyn
full_name: Drach, Kostiantyn
id: fe8209e2-906f-11eb-847d-950f8fc09115
last_name: Drach
orcid: 0000-0002-9156-8616
- first_name: Dierk
full_name: Schleicher, Dierk
last_name: Schleicher
citation:
ama: Drach K, Schleicher D. Rigidity of Newton dynamics. Advances in Mathematics.
2022;408(Part A). doi:10.1016/j.aim.2022.108591
apa: Drach, K., & Schleicher, D. (2022). Rigidity of Newton dynamics. Advances
in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2022.108591
chicago: Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.”
Advances in Mathematics. Elsevier, 2022. https://doi.org/10.1016/j.aim.2022.108591.
ieee: K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” Advances in
Mathematics, vol. 408, no. Part A. Elsevier, 2022.
ista: Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics.
408(Part A), 108591.
mla: Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” Advances
in Mathematics, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:10.1016/j.aim.2022.108591.
short: K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).
date_created: 2022-08-01T17:08:16Z
date_published: 2022-10-29T00:00:00Z
date_updated: 2023-08-03T12:36:07Z
day: '29'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1016/j.aim.2022.108591
ec_funded: 1
external_id:
isi:
- '000860924200005'
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- access_level: open_access
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creator: dernst
date_created: 2023-02-02T07:39:09Z
date_updated: 2023-02-02T07:39:09Z
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file_name: 2022_AdvancesMathematics_Drach.pdf
file_size: 2164036
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has_accepted_license: '1'
intvolume: ' 408'
isi: 1
issue: Part A
keyword:
- General Mathematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rigidity of Newton dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 408
year: '2022'
...