---
_id: '9929'
abstract:
- lang: eng
text: 'The evolution of assortative mating is a key part of the speciation process.
Stronger assortment, or greater divergence in mating traits, between species pairs
with overlapping ranges is commonly observed, but possible causes of this pattern
of reproductive character displacement are difficult to distinguish. We use a
multidisciplinary approach to provide a rare example where it is possible to distinguish
among hypotheses concerning the evolution of reproductive character displacement.
We build on an earlier comparative analysis that illustrated a strong pattern
of greater divergence in penis form between pairs of sister species with overlapping
ranges than between allopatric sister-species pairs, in a large clade of marine
gastropods (Littorinidae). We investigate both assortative mating and divergence
in male genitalia in one of the sister-species pairs, discriminating among three
contrasting processes each of which can generate a pattern of reproductive character
displacement: reinforcement, reproductive interference and the Templeton effect.
We demonstrate reproductive character displacement in assortative mating, but
not in genital form between this pair of sister species and use demographic models
to distinguish among the different processes. Our results support a model with
no gene flow since secondary contact and thus favour reproductive interference
as the cause of reproductive character displacement for mate choice, rather than
reinforcement. High gene flow within species argues against the Templeton effect.
Secondary contact appears to have had little impact on genital divergence.'
article_processing_charge: No
author:
- first_name: Johan
full_name: Hollander, Johan
last_name: Hollander
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Giuseppe
full_name: Bianco, Giuseppe
last_name: Bianco
- first_name: Xi
full_name: Yang, Xi
last_name: Yang
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Ludovic
full_name: Duvaux, Ludovic
last_name: Duvaux
- first_name: David G.
full_name: Reid, David G.
last_name: Reid
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative
mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5'
apa: 'Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux,
L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence
driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5'
chicago: 'Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja
M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are
Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018.
https://doi.org/10.5061/dryad.51sd2p5.'
ieee: 'J. Hollander et al., “Data from: Are assortative mating and genital
divergence driven by reinforcement?” Dryad, 2018.'
ista: 'Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid
DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence
driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.'
mla: 'Hollander, Johan, et al. Data from: Are Assortative Mating and Genital
Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5.'
short: J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux,
D.G. Reid, R.K. Butlin, (2018).
date_created: 2021-08-17T08:51:06Z
date_published: 2018-10-17T00:00:00Z
date_updated: 2024-10-21T06:02:42Z
day: '17'
department:
- _id: BeVi
doi: 10.5061/dryad.51sd2p5
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.51sd2p5
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9915'
relation: used_in_publication
status: public
status: public
title: 'Data from: Are assortative mating and genital divergence driven by reinforcement?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9930'
abstract:
- lang: eng
text: Adaptive divergence and speciation may happen despite opposition by gene flow.
Identifying the genomic basis underlying divergence with gene flow is a major
task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic
regions of high differentiation. However, not all genomic architectures potentially
underlying divergence are expected to show extreme differentiation. Here, we develop
an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns
of allele frequency change) with system-specific simulations to identify loci
inconsistent with neutral evolution. We apply this to a genome-wide SNP set from
an ideally-suited study organism, the intertidal snail Littorina saxatilis, which
shows primary divergence between ecotypes associated with different shore habitats.
We detect many SNPs with clinal patterns, most of which are consistent with neutrality.
Among non-neutral SNPs, most are located within three large putative inversions
differentiating ecotypes. Many non-neutral SNPs show relatively low levels of
differentiation. We discuss potential reasons for this pattern, including loose
linkage to selected variants, polygenic adaptation and a component of balancing
selection within populations (which may be expected for inversions). Our work
is in line with theory predicting a role for inversions in divergence, and emphasises
that genomic regions contributing to divergence may not always be accessible with
methods purely based on allele frequency differences. These conclusions call for
approaches that take spatial patterns of allele frequency change into account
in other systems.
article_processing_charge: No
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anders
full_name: Blomberg, Anders
last_name: Blomberg
- first_name: Bernhard
full_name: Mehlig, Bernhard
last_name: Mehlig
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore:
the genomic architecture underlying rapid divergence in the face of gene flow.
2018. doi:10.5061/dryad.bp25b65'
apa: 'Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova,
M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture
underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65'
chicago: 'Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson,
Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic
Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018.
https://doi.org/10.5061/dryad.bp25b65.'
ieee: 'A. M. Westram et al., “Data from: Clines on the seashore: the genomic
architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.'
ista: 'Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet
M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the
seashore: the genomic architecture underlying rapid divergence in the face of
gene flow, Dryad, 10.5061/dryad.bp25b65.'
mla: 'Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic
Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad,
2018, doi:10.5061/dryad.bp25b65.'
short: A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova,
M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).
date_created: 2021-08-17T08:58:47Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2024-10-21T06:02:42Z
day: '23'
department:
- _id: BeVi
doi: 10.5061/dryad.bp25b65
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.bp25b65
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9917'
relation: used_in_publication
status: public
status: public
title: 'Data from: Clines on the seashore: the genomic architecture underlying rapid
divergence in the face of gene flow'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '35'
abstract:
- lang: eng
text: 'We consider planning problems for graphs, Markov decision processes (MDPs),
and games on graphs. While graphs represent the most basic planning model, MDPs
represent interaction with nature and games on graphs represent interaction with
an adversarial environment. We consider two planning problems where there are
k different target sets, and the problems are as follows: (a) the coverage problem
asks whether there is a plan for each individual target set; and (b) the sequential
target reachability problem asks whether the targets can be reached in sequence.
