---
_id: '438'
abstract:
- lang: eng
text: The MazF toxin sequence-specifically cleaves single-stranded RNA upon various
stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin
module in Escherichia coli. Although autoregulation of mazEF expression through
the MazE antitoxin-dependent transcriptional repression has been biochemically
characterized, less is known about post-transcriptional autoregulation, as well
as how both of these autoregulatory features affect growth of single cells during
conditions that promote MazF production. Here, we demonstrate post-transcriptional
autoregulation of mazF expression dynamics by MazF cleaving its own transcript.
Single-cell analyses of bacterial populations during ectopic MazF production indicated
that two-level autoregulation of mazEF expression influences cell-to-cell growth
rate heterogeneity. The increase in growth rate heterogeneity is governed by the
MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both
autoregulatory features grant rapid exit from the stress caused by mazF overexpression.
Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads
to increased temporal variability in length of individual cells during ectopic
mazF overexpression, as explained by a stochastic model indicating that mazEF
mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Alexandra
full_name: Vandervelde, Alexandra
last_name: Vandervelde
- first_name: Tanino
full_name: Albanese, Tanino
last_name: Albanese
- first_name: Lendert
full_name: Gelens, Lendert
last_name: Gelens
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation
of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic
Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079
apa: Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &
Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity
in bacterial populations. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gky079
chicago: Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese,
Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies
Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research.
Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.
ieee: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I.
Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University
Press, pp. 2918–2931, 2018.
ista: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018.
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations. Nucleic Acids Research. 46(6), 2918–2931.
mla: Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth
Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46,
no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.
short: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll,
Nucleic Acids Research 46 (2018) 2918–2931.
date_created: 2018-12-11T11:46:29Z
date_published: 2018-04-06T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '06'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/nar/gky079
external_id:
isi:
- '000429009500021'
file:
- access_level: open_access
checksum: 3ff4f545c27e11a4cd20ccb30778793e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5151'
file_name: IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf
file_size: 5027978
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2918-2931
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
pubrep_id: '971'
quality_controlled: '1'
related_material:
record:
- id: '5569'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2018'
...
---
_id: '131'
abstract:
- lang: eng
text: 'XY systems usually show chromosome-wide compensation of X-linked genes, while
in many ZW systems, compensation is restricted to a minority of dosage-sensitive
genes. Why such differences arose is still unclear. Here, we combine comparative
genomics, transcriptomics and proteomics to obtain a complete overview of the
evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare
the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium)
and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary
strata. We use these to assess gene expression evolution following sex-linkage.
The resulting patterns suggest a reduction in expression of Z-linked genes in
females, combined with upregulation of the Z in both sexes, in line with the first
step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics
suggest that post-transcriptional mechanisms do not play a major role in balancing
the expression of Z-linked genes. '
acknowledgement: We are grateful to Lu Dabing (Soochow University, Suzhou, China)
for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette
Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for
providing optimal environment to bioinformatic analyses, and to the Vicoso lab for
comments on the manuscript.
article_number: e35684
article_processing_charge: No
article_type: original
author:
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Celine
full_name: Cosseau, Celine
last_name: Cosseau
- first_name: Sabrina
full_name: Ferré, Sabrina
last_name: Ferré
- first_name: Thomas
full_name: Quack, Thomas
last_name: Quack
- first_name: Christoph
full_name: Grevelding, Christoph
last_name: Grevelding
- first_name: Yohann
full_name: Couté, Yohann
last_name: Couté
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome
of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684
apa: Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté,
Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome
parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684
chicago: Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph
Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the
Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications,
2018. https://doi.org/10.7554/eLife.35684.
ieee: M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome
of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications,
2018.
ista: Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B.
2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife.
7, e35684.
mla: Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome
of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications,
2018, doi:10.7554/eLife.35684.
short: M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B.
Vicoso, ELife 7 (2018).
date_created: 2018-12-11T11:44:47Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '13'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.7554/eLife.35684
external_id:
isi:
- '000441388200001'
file:
- access_level: open_access
checksum: d6331d4385b1fffd6b47b45d5949d841
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T11:55:05Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5695'
file_name: 2018_eLife_Picard.pdf
file_size: 3158125
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7792'
quality_controlled: '1'
related_material:
record:
- id: '5586'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Evolution of gene dosage on the Z-chromosome of schistosome parasites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '5584'
abstract:
- lang: eng
text: "This package contains data for the publication \"Nonlinear decoding of a
complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018).
