---
_id: '5911'
abstract:
- lang: eng
text: Empirical data suggest that inversions in many species contain genes important
for intraspecific divergence and speciation, yet mechanisms of evolution remain
unclear. While genes inside an inversion are tightly linked, inversions are not
static but evolve separately from the rest of the genome by new mutations, recombination
within arrangements, and gene flux between arrangements. Inversion polymorphisms
are maintained by different processes, for example, divergent or balancing selection,
or a mix of multiple processes. Moreover, the relative roles of selection, drift,
mutation, and recombination will change over the lifetime of an inversion and
within its area of distribution. We believe inversions are central to the evolution
of many species, but we need many more data and new models to understand the complex
mechanisms involved.
article_processing_charge: No
article_type: original
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends
in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005
apa: Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving
inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005
chicago: Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving
Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.
ieee: R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,”
Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248,
2019.
ista: Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions.
Trends in Ecology and Evolution. 34(3), 239–248.
mla: Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution,
vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.
short: R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and
Evolution 34 (2019) 239–248.
date_created: 2019-02-03T22:59:15Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-24T14:29:48Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tree.2018.12.005
ec_funded: 1
external_id:
isi:
- '000459899000013'
file:
- access_level: open_access
checksum: ef24572d6ebcc1452c067e05410cc4a2
content_type: application/pdf
creator: cziletti
date_created: 2020-01-09T10:55:58Z
date_updated: 2020-07-14T12:47:13Z
file_id: '7245'
file_name: 2019_Trends_Evolution_Faria.pdf
file_size: 1946795
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 239-248
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Trends in Ecology and Evolution
publication_identifier:
issn:
- '01695347'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolving inversions
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 34
year: '2019'
...
---
_id: '439'
abstract:
- lang: eng
text: "We count points over a finite field on wild character varieties,of Riemann
surfaces for singularities with regular semisimple leading term. The new feature
in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras.
Our result leads to the conjecture that the mixed Hodge polynomials of these character
varieties agree with previously conjectured perverse Hodge polynomials of certain
twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P =
W conjecture for a suitable wild Hitchin system."
article_processing_charge: No
article_type: original
author:
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Martin
full_name: Mereb, Martin
id: 43D735EE-F248-11E8-B48F-1D18A9856A87
last_name: Mereb
- first_name: Michael
full_name: Wong, Michael
last_name: Wong
citation:
ama: Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character
varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052.
doi:10.4171/JEMS/896
apa: Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation
theory of wild character varieties. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/896
chicago: Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation
Theory of Wild Character Varieties.” Journal of the European Mathematical Society.
European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.
ieee: T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of
wild character varieties,” Journal of the European Mathematical Society,
vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.
ista: Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild
character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.
mla: Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character
Varieties.” Journal of the European Mathematical Society, vol. 21, no.
10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.
short: T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society
21 (2019) 2995–3052.
date_created: 2018-12-11T11:46:29Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-24T14:24:49Z
day: '01'
department:
- _id: TaHa
doi: 10.4171/JEMS/896
ec_funded: 1
external_id:
arxiv:
- '1604.03382'
isi:
- '000480413600002'
intvolume: ' 21'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.03382
month: '10'
oa: 1
oa_version: Preprint
page: 2995-3052
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Journal of the European Mathematical Society
publication_identifier:
eissn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society
publist_id: '7384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic and representation theory of wild character varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2019'
...
---
_id: '105'
abstract:
- lang: eng
text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar
hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease:
615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2
at 1p13.3. 4. OMIM# of the Gene(s): 102771.'
acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing
as part of health care”), a Coordination Action under FP7 (Grant Agreement Number
261469) and the European Society of Human Genetics. We acknowledge the participation
of the patients and their families in these studies, as well as the generous financial
support of the Lefroy and Handbury families. APLM was supported by an Australian
Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364).
RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.'
article_processing_charge: No
article_type: original
author:
- first_name: Ashley
full_name: Marsh, Ashley
last_name: Marsh
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Paul
full_name: Lockhart, Paul
last_name: Lockhart
- first_name: Richard
full_name: Leventer, Richard
last_name: Leventer
citation:
ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia
type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166.
doi:10.1038/s41431-018-0231-2
apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for
pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal
of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2
chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC
for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European
Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.
ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar
hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics,
vol. 27. Springer Nature, pp. 161–166, 2019.
ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar
hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics.
27, 161–166.
mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic
Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature,
2019, pp. 161–66, doi:10.1038/s41431-018-0231-2.
short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human
Genetics 27 (2019) 161–166.
date_created: 2018-12-11T11:44:39Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:28:24Z
day: '01'
department:
- _id: GaNo
doi: 10.1038/s41431-018-0231-2
external_id:
isi:
- '000454111500019'
pmid:
- '30089829'
intvolume: ' 27'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41431-018-0231-2
month: '01'
oa: 1
oa_version: Published Version
page: 161-166
pmid: 1
publication: European Journal of Human Genetics
publication_status: published
publisher: Springer Nature
publist_id: '7949'
quality_controlled: '1'
scopus_import: '1'
status: public
title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2019'
...