For the coverage problem, we present a linear-time algorithm for graphs, and quadratic
conditional lower bound for MDPs and games on graphs. For the sequential target
problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm
for MDPs, and a quadratic conditional lower bound for games on graphs. Our results
with conditional lower bounds establish (i) model-separation results showing that
for the coverage problem MDPs and games on graphs are harder than graphs and for
the sequential reachability problem games on graphs are harder than MDPs and graphs;
and (ii) objective-separation results showing that for MDPs the coverage problem
is harder than the sequential target problem.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger M, Svozil A. Algorithms and conditional
lower bounds for planning problems. In: 28th International Conference on Automated
Planning and Scheduling . AAAI Press; 2018.'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M., & Svozil, A. (2018). Algorithms
and conditional lower bounds for planning problems. In 28th International Conference
on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Alexander
Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th
International Conference on Automated Planning and Scheduling . AAAI Press,
2018.
ieee: K. Chatterjee, W. Dvorák, M. Henzinger, and A. Svozil, “Algorithms and conditional
lower bounds for planning problems,” in 28th International Conference on Automated
Planning and Scheduling , Delft, Netherlands, 2018.
ista: 'Chatterjee K, Dvorák W, Henzinger M, Svozil A. 2018. Algorithms and conditional
lower bounds for planning problems. 28th International Conference on Automated
Planning and Scheduling . ICAPS: International Conference on Automated Planning
and Scheduling.'
mla: Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for
Planning Problems.” 28th International Conference on Automated Planning and
Scheduling , AAAI Press, 2018.
short: K. Chatterjee, W. Dvorák, M. Henzinger, A. Svozil, in:, 28th International
Conference on Automated Planning and Scheduling , AAAI Press, 2018.
conference:
end_date: 2018-06-29
location: Delft, Netherlands
name: 'ICAPS: International Conference on Automated Planning and Scheduling'
start_date: 2018-06-24
date_created: 2018-12-11T11:44:17Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2025-07-10T11:52:30Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1804.07031'
isi:
- '000492986200007'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07031
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: '28th International Conference on Automated Planning and Scheduling '
publication_status: published
publisher: AAAI Press
publist_id: '8020'
quality_controlled: '1'
related_material:
record:
- id: '9293'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Algorithms and conditional lower bounds for planning problems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '36'
abstract:
- lang: eng
text: Wheat (Triticum ssp.) is one of the most important human food sources. However,
this crop is very sensitive to temperature changes. Specifically, processes during
wheat leaf, flower, and seed development and photosynthesis, which all contribute
to the yield of this crop, are affected by high temperature. While this has to
some extent been investigated on physiological, developmental, and molecular levels,
very little is known about early signalling events associated with an increase
in temperature. Phosphorylation-mediated signalling mechanisms, which are quick
and dynamic, are associated with plant growth and development, also under abiotic
stress conditions. Therefore, we probed the impact of a short-term and mild increase
in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822
(containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites)
were identified in leaf and spikelet samples, respectively. Following statistical
analysis, the resulting data set provides the scientific community with a first
large-scale plant phosphoproteome under the control of higher ambient temperature.
This community resource on the high temperature-mediated wheat phosphoproteome
will be valuable for future studies. Our analyses also revealed a core set of
common proteins between leaf and spikelet, suggesting some level of conserved
regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion
of phosphoforms, which probably impacts protein activity.
acknowledgement: TZ is supported by a grant from the Chinese Scholarship Council.
article_processing_charge: No
author:
- first_name: Lam
full_name: Vu, Lam
last_name: Vu
- first_name: Tingting
full_name: Zhu, Tingting
last_name: Zhu
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Brigitte
full_name: Van De Cotte, Brigitte
last_name: Van De Cotte
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
citation:
ama: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced
changes in the wheat phosphoproteome reveal temperature-regulated interconversion
of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624.
doi:10.1093/jxb/ery204
apa: Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet,
I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms. Journal of Experimental Botany. Oxford
University Press. https://doi.org/10.1093/jxb/ery204
chicago: Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert,
and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal
Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental
Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.
ieee: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet,
“Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms,” Journal of Experimental Botany, vol.
69, no. 19. Oxford University Press, pp. 4609–4624, 2018.
ista: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced
changes in the wheat phosphoproteome reveal temperature-regulated interconversion
of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.
mla: Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal
Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental
Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.
short: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal
of Experimental Botany 69 (2018) 4609–4624.
date_created: 2018-12-11T11:44:17Z
date_published: 2018-08-31T00:00:00Z
date_updated: 2023-09-19T10:00:46Z
day: '31'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1093/jxb/ery204
external_id:
isi:
- '000443568700010'
file:
- access_level: open_access
checksum: 34cb0a1611588b75bd6f4913fb4e30f1
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:47:51Z
date_updated: 2020-07-14T12:46:13Z
file_id: '5741'
file_name: 2018_JournalExperimBotany_Vu.pdf
file_size: 3359316
relation: main_file
file_date_updated: 2020-07-14T12:46:13Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
issue: '19'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 4609 - 4624
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '8019'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms
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: 69
year: '2018'
...
---
_id: '37'
abstract:
- lang: eng
text: Developmental processes are inherently dynamic and understanding them requires
quantitative measurements of gene and protein expression levels in space and time.