\r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion
cells that pass stability and quality criteria, recorded on the multi-electrode
array, in response to the presentation of the complex movie with many randomly
moving dark discs. The responses are represented as 648000 x 91 binary matrix,
where the first index indicates the timebin of duration 12.5 ms, and the second
index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike
in the particular time bin.\r\n(ii) README file and a graphical illustration of
the structure of the experiment, specifying how the 648000 timebins are split
into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments
are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix
of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie
frame, with time that is locked to the recorded raster. The luminance traces are
produced as described in the manuscript by filtering the raw disc movie with a
small gaussian spatial kernel. "
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Vicente
full_name: Botella-Soler, Vicente
last_name: Botella-Soler
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
apa: Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98
chicago: Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
ieee: S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina.” Institute of Science and
Technology Austria, 2018.
ista: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:98.
mla: Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian
Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.
short: S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
datarep_id: '98'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2024-02-21T13:45:26Z
day: '29'
ddc:
- '570'
department:
- _id: ChLa
- _id: GaTk
doi: 10.15479/AT:ISTA:98
file:
- access_level: open_access
checksum: 6808748837b9afbbbabc2a356ca2b88a
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:24Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5590'
file_name: IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat
file_size: 1142543971
relation: main_file
- access_level: open_access
checksum: d6d6cd07743038fe3a12352983fcf9dd
content_type: application/pdf
creator: system
date_created: 2018-12-12T13:02:25Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5591'
file_name: IST-2018-98-v1+2_ExperimentStructure.pdf
file_size: 702336
relation: main_file
- access_level: open_access
checksum: 0c9cfb4dab35bb3dc25a04395600b1c8
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5592'
file_name: IST-2018-98-v1+3_GoodLocations_area2_20x20.mat
file_size: 432
relation: main_file
- access_level: open_access
checksum: 2a83b011012e21e934b4596285b1a183
content_type: text/plain
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5593'
file_name: IST-2018-98-v1+4_README.txt
file_size: 986
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
keyword:
- retina
- decoding
- regression
- neural networks
- complex stimulus
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '292'
relation: used_in_publication
status: public
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '286'
abstract:
- lang: eng
text: 'Pedigree and sibship reconstruction are important methods in quantifying
relationships and fitness of individuals in natural populations. Current methods
employ a Markov chain-based algorithm to explore plausible possible pedigrees
iteratively. This provides accurate results, but is time-consuming. Here, we develop
a method to infer sibship and paternity relationships from half-sibling arrays
of known maternity using hierarchical clustering. Given 50 or more unlinked SNP
markers and empirically derived error rates, the method performs as well as the
widely used package Colony, but is faster by two orders of magnitude. Using simulations,
we show that the method performs well across contrasting mating scenarios, even
when samples are large. We then apply the method to open-pollinated arrays of
the snapdragon Antirrhinum majus and find evidence for a high degree of multiple
mating. Although we focus on diploid SNP data, the method does not depend on marker
type and as such has broad applications in nonmodel systems. '
acknowledgement: 'ERC, Grant/Award Number: 250152'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- 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: Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference
given known maternity via hierarchical clustering. Molecular Ecology Resources.
2018;18(5):988-999. doi:10.1111/1755-0998.12782
apa: Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity
and sibship inference given known maternity via hierarchical clustering. Molecular
Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782
chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference
of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.”
Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.
ieee: T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and
sibship inference given known maternity via hierarchical clustering,” Molecular
Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.
ista: Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship
inference given known maternity via hierarchical clustering. Molecular Ecology
Resources. 18(5), 988–999.
mla: Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference
given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources,
vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.
short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-02-21T13:45:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/1755-0998.12782
ec_funded: 1
external_id:
isi:
- '000441753000007'
intvolume: ' 18'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 988 - 999
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology Resources
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '5583'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Efficient inference of paternity and sibship inference given known maternity
via hierarchical clustering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2018'
...
---
_id: '5586'
abstract:
- lang: eng
text: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018).
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome
of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109
apa: Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on
the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109
chicago: Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.
ieee: B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the
Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute
of Science and Technology Austria, 2018.
ista: Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on
the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute
of Science and Technology Austria, 10.15479/AT:ISTA:109.
mla: Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018).
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.
short: B. Vicoso, (2018).
contributor:
- first_name: Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
datarep_id: '109'
date_created: 2018-12-12T12:31:40Z
date_published: 2018-07-24T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '24'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:109
file:
- access_level: open_access
checksum: e60b484bd6f55c08eb66a189cb72c923
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:35Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5601'
file_name: IST-2018-109-v1+1_SupplementaryMethods.zip
file_size: 11918144
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- schistosoma
- Z-chromosome
- gene expression
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '131'
relation: research_paper
status: public
status: public
title: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018)
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5583'
abstract:
- lang: eng
text: "Data and scripts are provided in support of the manuscript \"Efficient inference
of paternity and sibship inference given known maternity via hierarchical clustering\",
and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation
scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison
with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe
final script covers the analysis of half-sib arrays from wild-pollinated seed
in an Antirrhinum majus hybrid zone."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95
apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95
chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.
ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute
of Science and Technology Austria, 2018.
ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:95.
mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.
short: T. Ellis, (2018).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
datarep_id: '95'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-02-12T00:00:00Z
date_updated: 2024-02-21T13:45:01Z
day: '12'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:95
file:
- access_level: open_access
checksum: fc6aab51439f2622ba6df8632e66fd4f
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:41Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5606'
file_name: IST-2018-95-v1+1_amajus_GPS_2012.csv
file_size: 122048
relation: main_file
- access_level: open_access
checksum: 92347586ae4f8a6eb7c04354797bf314
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:42Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5607'
file_name: IST-2018-95-v1+2_offspring_SNPs_2012.csv
file_size: 235980
relation: main_file
- access_level: open_access
checksum: 3300813645a54e6c5c39f41917228354
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:43Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5608'
file_name: IST-2018-95-v1+3_parents_SNPs_2012.csv
file_size: 311712
relation: main_file
- access_level: open_access
checksum: e739fc473567fd8f39438b445fc46147
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:44Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5609'
file_name: IST-2018-95-v1+4_faps_scripts.zip
file_size: 342090
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '286'
relation: research_paper
status: public
status: public
title: Data and Python scripts supporting Python package FAPS
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5569'
abstract:
- lang: eng
text: "Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese,
Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression
underlies growth heterogeneity in bacterial populations” Nucleic Acids Research,
doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image
and data analysis by Nela Nikolic."
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
citation:
ama: Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74
apa: Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74
chicago: Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute
of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.
ieee: T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science
and Technology Austria, 2018.
ista: Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:74.
mla: Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute
of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.
short: T. Bergmiller, N. Nikolic, (2018).
datarep_id: '74'
date_created: 2018-12-12T12:31:35Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '07'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:74
file:
- access_level: open_access
checksum: 61ebb92213cfffeba3ddbaff984b81af
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:39Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5637'
file_name: IST-2018-74-v1+2_15-11-05.zip
file_size: 3558703796
relation: main_file
- access_level: open_access
checksum: bf26649af310ef6892d68576515cde6d
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:55Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5638'
file_name: IST-2018-74-v1+3_15-07-31.zip
file_size: 1830422606
relation: main_file
- access_level: open_access
checksum: 8e46eedce06f22acb2be1a9b9d3f56bd
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:11Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5639'
file_name: IST-2018-74-v1+4_Images_for_analysis.zip
file_size: 2140849248
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
keyword:
- microscopy
- microfluidics
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '7385'
related_material:
record:
- id: '438'
relation: research_paper
status: public
status: public
title: Time-lapse microscopy data
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '161'
abstract:
- lang: eng
text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
Predictive results have been obtained by flux balance analysis (FBA), by postulating
that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
of FBA to single-cell level using maximum entropy modeling, which we extend and
test experimentally. Specifically, we define for Escherichia coli metabolism a
flux distribution that yields the experimental growth rate: the model, containing
FBA as a limit, provides a better match to measured fluxes and it makes a wide
range of predictions: on flux variability, regulation, and correlations; on the
relative importance of stoichiometry vs. optimization; on scaling relations for
growth rate distributions. We validate the latter here with single-cell data at
different sub-inhibitory antibiotic concentrations. The model quantifies growth
optimization as emerging from the interplay of competitive dynamics in the population
and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Andersson Anna
full_name: Mc, Andersson Anna
last_name: Mc
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications.
2018;9(1). doi:10.1038/s41467-018-05417-9
apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018).
Statistical mechanics for metabolic networks during steady state growth. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9
chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
mechanics for metabolic networks during steady state growth,” Nature Communications,
vol. 9, no. 1. Springer Nature, 2018.
ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications. 9(1),
2988.
mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer
Nature, 2018, doi:10.1038/s41467-018-05417-9.
short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
9 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41467-018-05417-9
ec_funded: 1
external_id:
isi:
- '000440149300021'
file:
- access_level: open_access
checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:44:28Z
date_updated: 2020-07-14T12:45:06Z
file_id: '5728'
file_name: 2018_NatureComm_DeMartino.pdf
file_size: 1043205
relation: main_file
file_date_updated: 2020-07-14T12:45:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Springer Nature
publist_id: '7760'
quality_controlled: '1'
related_material:
record:
- id: '5587'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '5587'
abstract:
- lang: eng
text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E.
coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix
enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose
limited minimal medium, \r\nobtained from the soichiometric matrix by standard
linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John
ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in
a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter
of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli
catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with
the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input
the polytope of the feasible steady states of a metabolic network, \r\n(matrix
and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding
the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults
to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we
refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++
code file receives in input the polytope of the feasible steady states of a metabolic
network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point
inside and \r\nit gives in output a max entropy sampling at fixed average growth
rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov
chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli
network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:62
chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.
ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology
Austria, 2018.
ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:62.
mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
short: D. De Martino, G. Tkačik, (2018).
datarep_id: '111'
date_created: 2018-12-12T12:31:41Z
date_published: 2018-09-21T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '21'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:62
ec_funded: 1
file:
- access_level: open_access
checksum: 97992e3e8cf8544ec985a48971708726
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:13Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5641'
file_name: IST-2018-111-v1+1_CODES.zip
file_size: 14376
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- metabolic networks
- e.coli core
- maximum entropy
- monte carlo markov chain sampling
- ellipsoidal rounding
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '161'
relation: research_paper
status: public
status: public
title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE
GROWTH"
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '542'
abstract:
- lang: eng
text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a
model for autosomal segregation distortion for close to a century, but several
questions remain regarding its biology and evolutionary history. A recently published
set of population genomics resources for wild mice includes several individuals
heterozygous for the t-haplotype, which we use to characterize this selfish element
at the genomic and transcriptomic level. Our results show that large sections
of the t-haplotype have been replaced by standard homologous sequences, possibly
due to occasional events of recombination, and that this complicates the inference
of its history. As expected for a long genomic segment of very low recombination,
the t-haplotype carries an excess of fixed nonsynonymous mutations compared to
the standard chromosome. This excess is stronger for regions that have not undergone
recent recombination, suggesting that occasional gene flow between the t and the
standard chromosome may provide a mechanism to regenerate coding sequences that
have accumulated deleterious mutations. Finally, we find that t-complex genes
with altered expression largely overlap with deleted or amplified regions, and
that carrying a t-haplotype alters the testis expression of genes outside of the
t-complex, providing new leads into the pathways involved in the biology of this
segregation distorter.
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype,
a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513
apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation
patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.117.300513
chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics
Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.
ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns
of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1.
Genetics Society of America, pp. 365–375, 2018.
ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of
the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.
mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208,
no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.
short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-02-21T13:48:27Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1534/genetics.117.300513
ec_funded: 1
external_id:
isi:
- '000419356300024'
file:
- access_level: open_access
checksum: 2123845e7031a0cf043905be160f9e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:14Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5132'
file_name: IST-2018-1058-v1+1_365.full__1_.pdf
file_size: 1311661
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 365 - 375
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7274'
pubrep_id: '1058'
quality_controlled: '1'
related_material:
record:
- id: '5571'
relation: popular_science
status: public
- id: '5572'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic
driver
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '5751'
abstract:
- lang: eng
text: 'Because of the intrinsic randomness of the evolutionary process, a mutant
with a fitness advantage has some chance to be selected but no certainty. Any
experiment that searches for advantageous mutants will lose many of them due to
random drift. It is therefore of great interest to find population structures
that improve the odds of advantageous mutants. Such structures are called amplifiers
of natural selection: they increase the probability that advantageous mutants
are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous
mutants, even for very small fitness advantage. Despite intensive research over
the past decade, arbitrarily strong amplifiers have remained rare. Here we show
how to construct a large variety of them. Our amplifiers are so simple that they
could be useful in biotechnology, when optimizing biological molecules, or as
a diagnostic tool, when searching for faster dividing cells or viruses. They could
also occur in natural population structures.'
article_number: '71'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection
Using Evolutionary Graph Theory.” Communications Biology. Springer Nature,
2018. https://doi.org/10.1038/s42003-018-0078-7.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 1(1), 71.
mla: Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers
of Natural Selection Using Evolutionary Graph Theory.” Communications Biology,
vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology
1 (2018).
date_created: 2018-12-18T13:22:58Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2024-02-21T13:48:42Z
day: '14'
ddc:
- '004'
- '519'
- '576'
department:
- _id: KrCh
doi: 10.1038/s42003-018-0078-7
ec_funded: 1
external_id:
isi:
- '000461126500071'
file:
- access_level: open_access
checksum: a9db825fa3b64a51ff3de035ec973b3e
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:37:04Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5752'
file_name: 2018_CommBiology_Pavlogiannis.pdf
file_size: 1804194
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 1'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
pubrep_id: '1045'
quality_controlled: '1'
related_material:
record:
- id: '7196'
relation: part_of_dissertation
status: public
- id: '5559'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Construction of arbitrarily strong amplifiers of natural selection using evolutionary
graph theory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1
year: '2018'
...