---
_id: '65'
abstract:
- lang: eng
text: We provide an entropy formulation for porous medium-type equations with a
stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction
is obtained in the class of entropy solutions. Our scope allows for porous medium
operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity
with exponent 1/2.
article_processing_charge: No
article_type: original
author:
- first_name: Konstantinos
full_name: Dareiotis, Konstantinos
last_name: Dareiotis
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Benjamin
full_name: Gess, Benjamin
last_name: Gess
citation:
ama: Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media
equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012
apa: Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for
stochastic porous media equations. Journal of Differential Equations. Elsevier.
https://doi.org/10.1016/j.jde.2018.09.012
chicago: Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions
for Stochastic Porous Media Equations.” Journal of Differential Equations.
Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.
ieee: K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic
porous media equations,” Journal of Differential Equations, vol. 266, no.
6. Elsevier, pp. 3732–3763, 2019.
ista: Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous
media equations. Journal of Differential Equations. 266(6), 3732–3763.
mla: Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media
Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier,
2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012.
short: K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266
(2019) 3732–3763.
date_created: 2018-12-11T11:44:26Z
date_published: 2019-03-05T00:00:00Z
date_updated: 2023-08-24T14:30:16Z
day: '5'
department:
- _id: JaMa
doi: 10.1016/j.jde.2018.09.012
external_id:
arxiv:
- '1803.06953'
isi:
- '000456332500026'
intvolume: ' 266'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1803.06953
month: '03'
oa: 1
oa_version: Preprint
page: 3732-3763
publication: Journal of Differential Equations
publication_status: published
publisher: Elsevier
publist_id: '7989'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Entropy solutions for stochastic porous media equations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 266
year: '2019'
...
---
_id: '5907'
abstract:
- lang: eng
text: Microalgae of the genus Chlorella vulgaris are candidates for the production
of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed
as protein and vitamin rich food additive. Its potential as a novel expression
system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides
(N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic
N-glycans with up to nine mannoses were the structures found in culture collection
strains as well as several commercial products. These glycans co-eluted with plant
N-glycans in the highly shape selective porous graphitic carbon chromatography.
Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural
type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as
substrate for GlcNAc-transferase I and a trace of an endogenous structure with
terminal GlcNAc was seen. The unusual more linear Man5 structure recently found
on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces
only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated
with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This
modification has so far been neither found on plant nor vertebrate N-glycans.
It’s possible immunogenicity raises concerns as to the use of C. vulgaris for
production of pharmaceutical glycoproteins.
article_number: '331'
article_processing_charge: No
author:
- first_name: Réka
full_name: Mócsai, Réka
last_name: Mócsai
- first_name: Rudolf
full_name: Figl, Rudolf
last_name: Figl
- first_name: Clemens
full_name: Troschl, Clemens
last_name: Troschl
- first_name: Richard
full_name: Strasser, Richard
last_name: Strasser
- first_name: Elisabeth
full_name: Svehla, Elisabeth
last_name: Svehla
- first_name: Markus
full_name: Windwarder, Markus
last_name: Windwarder
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Friedrich
full_name: Altmann, Friedrich
last_name: Altmann
citation:
ama: Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris
are of the oligomannosidic type but highly methylated. Scientific Reports.
2019;9(1). doi:10.1038/s41598-018-36884-1
apa: Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M.,
… Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the
oligomannosidic type but highly methylated. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/s41598-018-36884-1
chicago: Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth
Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of
the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.”
Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1.
ieee: R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are
of the oligomannosidic type but highly methylated,” Scientific Reports,
vol. 9, no. 1. Nature Publishing Group, 2019.
ista: Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A,
Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic
type but highly methylated. Scientific Reports. 9(1), 331.
mla: Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of
the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol.
9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.
short: R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A.
Thader, F. Altmann, Scientific Reports 9 (2019).
date_created: 2019-02-03T22:59:13Z
date_published: 2019-01-23T00:00:00Z
date_updated: 2023-08-24T14:33:16Z
day: '23'
ddc:
- '580'
department:
- _id: FlSc
doi: 10.1038/s41598-018-36884-1
external_id:
isi:
- '000456392400012'
file:
- access_level: open_access
checksum: 4129c7d7663d1f8a1edf8c4232372f66
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T13:10:02Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5923'
file_name: 2019_ScientificReports_Mocsai.pdf
file_size: 2124292
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type
but highly methylated
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '5908'
abstract:
- lang: eng
text: The interorganelle communication mediated by membrane contact sites (MCSs)
is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular
exchange of information between organelles and allow them to coordinate responses
to changing cellular environments. In plants, the importance of MCS components
in the responses to environmental stress has been widely established, but the
molecular mechanisms regulating interorganelle connectivity during stress still
remain opaque. In this report, we use the model plant Arabidopsis thaliana to
show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM)
connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched
ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton
in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the
accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as
a molecular signal associated with the ER–PM connectivity changes. Our study highlights
the functional conservation of EPCS components and PM phosphoinositides as modulators
of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal
regulation of ER–PM connectivity in plants.