While live imaging is a powerful approach for obtaining such data, it is still
a challenge to apply it over long periods of time to large tissues, such as the
embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression
and signaling activity patterns in this organ can be studied by collecting tissue
sections at different developmental stages. In combination with immunohistochemistry,
this allows for measuring the levels of multiple developmental regulators in a
quantitative manner with high spatiotemporal resolution. The mean protein expression
levels over time, as well as embryo-to-embryo variability can be analyzed. A key
aspect of the approach is the ability to compare protein levels across different
samples. This requires a number of considerations in sample preparation, imaging
and data analysis. Here we present a protocol for obtaining time course data of
dorsoventral expression patterns from mouse and chick neural tube in the first
3 days of neural tube development. The described workflow starts from embryo dissection
and ends with a processed dataset. Software scripts for data analysis are included.
The protocol is adaptable and instructions that allow the user to modify different
steps are provided. Thus, the procedure can be altered for analysis of time-lapse
images and applied to systems other than the neural tube.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: 'Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling
profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863.
MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4'
apa: Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and
morphogen signaling profiles in the growing neural tube. In Morphogen Gradients
(Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4
chicago: Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients
, 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.
ieee: M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube,” in Morphogen Gradients ,
vol. 1863, Springer Nature, 2018, pp. 47–63.
ista: 'Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen
signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods
in Molecular Biology, vol. 1863, 47–63.'
mla: Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and
Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients
, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.
short: M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018,
pp. 47–63.
date_created: 2018-12-11T11:44:17Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2025-04-14T07:27:29Z
day: '16'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1007/978-1-4939-8772-6_4
ec_funded: 1
file:
- access_level: open_access
checksum: 2a97d0649fdcfcf1bdca7c8ad1dce71b
content_type: application/pdf
creator: dernst
date_created: 2020-10-13T14:20:37Z
date_updated: 2020-10-13T14:20:37Z
file_id: '8656'
file_name: 2018_MIMB_Zagorski.pdf
file_size: 4906815
relation: main_file
success: 1
file_date_updated: 2020-10-13T14:20:37Z
has_accepted_license: '1'
intvolume: ' 1863'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 47 - 63
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: 'Morphogen Gradients '
publication_identifier:
isbn:
- 978-1-4939-8771-9
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
publist_id: '8018'
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Measuring dorsoventral pattern and morphogen signaling profiles in the growing
neural tube
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1863
year: '2018'
...
---
_id: '38'
abstract:
- lang: eng
text: 'Genomes of closely-related species or populations often display localized
regions of enhanced relative sequence divergence, termed genomic islands. It has
been proposed that these islands arise through selective sweeps and/or barriers
to gene flow. Here, we genetically dissect a genomic island that controls flower
color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum
and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid
zone. We show that selective sweeps likely raised relative divergence at two tightly-linked
MYB-like transcription factors, leading to distinct flower patterns in the two
subspecies. The two patterns provide alternate floral guides and create a strong
barrier to gene flow where populations come into contact. This barrier affects
the selected flower color genes and tightlylinked loci, but does not extend outside
of this domain, allowing gene flow to lower relative divergence for the rest of
the chromosome. Thus, both selective sweeps and barriers to gene flow play a role
in shaping genomic islands: sweeps cause elevation in relative divergence, while
heterogeneous gene flow flattens the surrounding "sea," making the island of divergence
stand out. By showing how selective sweeps establish alternative adaptive phenotypes
that lead to barriers to gene flow, our study sheds light on possible mechanisms
leading to reproductive isolation and speciation.'
acknowledgement: ' ERC Grant 201252 (to N.H.B.)'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Annabel
full_name: Whitley, Annabel
last_name: Whitley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Joane
full_name: Elleouet, Joane
last_name: Elleouet
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Alexandra B
full_name: Rebocho, Alexandra B
last_name: Rebocho
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic
islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115
apa: Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L.,
… Coen, E. (2018). Selection and gene flow shape genomic islands that control
floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115
chicago: Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman,
Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands
That Control Floral Guides.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1801832115.
ieee: H. Tavares et al., “Selection and gene flow shape genomic islands that
control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences,
pp. 11006–11011, 2018.
ista: Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J,
Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection
and gene flow shape genomic islands that control floral guides. PNAS. 115(43),
11006–11011.
mla: Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control
Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018,
pp. 11006–11, doi:10.1073/pnas.1801832115.
short: H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J.
Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton,
E. Coen, PNAS 115 (2018) 11006–11011.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2025-07-10T11:52:32Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.1801832115
external_id:
isi:
- '000448040500065'
pmid:
- '30297406'
file:
- access_level: open_access
checksum: d2305d0cc81dbbe4c1c677d64ad6f6d1
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:44:03Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5683'
file_name: 11006.full.pdf
file_size: 1911302
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '43'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 11006 - 11011
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '8017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection and gene flow shape genomic islands that control floral guides
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '384'
abstract:
- lang: eng
text: Can orthologous proteins differ in terms of their ability to be secreted?
To answer this question, we investigated the distribution of signal peptides within
the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons
revealed a large number of signal peptide gain and loss events, in which signal
peptides emerge or disappear in the course of evolution. Signal peptide losses
prevail over gains, an effect which is especially pronounced in the transition
from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate
decline in the number of signal peptide-containing proteins in endosymbionts cannot
be explained by the overall reduction of their genomes. Signal peptides can be
gained and lost either by acquisition/elimination of the corresponding N-terminal
regions or by gradual accumulation of mutations. The evolutionary dynamics of
signal peptides in bacterial proteins represents a powerful mechanism of functional
diversification.
acknowledgement: "his work was supported by the Deutsche Forschungsgemeinschaft (grant
\ number FR 1411/9-1). This work was supported by the German Research Foundation
(DFG) and the Technical University of Munich within the fund- ing programme Open
Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont
status of the organisms and Michael Galperin for\r\nuseful comments. T"
article_processing_charge: No
author:
- first_name: Peter
full_name: Hönigschmid, Peter
last_name: Hönigschmid
- first_name: Nadya
full_name: Bykova, Nadya
last_name: Bykova
- first_name: René
full_name: Schneider, René
last_name: Schneider
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Dmitrij
full_name: Frishman, Dmitrij
last_name: Frishman
citation:
ama: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay
between symbiotic relationships and patterns of signal peptide gain and loss.
Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049
apa: Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D.
(2018). Evolutionary interplay between symbiotic relationships and patterns of
signal peptide gain and loss. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evy049
chicago: Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij
Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns
of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford
University Press, 2018. https://doi.org/10.1093/gbe/evy049.
ieee: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University
Press, pp. 928–938, 2018.
ista: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss. Genome Biology and Evolution. 10(3), 928–938.
mla: Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships
and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution,
vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.
short: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome
Biology and Evolution 10 (2018) 928–938.
date_created: 2018-12-11T11:46:10Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:56:52Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1093/gbe/evy049
external_id:
isi:
- '000429483700022'
file:
- access_level: open_access
checksum: 458a7c2c2e79528567edfeb0f326cbe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:07Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4667'
file_name: IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf
file_size: 691602
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 928 - 938
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7445'
pubrep_id: '999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interplay between symbiotic relationships and patterns of signal
peptide gain and loss
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: 10
year: '2018'
...
---
_id: '39'
abstract:
- lang: eng
text: We study how a block of genome with a large number of weakly selected loci
introgresses under directional selection into a genetically homogeneous population.
We derive exact expressions for the expected rate of growth of any fragment of
the introduced block during the initial phase of introgression, and show that
the growth rate of a single-locus variant is largely insensitive to its own additive
effect, but depends instead on the combined effect of all loci within a characteristic
linkage scale. The expected growth rate of a fragment is highly correlated with
its long-term introgression probability in populations of moderate size, and can
hence identify variants that are likely to introgress across replicate populations.
We clarify how the introgression probability of an individual variant is determined
by the interplay between hitchhiking with relatively large fragments during the
early phase of introgression and selection on fine-scale variation within these,
which at longer times results in differential introgression probabilities for
beneficial and deleterious loci within successful fragments. By simulating individuals,
we also investigate how introgression probabilities at individual loci depend
on the variance of fitness effects, the net fitness of the introduced block, and
the size of the recipient population, and how this shapes the net advance under
selection. Our work suggests that even highly replicable substitutions may be
associated with a range of selective effects, which makes it challenging to fine
map the causal loci that underlie polygenic adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- 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: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic
selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429
apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under
linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429
chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression
under Linked, Polygenic Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301429.
ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked,
polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America,
pp. 1411–1427, 2018.
ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked,
polygenic selection. Genetics. 210(4), 1411–1427.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under
Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society
of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.
short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-04T00:00:00Z
date_updated: 2025-07-10T11:52:33Z
day: '04'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301429
external_id:
isi:
- '000452315900021'
intvolume: ' 210'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/379578v1
month: '12'
oa: 1
oa_version: Preprint
page: 1411-1427
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Replicability of introgression under linked, polygenic selection
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 210
year: '2018'
...
---
_id: '394'
abstract:
- lang: eng
text: 'The valley pseudospin in monolayer transition metal dichalcogenides (TMDs)
has been proposed as a new way to manipulate information in various optoelectronic
devices. This relies on a large valley polarization that remains stable over long
time scales (hundreds of nanoseconds). However, time-resolved measurements report
valley lifetimes of only a few picoseconds. This has been attributed to mechanisms
such as phonon-mediated intervalley scattering and a precession of the valley
pseudospin through electron-hole exchange. Here we use transient spin grating
to directly measure the valley depolarization lifetime in monolayer MoSe2. We
find a fast valley decay rate that scales linearly with the excitation density
at different temperatures. This establishes the presence of strong exciton-exciton
Coulomb exchange interactions enhancing the valley depolarization. Our work highlights
the microscopic processes inhibiting the efficient use of the exciton valley pseudospin
in monolayer TMDs. '
arxiv: 1
author:
- first_name: Fahad
full_name: Mahmood, Fahad
last_name: Mahmood
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: Yi
full_name: Lee, Yi
last_name: Lee
- first_name: Jing
full_name: Kong, Jing
last_name: Kong
- first_name: Nuh
full_name: Gedik, Nuh
last_name: Gedik
citation:
ama: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton
interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters.
2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953
apa: Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation
of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2.
Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953
chicago: Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik.
“Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in
Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.
ieee: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of
exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,”
Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.
ista: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton
interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1),
223–228.
mla: Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated
Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1,
American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953.
short: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018)
223–228.
date_created: 2018-12-11T11:46:13Z
date_published: 2018-01-10T00:00:00Z
date_updated: 2021-01-12T07:53:20Z
day: '10'
doi: 10.1021/acs.nanolett.7b03953
extern: '1'
external_id:
arxiv:
- '1712.07925'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.07925
month: '01'
oa: 1
oa_version: Submitted Version
page: 223 - 228
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '7435'
quality_controlled: '1'
status: public
title: Observation of exciton-exciton interaction mediated valley Depolarization in
Monolayer MoSe2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2018'
...
---
_id: '397'
abstract:
- lang: eng
text: 'Concurrent sets with range query operations are highly desirable in applications
such as in-memory databases. However, few set implementations offer range queries.