---
_id: '5757'
abstract:
- lang: eng
text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences
of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference
genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid
sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile
S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous
polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous
divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants
were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions
with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic
sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS;
⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript
in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous
diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (#
of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total
# of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent
sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in
the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous
evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence
data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression
values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized
across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK ,
ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile
S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites,
excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all
covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with
the Eyre-Walker and Keightley method on binned data and using all variants."
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection
in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757
apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster.” Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:/5757
chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the
Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology
Austria, 2018. https://doi.org/10.15479/at:ista:/5757.
ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of
selection in Drosophila melanogaster.’” Institute of Science and Technology Austria,
2018.
ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster’, Institute of Science and Technology
Austria, 10.15479/at:ista:/5757.
mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy
of Selection in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2018, doi:10.15479/at:ista:/5757.
short: C. Fraisse, (2018).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
- first_name: Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2018-12-19T14:22:35Z
date_published: 2018-12-19T00:00:00Z
date_updated: 2024-02-21T13:59:18Z
day: '19'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/at:ista:/5757
ec_funded: 1
file:
- access_level: open_access
checksum: aed7ee9ca3f4dc07d8a66945f68e13cd
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:52Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5758'
file_name: FileS1.zip
file_size: 369837892
relation: main_file
- access_level: open_access
checksum: 3592e467b4d8206650860b612d6e12f3
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5759'
file_name: FileS2.zip
file_size: 84856909
relation: main_file
- access_level: open_access
checksum: c37ac5d5437c457338afc128c1240655
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5760'
file_name: FileS3.txt
file_size: 881133
relation: main_file
- access_level: open_access
checksum: 943dfd14da61817441e33e3e3cb8cdb9
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5761'
file_name: FileS4.txt
file_size: 883742
relation: main_file
- access_level: open_access
checksum: 1c669b6c4690ec1bbca3e2da9f566d17
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5762'
file_name: FileS5.txt
file_size: 2495437
relation: main_file
- access_level: open_access
checksum: f40f661b987ca6fb6b47f650cbbb04e6
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5763'
file_name: FileS6.txt
file_size: 15913457
relation: main_file
- access_level: open_access
checksum: 25f41e5b8a075669c6c88d4c6713bf6f
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5764'
file_name: FileS7.txt
file_size: 2584120
relation: main_file
- access_level: open_access
checksum: f6c0bd3e63e14ddf5445bd69b43a9152
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5765'
file_name: FileS8.txt
file_size: 2446059
relation: main_file
- access_level: open_access
checksum: 0fe7a58a030b11bf3b9c8ff7a7addcae
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5766'
file_name: FileS9.txt
file_size: 100737
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
keyword:
- (mal)adaptation
- pleiotropy
- selective constraint
- evo-devo
- gene expression
- Drosophila melanogaster
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6089'
relation: research_paper
status: public
status: public
title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in
Drosophila melanogaster"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '149'
abstract:
- lang: eng
text: The eigenvalue density of many large random matrices is well approximated
by a deterministic measure, the self-consistent density of states. In the present
work, we show this behaviour for several classes of random matrices. In fact,
we establish that, in each of these classes, the self-consistent density of states
approximates the eigenvalue density of the random matrix on all scales slightly
above the typical eigenvalue spacing. For large classes of random matrices, the
self-consistent density of states exhibits several universal features. We prove
that, under suitable assumptions, random Gram matrices and Hermitian random matrices
with decaying correlations have a 1/3-Hölder continuous self-consistent density
of states ρ on R, which is analytic, where it is positive, and has either a square
root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity
of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that
ρ is determined as the inverse Stieltjes transform of the normalized trace of
the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C
N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane,
a is a self-adjoint element of C N×N and S is a positivity-preserving operator
on C N×N encoding the first two moments of the random matrix. In order to analyze
a possible limit of ρ for N → ∞ and address some applications in free probability
theory, we also consider the Dyson equation on infinite dimensional von Neumann
algebras. We present two applications to random matrices. We first establish that,
under certain assumptions, large random matrices with independent entries have
a rotationally symmetric self-consistent density of states which is supported
on a centered disk in C. Moreover, it is infinitely often differentiable apart
from a jump on the boundary of this disk. Second, we show edge universality at
all regular (not necessarily extreme) spectral edges for Hermitian random matrices
with decaying correlations.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
citation:
ama: Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040
apa: Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040
chicago: Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.
ieee: J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute
of Science and Technology Austria, 2018.
ista: Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices.