article_processing_charge: No
article_type: original
author:
- first_name: Eunkyoung
full_name: Lee, Eunkyoung
last_name: Lee
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jessica
full_name: Pérez-Sancho, Jessica
last_name: Pérez-Sancho
- first_name: Francisco
full_name: Benitez-Fuente, Francisco
last_name: Benitez-Fuente
- first_name: Matthew
full_name: Strelau, Matthew
last_name: Strelau
- first_name: Alberto P.
full_name: Macho, Alberto P.
last_name: Macho
- first_name: Miguel A.
full_name: Botella, Miguel A.
last_name: Botella
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Abel
full_name: Rosado, Abel
last_name: Rosado
citation:
ama: Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity
via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings
of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429.
doi:10.1073/pnas.1818099116
apa: Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho,
A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated
SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1818099116
chicago: Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente,
Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado.
“Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1
Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2019. https://doi.org/10.1073/pnas.1818099116.
ieee: E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated
SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 4. National Academy
of Sciences, pp. 1420–1429, 2019.
ista: Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP,
Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity
via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings
of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.
mla: Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated
SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 4, National Academy
of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116.
short: E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P.
Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy
of Sciences of the United States of America 116 (2019) 1420–1429.
date_created: 2019-02-03T22:59:14Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-08-24T14:31:09Z
day: '22'
department:
- _id: JiFr
doi: 10.1073/pnas.1818099116
external_id:
isi:
- '000456336100050'
pmid:
- '30610176'
intvolume: ' 116'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1818099116
month: '01'
oa: 1
oa_version: Published Version
page: 1420-1429
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1
contact site expansion in Arabidopsis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 116
year: '2019'
...
---
_id: '5680'
abstract:
- lang: eng
text: Pollinators display a remarkable diversity of foraging strategies with flowering
plants, from primarily mutualistic interactions to cheating through nectar robbery.
Despite numerous studies on the effect of nectar robbing on components of plant
fitness, its contribution to reproductive isolation is unclear. We experimentally
tested the impact of different pollinator strategies in a natural hybrid zone
between two subspecies of Antirrhinum majus with alternate flower colour guides.
On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus
(magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral
visitors at different time points during the flowering season. Using long-run
camera surveys, we quantify the impact of nectar robbing on the number of flowers
visited per inflorescence and the flower probing time. We further experimentally
tested the effect of nectar robbing on female reproductive success by manipulating
the intensity of robbing. While robbing increased over time the number of legitimate
visitors tended to decrease concomitantly. We found that the number of flowers
pollinated on a focal inflorescence decreased with the number of prior robbing
events. However, in the manipulative experiment, fruit set and fruit volume did
not vary significantly between low robbing and control treatments. Our findings
challenge the idea that robbers have a negative impact on plant fitness through
female function. This study also adds to our understanding of the components of
pollinator-mediated reproductive isolation and the maintenance of Antirrhinum
hybrid zones.
article_processing_charge: No
author:
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Sandrine
full_name: Paute, Sandrine
last_name: Paute
- first_name: Christine
full_name: Lauzeral, Christine
last_name: Lauzeral
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate
pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum
majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142
apa: Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence
of legitimate pollinators and nectar robbers and the consequences for fruit set
in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis.
https://doi.org/10.1080/23818107.2018.1545142
chicago: Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral,
and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and
the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany
Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.
ieee: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of
legitimate pollinators and nectar robbers and the consequences for fruit set in
an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor
and Francis, pp. 80–92, 2019.
ista: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate
pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum
majus hybrid zone. Botany Letters. 166(1), 80–92.
mla: Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar
Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.”
Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.
short: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166
(2019) 80–92.
date_created: 2018-12-16T22:59:20Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:34:12Z
day: '01'
department:
- _id: NiBa
doi: 10.1080/23818107.2018.1545142
external_id:
isi:
- '000463802800009'
intvolume: ' 166'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 80-92
publication: Botany Letters
publication_identifier:
eissn:
- '23818115'
issn:
- '23818107'
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Prevalence of legitimate pollinators and nectar robbers and the consequences
for fruit set in an Antirrhinum majus hybrid zone
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 166
year: '2019'
...