Known techniques for augmenting data structures with range queries (or operations
that can be used to build range queries) have numerous problems that limit their
usefulness. For example, they impose high overhead or rely heavily on garbage
collection. In this work, we show how to augment data structures with highly efficient
range queries, without relying on garbage collection. We identify a property of
epoch-based memory reclamation algorithms that makes them ideal for implementing
range queries, and produce three algorithms, which use locks, transactional memory
and lock-free techniques, respectively. Our algorithms are applicable to more
data structures than previous work, and are shown to be highly efficient on a
large scale Intel system. '
alternative_title:
- PPoPP
article_processing_charge: No
author:
- first_name: Maya
full_name: Arbel Raviv, Maya
last_name: Arbel Raviv
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
citation:
ama: 'Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient
range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489'
apa: 'Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation
for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles
and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489'
chicago: Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation
for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.
ieee: 'M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient
range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming,
Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.'
ista: 'Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient
range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP,
vol. 53, 14–27.'
mla: Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation
for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.
short: M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.
conference:
end_date: 2018-02-28
location: Vienna, Austria
name: 'PPoPP: Principles and Practice of Parallel Programming'
start_date: 2018-02-24
date_created: 2018-12-11T11:46:14Z
date_published: 2018-02-10T00:00:00Z
date_updated: 2023-09-11T14:10:25Z
day: '10'
department:
- _id: DaAl
doi: 10.1145/3178487.3178489
external_id:
isi:
- '000446161100002'
intvolume: ' 53'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 14 - 27
publication_identifier:
isbn:
- 978-1-4503-4982-6
publication_status: published
publisher: ACM
publist_id: '7430'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Harnessing epoch-based reclamation for efficient range queries
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 53
year: '2018'
...
---
_id: '398'
abstract:
- lang: eng
text: 'Objective: To report long-term results after Pipeline Embolization Device
(PED) implantation, characterize complex and standard aneurysms comprehensively,
and introduce a modified flow disruption scale. Methods: We retrospectively reviewed
a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs.
Aneurysm complexity was assessed using our proposed classification. Immediate
angiographic results were analyzed using previously published grading scales and
our novel flow disruption scale. Results: According to our new definition, 46
(78%) aneurysms were classified as complex. Most PED interventions were performed
in the paraophthalmic and cavernous internal carotid artery segments. Excellent
neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients.
Our data showed low permanent procedure-related mortality (0%) and morbidity (3%)
rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total
obliteration in a further 14%. Complete obliteration after deployment of a single
PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale
was an independent predictor of aneurysm occlusion in a multivariable analysis.
All aneurysms with a high flow disruption grade showed complete occlusion at follow-up
regardless of PED number or aneurysm complexity. Conclusions: Treatment with the
PED should be recognized as a primary management strategy for a highly selected
cohort with predominantly complex intracranial aneurysms. We further show that
a priori assessment of aneurysm complexity and our new postinterventional angiographic
flow disruption scale predict occlusion probability and may help to determine
the adequate number of per-aneurysm devices.'
article_processing_charge: No
author:
- first_name: Philippe
full_name: Dodier, Philippe
last_name: Dodier
- first_name: Josa
full_name: Frischer, Josa
last_name: Frischer
- first_name: Wei
full_name: Wang, Wei
last_name: Wang
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Ammar
full_name: Mallouhi, Ammar
last_name: Mallouhi
- first_name: Wolfgang
full_name: Serles, Wolfgang
last_name: Serles
- first_name: Andreas
full_name: Gruber, Andreas
last_name: Gruber
- first_name: Engelbert
full_name: Knosp, Engelbert
last_name: Knosp
- first_name: Gerhard
full_name: Bavinzski, Gerhard
last_name: Bavinzski
citation:
ama: Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic
factor after flow diverter treatment long term experience with the pipeline embolization
device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096
apa: Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W.,
… Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096
chicago: Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi,
Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate
Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term
Experience with the Pipeline Embolization Device.” World Neurosurgery.
Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.
ieee: P. Dodier et al., “Immediate flow disruption as a prognostic factor
after flow diverter treatment long term experience with the pipeline embolization
device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.
ista: Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A,
Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. 13, e568–e578.
mla: Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor
after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization
Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.
short: P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A.
Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:12:33Z
day: '01'
department:
- _id: BeBi
doi: 10.1016/j.wneu.2018.02.096
external_id:
isi:
- '000432942700070'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: e568-e578
publication: World Neurosurgery
publication_status: published
publisher: Elsevier
publist_id: '7431'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Immediate flow disruption as a prognostic factor after flow diverter treatment
long term experience with the pipeline embolization device
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '399'
abstract:
- lang: eng
text: Following an earlier calculation in 3D, we calculate the 2D critical temperature
of a dilute, translation-invariant Bose gas using a variational formulation of
the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This
provides the first analytical calculation of the Kosterlitz-Thouless transition
temperature that includes the constant in the logarithm.
acknowledgement: We thank Robert Seiringer and Daniel Ueltschi for bringing the issue
of the change in critical temperature to our attention. We also thank the Erwin
Schrödinger Institute (all authors) and the Department of Mathematics, University
of Copenhagen (MN) for the hospitality during the period this work was carried out.
We gratefully acknowledge the financial support by the European Unions Seventh Framework
Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR)
as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant
No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430
and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).
article_number: '10007'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature
of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1).
doi:10.1209/0295-5075/121/10007
apa: Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of
the critical temperature of a dilute Bose gas in the Bogoliubov approximation.