Institute of Science and Technology Austria.
mla: Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.
short: J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-07-12T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '12'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:TH_1040
ec_funded: 1
file:
- access_level: open_access
checksum: d4dad55a7513f345706aaaba90cb1bb8
content_type: application/pdf
creator: dernst
date_created: 2019-04-08T13:55:20Z
date_updated: 2020-07-14T12:44:57Z
file_id: '6241'
file_name: 2018_thesis_Alt.pdf
file_size: 5801709
relation: main_file
- access_level: closed
checksum: d73fcf46300dce74c403f2b491148ab4
content_type: application/zip
creator: dernst
date_created: 2019-04-08T13:55:20Z
date_updated: 2020-07-14T12:44:57Z
file_id: '6242'
file_name: 2018_thesis_Alt_source.zip
file_size: 3802059
relation: source_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '456'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7772'
pubrep_id: '1040'
related_material:
record:
- id: '1677'
relation: part_of_dissertation
status: public
- id: '550'
relation: part_of_dissertation
status: public
- id: '6183'
relation: part_of_dissertation
status: public
- id: '566'
relation: part_of_dissertation
status: public
- id: '1010'
relation: part_of_dissertation
status: public
- id: '6240'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: Dyson equation and eigenvalue statistics of random matrices
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '415'
abstract:
- lang: eng
text: Recently it was shown that a molecule rotating in a quantum solvent can be
described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett.
118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules
possessing an additional spin-1/2 degree of freedom and study the behavior of
the system in the presence of a static magnetic field. We show that exchange of
angular momentum between the molecule and the solvent can be altered by the field,
even though the solvent itself is non-magnetic. In particular, we demonstrate
a possibility to control resonant emission of phonons with a given angular momentum
using a magnetic field.
acknowledgement: "We acknowledge insightful discussions with Giacomo Bighin, Igor
Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the
Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish
Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No. 665385.\r\n"
article_number: '104307'
article_processing_charge: No
article_type: original
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular
momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591
apa: Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent
angular momentum transfer. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.5017591
chicago: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field
on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics.
AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.
ieee: W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent
angular momentum transfer,” The Journal of Chemical Physics, vol. 148,
no. 10. AIP Publishing, 2018.
ista: Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent
angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.
mla: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on
Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics,
vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.
short: W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).
date_created: 2018-12-11T11:46:21Z
date_published: 2018-03-14T00:00:00Z
date_updated: 2024-02-28T13:01:59Z
day: '14'
department:
- _id: MiLe
doi: 10.1063/1.5017591
ec_funded: 1
external_id:
arxiv:
- '1711.09904'
isi:
- '000427517200065'
intvolume: ' 148'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.09904
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Chemical Physics
publication_status: published
publisher: AIP Publishing
publist_id: '7408'
quality_controlled: '1'
related_material:
record:
- id: '10759'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Effect of a magnetic field on molecule–solvent angular momentum transfer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 148
year: '2018'
...
---
_id: '134'
abstract:
- lang: eng
text: "The current state of the art in real-time two-dimensional water wave simulation
requires developers to choose between efficient Fourier-based methods, which lack
interactions with moving obstacles, and finite-difference or finite element methods,
which handle environmental interactions but are significantly more expensive.
This paper attempts to bridge this long-standing gap between complexity and performance,
by proposing a new wave simulation method that can faithfully simulate wave interactions
with moving obstacles in real time while simultaneously preserving minute details
and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating
2D water waves directly compute the change in height of the water surface, a strategy
which imposes limitations based on the CFL condition (fast moving waves require
small time steps) and Nyquist's limit (small wave details require closely-spaced
simulation variables). This paper proposes a novel wavelet transformation that
discretizes the liquid motion in terms of amplitude-like functions that vary over
space, frequency, and direction, effectively generalizing Fourier-based methods
to handle local interactions. Because these new variables change much more slowly
over space than the original water height function, our change of variables drastically
reduces the limitations of the CFL condition and Nyquist limit, allowing us to
simulate highly detailed water waves at very large visual resolutions. Our discretization
is amenable to fast summation and easy to parallelize. We also present basic extensions
like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue
that our discretization provides a convenient set of variables for artistic manipulation,
which we illustrate with a novel wave-painting interface."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- SIGGRAPH
article_number: '94'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Matthias
full_name: Mueller Fischer, Matthias
last_name: Mueller Fischer
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336
apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M.,
& Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3197517.3201336
chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez,
Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions
on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.
ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and
C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol.
37, no. 4. ACM, 2018.
ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.
mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics,
vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.
short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C.