---
_id: '5790'
abstract:
- lang: eng
text: The partial representation extension problem is a recently introduced generalization
of the recognition problem. A circle graph is an intersection graph of chords
of a circle. We study the partial representation extension problem for circle
graphs, where the input consists of a graph G and a partial representation R′
giving some predrawn chords that represent an induced subgraph of G. The question
is whether one can extend R′ to a representation R of the entire graph G, that
is, whether one can draw the remaining chords into a partially predrawn representation
to obtain a representation of G. Our main result is an O(n3) time algorithm for
partial representation extension of circle graphs, where n is the number of vertices.
To show this, we describe the structure of all representations of a circle graph
using split decomposition. This can be of independent interest.
article_processing_charge: No
article_type: original
author:
- first_name: Steven
full_name: Chaplick, Steven
last_name: Chaplick
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Pavel
full_name: Klavík, Pavel
last_name: Klavík
citation:
ama: Chaplick S, Fulek R, Klavík P. Extending partial representations of circle
graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436
apa: Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations
of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436
chicago: Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial
Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019.
https://doi.org/10.1002/jgt.22436.
ieee: S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of
circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394,
2019.
ista: Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of
circle graphs. Journal of Graph Theory. 91(4), 365–394.
mla: Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.”
Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.
short: S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.
date_created: 2018-12-30T22:59:15Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-24T14:30:43Z
day: '01'
department:
- _id: UlWa
doi: 10.1002/jgt.22436
ec_funded: 1
external_id:
arxiv:
- '1309.2399'
isi:
- '000485392800004'
intvolume: ' 91'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.2399
month: '08'
oa: 1
oa_version: Preprint
page: 365-394
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Graph Theory
publication_identifier:
issn:
- '03649024'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending partial representations of circle graphs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 91
year: '2019'
...
---
_id: '405'
abstract:
- lang: eng
text: We investigate the quantum Jensen divergences from the viewpoint of joint
convexity. It turns out that the set of the functions which generate jointly convex
quantum Jensen divergences on positive matrices coincides with the Matrix Entropy
Class which has been introduced by Chen and Tropp quite recently.
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technology Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office – NKFIH (grant
no. K124152)
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and
Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002
apa: Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear
Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002
chicago: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear
Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002.
ieee: D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra
and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.
ista: Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra
and Its Applications. 576, 67–78.
mla: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra
and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.
short: D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.
date_created: 2018-12-11T11:46:17Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-24T14:31:47Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.laa.2018.03.002
ec_funded: 1
external_id:
arxiv:
- '1712.05324'
isi:
- '000470955300005'
intvolume: ' 576'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.05324
month: '09'
oa: 1
oa_version: Preprint
page: 67-78
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Linear Algebra and Its Applications
publication_status: published
publisher: Elsevier
publist_id: '7424'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Jointly convex quantum Jensen divergences
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 576
year: '2019'
...
---
_id: '175'
abstract:
- lang: eng
text: An upper bound sieve for rational points on suitable varieties isdeveloped,
together with applications tocounting rational points in thin sets,to local solubility
in families, and to the notion of “friable” rational pointswith respect to divisors.
In the special case of quadrics, sharper estimates areobtained by developing a
version of the Selberg sieve for rational points.
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Daniel
full_name: Loughran, Daniel
last_name: Loughran
citation:
ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions
of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514
apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/7514
chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.”
Transactions of the American Mathematical Society. American Mathematical
Society, 2019. https://doi.org/10.1090/tran/7514.
ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions
of the American Mathematical Society, vol. 371, no. 8. American Mathematical
Society, pp. 5757–5785, 2019.
ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions
of the American Mathematical Society. 371(8), 5757–5785.
mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.”
Transactions of the American Mathematical Society, vol. 371, no. 8, American
Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.
short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society
371 (2019) 5757–5785.
date_created: 2018-12-11T11:45:01Z
date_published: 2019-04-15T00:00:00Z
date_updated: 2023-08-24T14:34:56Z
day: '15'
department:
- _id: TiBr
doi: 10.1090/tran/7514
external_id:
arxiv:
- '1705.01999'
isi:
- '000464034200019'
intvolume: ' 371'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.01999
month: '04'
oa: 1
oa_version: Preprint
page: 5757-5785
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- '10886850'
issn:
- '00029947'
publication_status: published
publisher: American Mathematical Society
publist_id: '7746'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sieving rational points on varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 371
year: '2019'
...
---
_id: '319'
abstract:
- lang: eng
text: We study spaces of modelled distributions with singular behaviour near the
boundary of a domain that, in the context of the theory of regularity structures,
allow one to give robust solution theories for singular stochastic PDEs with boundary
conditions. The calculus of modelled distributions established in Hairer (Invent
Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended
to this setting. We formulate and solve fixed point problems in these spaces with
a class of kernels that is sufficiently large to cover in particular the Dirichlet
and Neumann heat kernels. These results are then used to provide solution theories
for the KPZ equation with Dirichlet and Neumann boundary conditions and for the
2D generalised parabolic Anderson model with Dirichlet boundary conditions. In
the case of the KPZ equation with Neumann boundary conditions, we show that, depending
on the class of mollifiers one considers, a “boundary renormalisation” takes place.