EPL. IOP Publishing. https://doi.org/10.1209/0295-5075/121/10007
chicago: Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of
the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.”
EPL. IOP Publishing, 2018. https://doi.org/10.1209/0295-5075/121/10007.
ieee: M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical
temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL,
vol. 121, no. 1. IOP Publishing, 2018.
ista: Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature
of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.
mla: Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of
a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no.
1, 10007, IOP Publishing, 2018, doi:10.1209/0295-5075/121/10007.
short: M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).
date_created: 2018-12-11T11:46:15Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T08:26:14Z
day: '01'
department:
- _id: RoSe
doi: 10.1209/0295-5075/121/10007
external_id:
arxiv:
- '1706.01822'
isi:
- '000460003000003'
intvolume: ' 121'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.01822
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: EPL
publication_status: published
publisher: IOP Publishing
publist_id: '7432'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov
approximation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '4'
abstract:
- lang: eng
text: We present a data-driven technique to instantly predict how fluid flows around
various three-dimensional objects. Such simulation is useful for computational
fabrication and engineering, but is usually computationally expensive since it
requires solving the Navier-Stokes equation for many time steps. To accelerate
the process, we propose a machine learning framework which predicts aerodynamic
forces and velocity and pressure fields given a threedimensional shape input.
Handling detailed free-form three-dimensional shapes in a data-driven framework
is challenging because machine learning approaches usually require a consistent
parametrization of input and output. We present a novel PolyCube maps-based parametrization
that can be computed for three-dimensional shapes at interactive rates. This allows
us to efficiently learn the nonlinear response of the flow using a Gaussian process
regression. We demonstrate the effectiveness of our approach for the interactive
design and optimization of a car body.
article_number: '89'
article_processing_charge: No
author:
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic
design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325
apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325
chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for
Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.
ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive
aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.
ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. 37(4), 89.
mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive
Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018,
doi:10.1145/3197517.3201325.
short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:06Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2025-04-14T07:28:55Z
day: '04'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201325
ec_funded: 1
external_id:
isi:
- '000448185000050'
file:
- access_level: open_access
checksum: 7a2243668f215821bc6aecad0320079a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5216'
file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf
file_size: 22803163
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8053'
pubrep_id: '1049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/
scopus_import: '1'
status: public
title: Learning three-dimensional flow for interactive aerodynamic design
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '40'
abstract:
- lang: eng
text: Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences
of the introgression of an insecticide resistance allele into a mosquito population.
Linked alleles initially increased, but many of these later declined. It is hard
to determine whether this decline was due to counter‐selection, rather than simply
to chance.
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The consequences of an introgression event. Molecular Ecology.
2018;27(24):4973-4975. doi:10.1111/mec.14950
apa: Barton, N. H. (2018). The consequences of an introgression event. Molecular
Ecology. Wiley. https://doi.org/10.1111/mec.14950
chicago: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular
Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.
ieee: N. H. Barton, “The consequences of an introgression event,” Molecular Ecology,
vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.
ista: Barton NH. 2018. The consequences of an introgression event. Molecular Ecology.
27(24), 4973–4975.
mla: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular
Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.
short: N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.
corr_author: '1'
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2025-07-10T11:52:34Z
day: '31'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.14950
external_id:
isi:
- '000454600500001'
pmid:
- '30599087'
file:
- access_level: open_access
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-19T06:54:46Z
date_updated: 2020-07-14T12:46:22Z
file_id: '6652'
file_name: 2018_MolecularEcology_BartonNick.pdf
file_size: 295452
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4973-4975
pmid: 1
publication: Molecular Ecology
publication_identifier:
issn:
- 1365-294X
publication_status: published
publisher: Wiley
publist_id: '8014'
quality_controlled: '1'
related_material:
record:
- id: '9805'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The consequences of an introgression event
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2018'
...
---
_id: '400'
abstract:
- lang: eng
text: We consider the two-dimensional BCS functional with a radial pair interaction.
We show that the translational symmetry is not broken in a certain temperature
interval below the critical temperature. In the case of vanishing angular momentum,
our results carry over to the three-dimensional case.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Alissa
full_name: Geisinge, Alissa
last_name: Geisinge
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Michael
full_name: Loss, Michael
last_name: Loss
citation:
ama: Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry
in the BCS model with radial pair interaction. Annales Henri Poincare.
2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7
apa: Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence
of translational symmetry in the BCS model with radial pair interaction. Annales
Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7
chicago: Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss.
“Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.”
Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.
ieee: A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational
symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare,
vol. 19, no. 5. Springer, pp. 1507–1527, 2018.
ista: Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational
symmetry in the BCS model with radial pair interaction. Annales Henri Poincare.
19(5), 1507–1527.
mla: Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS
Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no.
5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.
short: A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018)
1507–1527.
corr_author: '1'
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2025-04-14T07:26:53Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00023-018-0665-7
ec_funded: 1
external_id:
isi:
- '000429799900008'
file:
- access_level: open_access
checksum: 04d2c9bd7cbf3ca1d7acaaf4e7dca3e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:47Z
date_updated: 2020-07-14T12:46:22Z
file_id: '4966'
file_name: IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf
file_size: 582680
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1507 - 1527
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_status: published
publisher: Springer
publist_id: '7429'
pubrep_id: '1011'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistence of translational symmetry in the BCS model with radial pair interaction
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: 19
year: '2018'
...
---
_id: '401'
abstract:
- lang: eng
text: The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells,
oscillates spontaneously in a wide variety of systems. Although much of the signal
cascade regulating myosin activity has been characterized, the origin of such
oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation
in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension,
but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase.
Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial
actomyosin cortex, and dynamically maintained by a self-activation loop reliant
on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin
phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling
Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic
biochemical oscillator at the core of myosin II regulatory network, shedding light
on the spatio-temporal dynamics of force generation.
article_number: '1210'
article_processing_charge: No
author:
- first_name: Xiang
full_name: Qin, Xiang
last_name: Qin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Thomas
full_name: Mangeat, Thomas
last_name: Mangeat
- first_name: Chang
full_name: Liu, Chang
last_name: Liu
- first_name: Pralay
full_name: Majumder, Pralay
last_name: Majumder
- first_name: Jjiaying
full_name: Liu, Jjiaying
last_name: Liu
- first_name: Valerie
full_name: Choesmel Cadamuro, Valerie
last_name: Choesmel Cadamuro
- first_name: Jocelyn
full_name: Mcdonald, Jocelyn
last_name: Mcdonald
- first_name: Yinyao
full_name: Liu, Yinyao
last_name: Liu
- first_name: Bin
full_name: Yi, Bin
last_name: Yi
- first_name: Xiaobo
full_name: Wang, Xiaobo
last_name: Wang
citation:
ama: Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal
myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5
apa: Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang,
X. (2018). A biochemical network controlling basal myosin oscillation. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5
chicago: Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder,
Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling
Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group,
2018. https://doi.org/10.1038/s41467-018-03574-5.
ieee: X. Qin et al., “A biochemical network controlling basal myosin oscillation,”
Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.
ista: Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro
V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal
myosin oscillation. Nature Communications. 9(1), 1210.
mla: Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.”
Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018,
doi:10.1038/s41467-018-03574-5.
short: X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel
Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).
date_created: 2018-12-11T11:46:16Z
date_published: 2018-03-23T00:00:00Z
date_updated: 2023-09-08T11:41:45Z
day: '23'
ddc:
- '539'
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-018-03574-5
external_id:
isi:
- '000428165400009'
file:
- access_level: open_access
checksum: 87a427bc2e8724be3dd22a4efdd21a33
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:45Z
date_updated: 2020-07-14T12:46:22Z
file_id: '4902'
file_name: IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf
file_size: 3780491
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '7427'
pubrep_id: '996'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A biochemical network controlling basal myosin oscillation
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: '403'
abstract:
- lang: eng
text: The ability to adapt growth and development to temperature variations is crucial
to generate plant varieties resilient to predicted temperature changes. However,
the mechanisms underlying plant response to progressive increases in temperature
have just started to be elucidated. Here, we report that the Cyclin-dependent
Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade
that transduces changes in ambient temperature into differential expression of
the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced
in a temperature-dependent manner. We found that this process is partly dependent
on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN
L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1
transcripts correlates with ambient temperature and possibly with different expression
levels of the associated protein isoforms. Both CDKG1 alternative transcripts
are necessary to fully complement the expression of ATU2AF65A across the temperature
range. Our data support a previously unidentified temperature-dependent mechanism
based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1.
We propose that changes in ambient temperature affect the relative abundance of
CDKG1 transcripts and this in turn translates into differential CDKG1 protein
expression coordinating the alternative splicing of ATU2AF65A. This article is
protected by copyright. All rights reserved.
acknowledgement: CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1).
NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and
Research and the City of Vienna. AB and AF were supported by the Austrian Science
Fund (FWF) [DK W1207; SFB RNAreg F43-P10]
article_processing_charge: No
author:
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Candida
full_name: Nibau, Candida
last_name: Nibau
- first_name: Armin
full_name: Fuchs, Armin
last_name: Fuchs
- first_name: Despoina
full_name: Dadarou, Despoina
last_name: Dadarou
- first_name: Andrea
full_name: Barta, Andrea
last_name: Barta
- first_name: John
full_name: Doonan, John
last_name: Doonan
citation:
ama: Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent
kinase G group defines a thermo‐sensitive alternative splicing circuit modulating
the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022.
doi:10.1111/tpj.13914
apa: Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan,
J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative
splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The
Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914
chicago: Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea
Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive
Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF
65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.
ieee: N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The
cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing
circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal,
vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.
ista: Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent
kinase G group defines a thermo‐sensitive alternative splicing circuit modulating
the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.
mla: Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive
Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF
65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.
short: N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant
Journal 94 (2018) 1010–1022.
corr_author: '1'
date_created: 2018-12-11T11:46:17Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2024-10-09T20:58:42Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1111/tpj.13914
external_id:
isi:
- '000434365500008'
file:
- access_level: open_access
checksum: d9d3ad3215ac0e581731443fca312266
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T11:40:54Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5934'
file_name: 2018_PlantJourn_Cavallari.pdf
file_size: 1543354
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 94'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1010 - 1022
publication: The Plant Journal
publication_status: published
publisher: Wiley
publist_id: '7426'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative
splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A
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: 94
year: '2018'
...
---
_id: '404'
abstract:
- lang: eng
text: "We construct martingale solutions to stochastic thin-film equations by introducing
a (spatial) semidiscretization and establishing convergence. The discrete scheme
allows for variants of the energy and entropy estimates in the continuous setting
as long as the discrete energy does not exceed certain threshold values depending
on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy
paths constant in time, arbitrary moments of coupled energy/entropy functionals
can be controlled. Having established Hölder regularity of approximate solutions,
the convergence proof is then based on compactness arguments---in particular on
Jakubowski's generalization of Skorokhod's theorem---weak convergence methods,
and recent tools on martingale convergence.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Günther
full_name: Grün, Günther
last_name: Grün
citation:
ama: Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796
apa: Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic
thin-film equations. SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796
chicago: Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to
Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.
ieee: J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic
thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no.
