---
_id: '6413'
abstract:
- lang: eng
text: Phase-field methods have long been used to model the flow of immiscible fluids.
Their ability to naturally capture interface topological changes is widely recognized,
but their accuracy in simulating flows of real fluids in practical geometries
is not established. We here quantitatively investigate the convergence of the
phase-field method to the sharp-interface limit with simulations of two-phase
pipe flow. We focus on core-annular flows, in which a highly viscous fluid is
lubricated by a less viscous fluid, and validate our simulations with an analytic
laminar solution, a formal linear stability analysis and also in the fully nonlinear
regime. We demonstrate the ability of the phase-field method to accurately deal
with non-rectangular geometry, strong advection, unsteady fluctuations and large
viscosity contrast. We argue that phase-field methods are very promising for quantitatively
studying moderately turbulent flows, especially at high concentrations of the
disperse phase.
article_processing_charge: No
article_type: original
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Carlos
full_name: Plana, Carlos
last_name: Plana
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular
pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027
apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field
simulation of core-annular pipe flow. International Journal of Multiphase Flow.
Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027
chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field
Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase
Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.
ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation
of core-annular pipe flow,” International Journal of Multiphase Flow, vol.
117. Elsevier, pp. 14–24, 2019.
ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of
core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.
mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International
Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.
short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of
Multiphase Flow 117 (2019) 14–24.
date_created: 2019-05-13T07:58:35Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-25T10:19:55Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.ijmultiphaseflow.2019.04.027
external_id:
arxiv:
- '1902.07351'
isi:
- '000474496000002'
intvolume: ' 117'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07351
month: '08'
oa: 1
oa_version: Preprint
page: 14-24
publication: International Journal of Multiphase Flow
publication_identifier:
issn:
- '03019322'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-field simulation of core-annular pipe flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2019'
...
---
_id: '6419'
abstract:
- lang: eng
text: Characterizing the fitness landscape, a representation of fitness for a large
set of genotypes, is key to understanding how genetic information is interpreted
to create functional organisms. Here we determined the evolutionarily-relevant
segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine
synthesis pathway, focusing on combinations of amino acid states found at orthologous
sites of extant species. Just 15% of amino acids found in yeast His3 orthologues
were always neutral while the impact on fitness of the remaining 85% depended
on the genetic background. Furthermore, at 67% of sites, amino acid replacements
were under sign epistasis, having both strongly positive and negative effect in
different genetic backgrounds. 46% of sites were under reciprocal sign epistasis.
The fitness impact of amino acid replacements was influenced by only a few genetic
backgrounds but involved interaction of multiple sites, shaping a rugged fitness
landscape in which many of the shortest paths between highly fit genotypes are
inaccessible.
article_number: e1008079
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the
interactions of amino acids from orthologous sequences shaping a complex fitness
landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions
of amino acids from orthologous sequences shaping a complex fitness landscape.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An
Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences
Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.
ieee: V. Pokusaeva et al., “An experimental assay of the interactions of
amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS
Genetics, vol. 15, no. 4. Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino
acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics.
15(4), e1008079.
mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino
Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS
Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:37Z
day: '10'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079
ec_funded: 1
external_id:
isi:
- '000466866000029'
file:
- access_level: open_access
checksum: cf3889c8a8a16053dacf9c3776cbe217
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:26:08Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6445'
file_name: 2019_PLOSGenetics_Pokusaeva.pdf
file_size: 3726017
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: PLoS Genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9789'
relation: research_data
status: public
- id: '9790'
relation: research_data
status: public
- id: '9797'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An experimental assay of the interactions of amino acids from orthologous sequences
shaping a complex fitness landscape
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: 15
year: '2019'
...
---
_id: '6412'
abstract:
- lang: eng
text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance
of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct
chromatin modifications to enforce gene silencing, but how transcriptional repression
is propagated through mitotic cell divisions remains a key unresolved question.
Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic
stem cells, here we show that PRC1 can trigger transcriptional repression and
Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1),
but not variant PRC1, maintains gene silencing through cell division upon reversal
of tethering. Propagation of gene repression is sustained by cis-acting histone
modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting
a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the
distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic
maintenance of gene silencing, potentially enabling dynamic heritable responses
to complex stimuli. Our findings reveal how PcG repression is potentially inherited
in vertebrates.
article_number: '1931'
article_processing_charge: No
author:
- first_name: Hagar F.
full_name: Moussa, Hagar F.
last_name: Moussa
- first_name: Daniel
full_name: Bsteh, Daniel
last_name: Bsteh
- first_name: Ramesh
full_name: Yelagandula, Ramesh
last_name: Yelagandula
- first_name: Carina
full_name: Pribitzer, Carina
last_name: Pribitzer
- first_name: Karin
full_name: Stecher, Karin
last_name: Stecher
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Luca
full_name: Michetti, Luca
last_name: Michetti
- first_name: Jingkui
full_name: Wang, Jingkui
last_name: Wang
- first_name: Jorge A.
full_name: Zepeda-Martinez, Jorge A.
last_name: Zepeda-Martinez
- first_name: Ulrich
full_name: Elling, Ulrich
last_name: Elling
- first_name: Jacob I.
full_name: Stuckey, Jacob I.
last_name: Stuckey
- first_name: Lindsey I.
full_name: James, Lindsey I.
last_name: James
- first_name: Stephen V.
full_name: Frye, Stephen V.
last_name: Frye
- first_name: Oliver
full_name: Bell, Oliver
last_name: Bell
citation:
ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing. Nature Communications.
2019;10(1). doi:10.1038/s41467-019-09628-6
apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska,
K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation
of Polycomb-mediated gene silencing. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-09628-6
chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin
Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent
Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications.
Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.
ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing,” Nature Communications,
vol. 10, no. 1. Springer Nature, 2019.
ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti
L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O.
2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing. Nature Communications. 10(1), 1931.
mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation
of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no.
1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.
short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska,
L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James,
S.V. Frye, O. Bell, Nature Communications 10 (2019).
date_created: 2019-05-13T07:58:35Z
date_published: 2019-04-29T00:00:00Z
date_updated: 2023-08-25T10:31:56Z
day: '29'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-019-09628-6
external_id:
isi:
- '000466118700002'
file:
- access_level: open_access
checksum: 6550a328335396c856db4cbdda7d2994
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:45:51Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6448'
file_name: 2019_NatureComm_Moussa.pdf
file_size: 1223647
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing
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: 10
year: '2019'
...
---
_id: '6415'
abstract:
- lang: eng
text: Ant invasions are often harmful to native species communities. Their pathogens
and host disease defense mechanisms may be one component of their devastating
success. First, they can introduce harmful diseases to their competitors in the
introduced range, to which they themselves are tolerant. Second, their supercolonial
social structure of huge multi-queen nest networks means that they will harbor
a broad pathogen spectrum and high pathogen load while remaining resilient, unlike
the smaller, territorial colonies of the native species. Thus, it is likely that
invasive ants act as a disease reservoir, promoting their competitive advantage
and invasive success.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011
apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current
Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011
chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.
ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion
in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.
ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 33, 63–68.
mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.
short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.
date_created: 2019-05-13T07:58:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:31:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2019.03.011
external_id:
isi:
- '000477666000012'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 63-68
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- '22145753'
issn:
- '22145745'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathogens and disease defense of invasive ants
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2019'
...
---
_id: '9790'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing
results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:50:15Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...