In other words, there are situations in which a certain boundary condition is
applied to an approximation to the KPZ equation, but the limiting process is the
Hopf–Cole solution to the KPZ equation with a different boundary condition.
acknowledgement: "MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Martin
full_name: Hairer, Martin
last_name: Hairer
citation:
ama: Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability
Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1
apa: Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries.
Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1
chicago: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.”
Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.
ieee: M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability
Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.
ista: Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability
Theory and Related Fields. 173(3–4), 697–758.
mla: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.”
Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019,
pp. 697–758, doi:10.1007/s00440-018-0841-1.
short: M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019)
697–758.
date_created: 2018-12-11T11:45:48Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-24T14:38:32Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00440-018-0841-1
external_id:
isi:
- '000463613800001'
file:
- access_level: open_access
checksum: 288d16ef7291242f485a9660979486e3
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:25:24Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5722'
file_name: 2018_ProbTheory_Gerencser.pdf
file_size: 893182
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 697–758
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '7546'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Singular SPDEs in domains with boundaries
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 173
year: '2019'
...
---
_id: '429'
abstract:
- lang: eng
text: We consider real symmetric or complex hermitian random matrices with correlated
entries. We prove local laws for the resolvent and universality of the local eigenvalue
statistics in the bulk of the spectrum. The correlations have fast decay but are
otherwise of general form. The key novelty is the detailed stability analysis
of the corresponding matrix valued Dyson equation whose solution is the deterministic
limit of the resolvent.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria).\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random
matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373.
doi:10.1007/s00440-018-0835-z
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix
Dyson equation and random matrices with correlations. Probability Theory and
Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the
Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory
and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation
and random matrices with correlations,” Probability Theory and Related Fields,
vol. 173, no. 1–2. Springer, pp. 293–373, 2019.
ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation
and random matrices with correlations. Probability Theory and Related Fields.
173(1–2), 293–373.
mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random
Matrices with Correlations.” Probability Theory and Related Fields, vol.
173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
173 (2019) 293–373.
date_created: 2018-12-11T11:46:25Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-24T14:39:00Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00440-018-0835-z
ec_funded: 1
external_id:
isi:
- '000459396500007'
file:
- access_level: open_access
checksum: f9354fa5c71f9edd17132588f0dc7d01
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:12:08Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5720'
file_name: 2018_ProbTheory_Ajanki.pdf
file_size: 1201840
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: 1-2
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 293–373
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '7394'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability of the matrix Dyson equation and random matrices with correlations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 173
year: '2019'
...
---
_id: '5947'
abstract:
- lang: eng
text: Graph algorithms applied in many applications, including social networks,
communication networks, VLSI design, graphics, and several others, require dynamic
modifications - addition and removal of vertices and/or edges - in the graph.
This paper presents a novel concurrent non-blocking algorithm to implement a dynamic
unbounded directed graph in a shared-memory machine. The addition and removal
operations of vertices and edges are lock-free. For a finite sized graph, the
lookup operations are wait-free. Most significant component of the presented algorithm
is the reachability query in a concurrent graph. The reachability queries in our
algorithm are obstruction-free and thus impose minimal additional synchronization
cost over other operations. We prove that each of the data structure operations
are linearizable. We extensively evaluate a sample C/C++ implementation of the
algorithm through a number of micro-benchmarks. The experimental results show
that the proposed algorithm scales well with the number of threads and on an average
provides 5 to 7x performance improvement over a concurrent graph implementation
using coarse-grained locking.
article_processing_charge: No
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Sathya
full_name: Peri, Sathya
last_name: Peri
- first_name: Muktikanta
full_name: Sa, Muktikanta
last_name: Sa
- first_name: Nandini
full_name: Singhal, Nandini
last_name: Singhal
citation:
ama: 'Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking
unbounded graph with linearizable reachability queries. In: ACM International
Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617'
apa: 'Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical
concurrent non-blocking unbounded graph with linearizable reachability queries.