1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.
ista: Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.
mla: Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic
Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no.
1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.
short: J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.
corr_author: '1'
date_created: 2018-12-11T11:46:17Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2024-10-09T20:58:25Z
day: '30'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1137/16M1098796
external_id:
isi:
- '000426630900015'
file:
- access_level: open_access
checksum: 89a8eae7c52bb356c04f52b44bff4b5a
content_type: application/pdf
creator: dernst
date_created: 2019-11-07T12:20:25Z
date_updated: 2020-07-14T12:46:22Z
file_id: '6992'
file_name: 2018_SIAM_Fischer.pdf
file_size: 557338
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 411 - 455
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7425'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Existence of positive solutions to stochastic thin-film equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '406'
abstract:
- lang: eng
text: 'Recent developments in automated tracking allow uninterrupted, high-resolution
recording of animal trajectories, sometimes coupled with the identification of
stereotyped changes of body pose or other behaviors of interest. Analysis and
interpretation of such data represents a challenge: the timing of animal behaviors
may be stochastic and modulated by kinematic variables, by the interaction with
the environment or with the conspecifics within the animal group, and dependent
on internal cognitive or behavioral state of the individual. Existing models for
collective motion typically fail to incorporate the discrete, stochastic, and
internal-state-dependent aspects of behavior, while models focusing on individual
animal behavior typically ignore the spatial aspects of the problem. Here we propose
a probabilistic modeling framework to address this gap. Each animal can switch
stochastically between different behavioral states, with each state resulting
in a possibly different law of motion through space. Switching rates for behavioral
transitions can depend in a very general way, which we seek to identify from data,
on the effects of the environment as well as the interaction between the animals.
We represent the switching dynamics as a Generalized Linear Model and show that:
(i) forward simulation of multiple interacting animals is possible using a variant
of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly,
the maximum likelihood inference of switching rate functions is tractably solvable
by gradient descent; (iii) model selection can be used to identify factors that
modulate behavioral state switching and to appropriately adjust model complexity
to data. To illustrate our framework, we apply it to two synthetic models of animal
motion and to real zebrafish tracking data. '
acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012
(GT, ES).
article_processing_charge: Yes
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models
of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Probabilistic models of individual and collective animal behavior. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0193049
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS
One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic
models of individual and collective animal behavior,” PLoS One, vol. 13,
no. 3. Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic
models of individual and collective animal behavior. PLoS One. 13(3).
mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective
Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science,
2018, doi:10.1371/journal.pone.0193049.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13
(2018).
corr_author: '1'
date_created: 2018-12-11T11:46:18Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '07'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049
external_id:
isi:
- '000426896800032'
file:
- access_level: open_access
checksum: 684229493db75b43e98a46cd922da497
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:43Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5165'
file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf
file_size: 6887358
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7423'
pubrep_id: '995'
quality_controlled: '1'
related_material:
record:
- id: '9831'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Probabilistic models of individual and collective animal behavior
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: 13
year: '2018'
...
---
_id: '407'
abstract:
- lang: eng
text: Isoprenoid cytokinins play a number of crucial roles in the regulation of
plant growth and development. To study cytokinin receptor properties in plants,
we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine
(N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2
or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels
included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B
(RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5).
All prepared compounds were screened for affinity for the Arabidopsis thaliana
cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels
to iP via the linkers mostly disrupted binding to the receptor, several fluorescent
derivatives interacted well. For this reason, three derivatives, two rhodamine
B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction
with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that
the three derivatives were able to activate transcription of cytokinin response
regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled
cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently
labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and
4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative
controls (19, 20 and 29, respectively) were used for in planta staining experiments
in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy.
acknowledgement: "This work was supported by the Ministry of Education Youth and Sports,
Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural
Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S
and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank
Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical
assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis
of some 2D NMR spectral data. \r\n"
article_processing_charge: No
author:
- first_name: Karolina
full_name: Kubiasová, Karolina
last_name: Kubiasová
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Jaroslav
full_name: Nisler, Jaroslav
last_name: Nisler
- first_name: Martin
full_name: Hönig, Martin
last_name: Hönig
- first_name: Alexandra
full_name: Husičková, Alexandra
last_name: Husičková
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
- first_name: Zuzana
full_name: Pěkná, Zuzana
last_name: Pěkná
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Lucie
full_name: Plíhalová, Lucie
last_name: Plíhalová
citation:
ama: Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently
labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015
apa: Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L.,
… Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled
isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015
chicago: Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra
Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception
of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier,
2018. https://doi.org/10.1016/j.phytochem.2018.02.015.
ieee: K. Kubiasová et al., “Design, synthesis and perception of fluorescently
labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp.
1–11, 2018.
ista: Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová
O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis
and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry.
150, 1–11.
mla: Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently
Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018,
pp. 1–11, doi:10.1016/j.phytochem.2018.02.015.
short: K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná,
O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry
150 (2018) 1–11.
date_created: 2018-12-11T11:46:18Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-11T12:53:11Z
day: '01'
department:
- _id: EvBe
doi: 10.1016/j.phytochem.2018.02.015
external_id:
isi:
- '000435623400001'
intvolume: ' 150'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 1-11
publication: Phytochemistry
publication_status: published
publisher: Elsevier
publist_id: '7422'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2018'
...