Wojtan, ACM Transactions on Graphics 37 (2018).
date_created: 2018-12-11T11:44:48Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-28T13:58:51Z
day: '30'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3197517.3201336
ec_funded: 1
external_id:
isi:
- '000448185000055'
file:
- access_level: open_access
checksum: db75ebabe2ec432bf41389e614d6ef62
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:59:23Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5744'
file_name: 2018_ACM_Jeschke.pdf
file_size: 22185016
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '7789'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/
scopus_import: '1'
status: public
title: Water surface wavelets
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2018'
...
---
_id: '6339'
abstract:
- lang: eng
text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties
of quantum many-particle systems possessing a macroscopic number of degrees of
freedom. The treatment is based on a diagrammatic expansion that merges the usual
Feynman diagrams with the angular momentum diagrams known from atomic and nuclear
structure theory, thereby incorporating the non-Abelian algebra inherent to quantum
rotations. Our approach is applicable at arbitrary coupling, is free of systematic
errors and of finite-size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model; however, the method is quite general and can be applied
to a broad variety of systems in which particles exchange quantum angular momentum
with their many-body environment.
article_number: '165301'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular
momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16).
doi:10.1103/physrevlett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to angular momentum in quantum many-particle systems. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo
Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review
Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems,” Physical Review Letters,
vol. 121, no. 16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems. Physical Review Letters.
121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum
in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no.
16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-04-17T10:53:38Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:15:09Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/physrevlett.121.165301
external_id:
arxiv:
- '1803.07990'
isi:
- '000447468400008'
intvolume: ' 121'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle
systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '417'
abstract:
- lang: eng
text: 'We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular
impurities with rotational degrees of freedom interacting with a many-particle
environment. The treatment is based on the diagrammatic expansion that merges
the usual Feynman diagrams with the angular momentum diagrams known from atomic
and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent
to quantum rotations. Our approach works at arbitrary coupling, is free of systematic
errors and of finite size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model, however, the method is quite general and can be applied
to a broad variety of quantum impurities possessing angular momentum degrees of
freedom. '
article_number: '165301'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating
molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to rotating molecular impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte
Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to rotating molecular impurities,” Physical Review Letters, vol. 121, no.
16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to rotating molecular impurities. Physical Review Letters. 121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular
Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2018-12-11T11:46:22Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:14:53Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.165301
external_id:
arxiv:
- '1803.07990'
intvolume: ' 121'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '8025'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to rotating molecular impurities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '412'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which
cargoes and lipids are internalized from the plasma membrane into vesicles coated
with clathrin and adaptor proteins. CME is essential for many developmental and
physiological processes in plants, but its underlying mechanism is not well characterised
compared to that in yeast and animal systems. Here, we searched for new factors
involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification
of proteins that interact with clathrin light chain, a principal component of
the clathrin coat. Among the confirmed interactors, we found two putative homologues
of the clathrin-coat uncoating factor auxilin previously described in non-plant
systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused
an arrest of seedling growth and development. This was concomitant with inhibited
endocytosis due to blocking of clathrin recruitment after the initial step of
adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2)
loss-of-function lines did not present endocytosis-related developmental or cellular
phenotypes under normal growth conditions. This work contributes to the on-going
characterization of the endocytotic machinery in plants and provides a robust
tool for conditionally and specifically interfering with CME in A. thaliana.
acknowledgement: We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner
at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9
construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek,
Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych,
Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for
help with correcting the manuscript. This work was supported by the European Research
Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC
Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project
NPUI-LO1417.
article_processing_charge: No
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional
study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis.
The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785
apa: Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml,
J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating
factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.17.00785
chicago: Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc,
Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two
Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American
Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.
ieee: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml,
“A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant
Biologists, pp. 700–716, 2018.
ista: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A
functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis. The Plant Cell. 30(3), 700–716.
mla: Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative
Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no.
3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.
short: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml,
The Plant Cell 30 (2018) 700–716.
date_created: 2018-12-11T11:46:20Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2024-03-28T23:30:06Z
day: '09'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1105/tpc.17.00785
ec_funded: 1
external_id:
isi:
- '000429441400018'
pmid:
- '29511054'
file:
- access_level: open_access
checksum: 4e165e653b67d3f0684697f21aace5a1
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T09:12:38Z
date_updated: 2022-05-23T09:12:38Z
file_id: '11406'
file_name: 2018_PlantCell_Adamowski.pdf
file_size: 4407538
relation: main_file
success: 1
file_date_updated: 2022-05-23T09:12:38Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 700 - 716
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7417'
quality_controlled: '1'
related_material:
record:
- id: '6269'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2018'
...