In ACM International Conference Proceeding Series (pp. 168–177). Bangalore,
India: ACM. https://doi.org/10.1145/3288599.3288617'
chicago: Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple
and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability
Queries.” In ACM International Conference Proceeding Series, 168–77. ACM,
2019. https://doi.org/10.1145/3288599.3288617.
ieee: B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent
non-blocking unbounded graph with linearizable reachability queries,” in ACM
International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.
ista: 'Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent
non-blocking unbounded graph with linearizable reachability queries. ACM International
Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking,
168–177.'
mla: Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded
Graph with Linearizable Reachability Queries.” ACM International Conference
Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.
short: B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference
Proceeding Series, ACM, 2019, pp. 168–177.
conference:
end_date: 2019-01-07
location: Bangalore, India
name: 'ICDCN: Conference on Distributed Computing and Networking'
start_date: 2019-01-04
date_created: 2019-02-10T22:59:17Z
date_published: 2019-01-04T00:00:00Z
date_updated: 2023-08-24T14:41:53Z
day: '04'
department:
- _id: DaAl
doi: 10.1145/3288599.3288617
external_id:
arxiv:
- '1809.00896'
isi:
- '000484491600019'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.00896
month: '01'
oa: 1
oa_version: Preprint
page: 168-177
publication: ACM International Conference Proceeding Series
publication_identifier:
isbn:
- '978-1-4503-6094-4 '
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: A simple and practical concurrent non-blocking unbounded graph with linearizable
reachability queries
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '5857'
abstract:
- lang: eng
text: 'A thrackle is a graph drawn in the plane so that every pair of its edges
meet exactly once: either at a common end vertex or in a proper crossing. We prove
that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are
defined similarly, except that every pair of edges that do not share a vertex
are allowed to cross an odd number of times. It is also shown that the maximum
number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1),
and that this bound is best possible for infinitely many values of n.'
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: János
full_name: Pach, János
last_name: Pach
citation:
ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics.
2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025'
apa: 'Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete
Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025'
chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.”
Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.'
ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied
Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.'
ista: 'Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied
Mathematics. 259(4), 266–231.'
mla: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete
Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.'
short: R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.
date_created: 2019-01-20T22:59:17Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-08-24T14:39:33Z
day: '30'
department:
- _id: UlWa
doi: 10.1016/j.dam.2018.12.025
external_id:
arxiv:
- '1708.08037'
isi:
- '000466061100020'
intvolume: ' 259'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08037
month: '04'
oa: 1
oa_version: Preprint
page: 266-231
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '433'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Thrackles: An improved upper bound'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 259
year: '2019'
...
---
_id: '5944'
abstract:
- lang: eng
text: Understanding the thermodynamics of the duplication process is a fundamental
step towards a comprehensive physical theory of biological systems. However, the
immense complexity of real cells obscures the fundamental tensions between energy
gradients and entropic contributions that underlie duplication. The study of synthetic,
feasible systems reproducing part of the key ingredients of living entities but
overcoming major sources of biological complexity is of great relevance to deepen
the comprehension of the fundamental thermodynamic processes underlying life and
its prevalence. In this paper an abstract—yet realistic—synthetic system made
of small synthetic protocell aggregates is studied in detail. A fundamental relation
between free energy and entropic gradients is derived for a general, non-equilibrium
scenario, setting the thermodynamic conditions for the occurrence and prevalence
of duplication phenomena. This relation sets explicitly how the energy gradients
invested in creating and maintaining structural—and eventually, functional—elements
of the system must always compensate the entropic gradients, whose contributions
come from changes in the translational, configurational, and macrostate entropies,
as well as from dissipation due to irreversible transitions. Work/energy relations
are also derived, defining lower bounds on the energy required for the duplication
event to take place. A specific example including real ternary emulsions is provided
in order to grasp the orders of magnitude involved in the problem. It is found
that the minimal work invested over the system to trigger a duplication event
is around ~ 10−13J , which results, in the case of duplication of all the vesicles
contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without
aiming to describe a truly biological process of duplication, this theoretical
contribution seeks to explicitly define and identify the key actors that participate
in it.
article_number: '9'
article_processing_charge: No
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
citation:
ama: Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell
systems. Life. 2019;9(1). doi:10.3390/life9010009
apa: Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic
protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009
chicago: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in
Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009.
ieee: B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic
protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.
ista: Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic
protocell systems. Life. 9(1), 9.
mla: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic
Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.
short: B. Corominas-Murtra, Life 9 (2019).
date_created: 2019-02-10T22:59:15Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-08-24T14:43:41Z
day: '15'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.3390/life9010009
external_id:
isi:
- '000464125500001'
file:
- access_level: open_access
checksum: 7d2322cd96ace41959909b66702d5cf4
content_type: application/pdf
creator: dernst
date_created: 2019-02-11T10:45:27Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5951'
file_name: 2019_Life_Corominas.pdf
file_size: 963454
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Life
publication_identifier:
eissn:
- '20751729'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermodynamics of duplication thresholds in synthetic protocell systems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6029'
abstract:
- lang: eng
text: Protein micropatterning has become an important tool for many biomedical applications
as well as in academic research. Current techniques that allow to reduce the feature
size of patterns below 1 μm are, however, often costly and require sophisticated
equipment. We present here a straightforward and convenient method to generate
highly condensed nanopatterns of proteins without the need for clean room facilities
or expensive equipment. Our approach is based on nanocontact printing and allows
for the fabrication of protein patterns with feature sizes of 80 nm and periodicities
down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane)
(X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle,
different proteins at various scales were printed and the pattern quality was
evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.
article_number: '655'
article_processing_charge: No
author:
- first_name: Marco
full_name: Lindner, Marco
last_name: Lindner
- first_name: Aliz
full_name: Tresztenyak, Aliz
last_name: Tresztenyak
- first_name: Gergö
full_name: Fülöp, Gergö
last_name: Fülöp
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- first_name: Adrian
full_name: Prinz, Adrian
last_name: Prinz
- first_name: Iris
full_name: Prinz, Iris
last_name: Prinz
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gerhard J.
full_name: Schütz, Gerhard J.
last_name: Schütz
- first_name: Eva
full_name: Sevcsik, Eva
last_name: Sevcsik
citation:
ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing
approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6.
doi:10.3389/fchem.2018.00655
apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., …
Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655
chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz,
Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple
Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in
Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655.
ieee: M. Lindner et al., “A fast and simple contact printing approach to
generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers
Media S.A., 2019.
ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz
GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D
protein nanopatterns. Frontiers in Chemistry. 6, 655.
mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate
2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers
Media S.A., 2019, doi:10.3389/fchem.2018.00655.
short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl,
G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).
date_created: 2019-02-17T22:59:24Z
date_published: 2019-01-24T00:00:00Z
date_updated: 2023-08-24T14:45:38Z
day: '24'
ddc:
- '540'
department:
- _id: JoDa
doi: 10.3389/fchem.2018.00655
external_id:
isi:
- '000456718000001'
file:
- access_level: open_access
checksum: 7841301d7c53b56ef873791b4b6f7b24
content_type: application/pdf
creator: dernst
date_created: 2019-02-18T15:10:34Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6039'
file_name: 2019_frontiers_Lindner.pdf
file_size: 1766820
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Frontiers in Chemistry
publication_identifier:
eissn:
- '22962646'
publication_status: published
publisher: Frontiers Media S.A.
quality_controlled: '1'
scopus_import: '1'
status: public
title: A fast and simple contact printing approach to generate 2D protein nanopatterns
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2019'
...
---
_id: '6028'
abstract:
- lang: eng
text: We give a construction allowing us to build local renormalized solutions to
general quasilinear stochastic PDEs within the theory of regularity structures,
thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking,
our construction covers quasilinear variants of all classes of equations for which
the general construction of [3, 4, 7] applies, including in particular one‐dimensional
systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less
singular and more specific case, we furthermore show that the counterterms introduced
by the renormalization procedure are given by local functionals of the solution.
The main feature of our construction is that it allows exploitation of a number
of existing results developed for the semilinear case, so that the number of additional
arguments it requires is relatively small.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Martin
full_name: Hairer, Martin
last_name: Hairer
citation:
ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications
on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816
apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular
SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816
chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear
Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley,
2019. https://doi.org/10.1002/cpa.21816.
ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,”
Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley,
pp. 1983–2005, 2019.
ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs.
Communications on Pure and Applied Mathematics. 72(9), 1983–2005.
mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular
SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9,
Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.
short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72
(2019) 1983–2005.
date_created: 2019-02-17T22:59:24Z
date_published: 2019-02-08T00:00:00Z
date_updated: 2023-08-24T14:44:31Z
day: '08'
ddc:
- '500'
department:
- _id: JaMa
doi: 10.1002/cpa.21816
external_id:
isi:
- '000475465000003'
file:
- access_level: open_access
checksum: 09aec427eb48c0f96a1cce9ff53f013b
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:25:55Z
date_updated: 2020-07-14T12:47:17Z
file_id: '7237'
file_name: 2019_Wiley_Gerencser.pdf
file_size: 381350
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 72'
isi: 1
issue: '9'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1983-2005
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A solution theory for quasilinear singular SPDEs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 72
year: '2019'
...
---
_id: '5948'
abstract:
- lang: eng
text: We study the termination problem for nondeterministic probabilistic programs.
We consider the bounded termination problem that asks whether the supremum of
the expected termination time over all schedulers is bounded. First, we show that
ranking supermartingales (RSMs) are both sound and complete for proving bounded
termination over nondeterministic probabilistic programs. For nondeterministic
probabilistic programs a previous result claimed that RSMs are not complete for
bounded termination, whereas our result corrects the previous flaw and establishes
completeness with a rigorous proof. Second, we present the first sound approach
to establish lower bounds on expected termination time through RSMs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs.
In: International Conference on Verification, Model Checking, and Abstract
Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22'
apa: 'Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic
programs. In International Conference on Verification, Model Checking, and
Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer
Nature. https://doi.org/10.1007/978-3-030-11245-5_22'
chicago: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic
Probabilistic Programs.” In International Conference on Verification, Model
Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019.
https://doi.org/10.1007/978-3-030-11245-5_22.
ieee: H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,”
in International Conference on Verification, Model Checking, and Abstract Interpretation,
Cascais, Portugal, 2019, vol. 11388, pp. 468–490.
ista: 'Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs.