---
_id: '5914'
abstract:
- lang: eng
text: With the advent of optogenetics, it became possible to change the activity
of a targeted population of neurons in a temporally controlled manner. To combine
the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics,
we have developed a closed-loop recording system that allows for the actual electrophysiological
signal to be used as a trigger for the laser light mediating the optogenetic intervention.
We have optimized the weight, size, and shape of the corresponding implant to
make it compatible with the size, force, and movements of a behaving mouse, and
we have shown that the system can efficiently block sharp wave ripple (SWR) events
using those events themselves as a trigger. To demonstrate the full potential
of the optogenetic recording system we present a pilot study addressing the contribution
of SWR events to learning in a complex behavioral task.
article_number: e0087
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
- first_name: James G.
full_name: Donnett, James G.
last_name: Donnett
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
orcid: 0000-0001-6251-1007
citation:
ama: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording
from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop
optogenetics: A technique to study the contribution of Hippocampal SWR events
to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018'
apa: 'Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K.
(2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal
SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018'
chicago: 'Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and
Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled
with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the
Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of
Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.'
ieee: 'D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode
recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal
SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience,
2018.'
ista: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording
from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop
optogenetics: A technique to study the contribution of Hippocampal SWR events
to learning. eNeuro. 5(4), e0087.'
mla: 'Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus
of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics:
A Technique to Study the Contribution of Hippocampal SWR Events to Learning.”
ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.'
short: D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).
date_created: 2019-02-03T22:59:16Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2024-03-28T23:30:10Z
day: '27'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1523/ENEURO.0087-18.2018
ec_funded: 1
external_id:
isi:
- '000443994700007'
file:
- access_level: open_access
checksum: f4915d45fc7ad4648b7b7a13fdecca01
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T12:48:36Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5921'
file_name: 2018_ENeuro_Guerrero.pdf
file_size: 3746884
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 257D4372-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2072-B27
name: Interneuron plasticity during spatial learning
publication: eNeuro
publication_status: published
publisher: Society of Neuroscience
quality_controlled: '1'
related_material:
record:
- id: '6849'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR
events to learning'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2018'
...
---
_id: '402'
abstract:
- lang: eng
text: During metastasis, malignant cells escape the primary tumor, intravasate lymphatic
vessels, and reach draining sentinel lymph nodes before they colonize distant
organs via the blood circulation. Although lymph node metastasis in cancer patients
correlates with poor prognosis, evidence is lacking as to whether and how tumor
cells enter the bloodstream via lymph nodes. To investigate this question, we
delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells
into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated
the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without
involvement of the thoracic duct. These results suggest that the lymph node blood
vessels can serve as an exit route for systemic dissemination of cancer cells
in experimental mouse models. Whether this form of tumor cell spreading occurs
in cancer patients remains to be determined.
acknowledged_ssus:
- _id: Bio
acknowledgement: "M.B. was supported by the Cell Communication in Health and Disease
graduate study program of the Austrian Science Fund (FWF) and the Medical University
of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556)
and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic
injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster
and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri
for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging,
the Sixt lab for intellectual input, M. Schunn for help with the design of the in
vivo experiments, F. Langer for technical assistance with the in vivo experiments,
the bioimaging facility of IST Austria for support, and R. Efferl for providing
the CT26 cell line."
article_processing_charge: No
article_type: original
author:
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Gabriele
full_name: Asfour, Gabriele
last_name: Asfour
- first_name: Zsuzsanna
full_name: Bagó Horváth, Zsuzsanna
last_name: Bagó Horváth
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
- first_name: Pavel
full_name: Uhrin, Pavel
last_name: Uhrin
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
citation:
ama: Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit
routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411.
doi:10.1126/science.aal3662
apa: Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G.,
… Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic
tumor cell dissemination in mice. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aal3662
chicago: Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner,
Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide
Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science.
American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.
ieee: M. Brown et al., “Lymph node blood vessels provide exit routes for
metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382.
American Association for the Advancement of Science, pp. 1408–1411, 2018.
ista: Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth
Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide
exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382),
1408–1411.
mla: Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic
Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American
Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.
short: M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z.
Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018)
1408–1411.
date_created: 2018-12-11T11:46:16Z
date_published: 2018-03-23T00:00:00Z
date_updated: 2024-03-28T23:30:09Z
day: '23'
department:
- _id: MiSi
doi: 10.1126/science.aal3662
ec_funded: 1
external_id:
isi:
- '000428043600047'
pmid:
- '29567714'
intvolume: ' 359'
isi: 1
issue: '6382'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.aal3662
month: '03'
oa: 1
oa_version: Published Version
page: 1408 - 1411
pmid: 1
project:
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7428'
quality_controlled: '1'
related_material:
record:
- id: '6947'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination
in mice
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 359
year: '2018'
...