International Conference on Verification, Model Checking, and Abstract Interpretation.
VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388,
468–490.'
mla: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic
Programs.” International Conference on Verification, Model Checking, and Abstract
Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22.
short: H. Fu, K. Chatterjee, in:, International Conference on Verification, Model
Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.
conference:
end_date: 2019-01-15
location: Cascais, Portugal
name: 'VMCAI: Verification, Model Checking, and Abstract Interpretation'
start_date: 2019-01-13
date_created: 2019-02-10T22:59:17Z
date_published: 2019-01-11T00:00:00Z
date_updated: 2023-08-24T14:42:22Z
day: '11'
department:
- _id: KrCh
doi: 10.1007/978-3-030-11245-5_22
external_id:
arxiv:
- '1701.02944'
isi:
- '000931943000022'
intvolume: ' 11388'
isi: 1
language:
- iso: eng
main_file_link:
- url: https://arxiv.org/abs/1701.02944
month: '01'
oa_version: Preprint
page: 468-490
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Conference on Verification, Model Checking, and Abstract
Interpretation
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Termination of nondeterministic probabilistic programs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11388
year: '2019'
...
---
_id: '5945'
abstract:
- lang: eng
text: In developing organisms, spatially prescribed cell identities are thought
to be determined by the expression levels of multiple genes. Quantitative tests
of this idea, however, require a theoretical framework capable of exposing the
rules and precision of cell specification over developmental time. We use the
gap gene network in the early fly embryo as an example to show how expression
levels of the four gap genes can be jointly decoded into an optimal specification
of position with 1% accuracy. The decoder correctly predicts, with no free parameters,
the dynamics of pair-rule expression patterns at different developmental time
points and in various mutant backgrounds. Precise cellular identities are thus
available at the earliest stages of development, contrasting the prevailing view
of positional information being slowly refined across successive layers of the
patterning network. Our results suggest that developmental enhancers closely approximate
a mathematically optimal decoding strategy.
article_processing_charge: No
article_type: original
author:
- first_name: Mariela D.
full_name: Petkova, Mariela D.
last_name: Petkova
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Eric F.
full_name: Wieschaus, Eric F.
last_name: Wieschaus
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of
cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15.
doi:10.1016/j.cell.2019.01.007
apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T.
(2019). Optimal decoding of cellular identities in a genetic network. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2019.01.007
chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus,
and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.”
Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.
ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal
decoding of cellular identities in a genetic network,” Cell, vol. 176,
no. 4. Cell Press, p. 844–855.e15, 2019.
ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding
of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.
mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic
Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019)
844–855.e15.
date_created: 2019-02-10T22:59:16Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-08-24T14:42:47Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.cell.2019.01.007
external_id:
isi:
- '000457969200015'
pmid:
- '30712870'
intvolume: ' 176'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.01.007
month: '02'
oa: 1
oa_version: Published Version
page: 844-855.e15
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Cell
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/
scopus_import: '1'
status: public
title: Optimal decoding of cellular identities in a genetic network
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 176
year: '2019'
...
---
_id: '5943'
abstract:
- lang: eng
text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow
velocity ratio is investigated experimentally for a velocity ratio range of R
∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral
analysis we characterize the Strouhal number and amplitude of the hairpin instability
as a function of R and ReD. We demonstrate that the dynamics of the hairpins is
well described by the Landau model, and, hence, that the instability occurs through
Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind
different bluff bodies. Using the Landau model, we determine the precise threshold
values of hairpin shedding. We also study the spatial dependence of this hydrodynamical
instability, which shows a global behaviour.
article_processing_charge: No
article_type: original
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Konrad
full_name: Gumowski, Konrad
last_name: Gumowski
- first_name: José Eduardo
full_name: Wesfreid, José Eduardo
last_name: Wesfreid
citation:
ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the
low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406.
doi:10.1017/jfm.2018.974
apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet
in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2018.974
chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments
on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid
Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.
ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow
in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863.
Cambridge University Press, pp. 386–406, 2019.
ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow
in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.
mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio
Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press,
2019, pp. 386–406, doi:10.1017/jfm.2018.974.
short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019)
386–406.
date_created: 2019-02-10T22:59:15Z
date_published: 2019-03-25T00:00:00Z
date_updated: 2023-08-24T14:43:13Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2018.974
ec_funded: 1
external_id:
arxiv:
- '1902.07931'
isi:
- '000526029100016'
intvolume: ' 863'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07931
month: '03'
oa: 1
oa_version: Preprint
page: 386-406
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experiments on a jet in a crossflow in the low-velocity-ratio regime
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 863
year: '2019'
...