---
_id: '9673'
abstract:
- lang: eng
text: Current strategies of computational crystal plasticity that focus on individual
atoms or dislocations are impractical for real-scale, large-strain problems even
with today’s computing power. Dislocation-density based approaches are a way forward
but a critical issue to address is a realistic description of the interactions
between dislocations. In this paper, a new scheme for computational dynamics of
dislocation-density functions is proposed, which takes full consideration of the
mutual elastic interactions between dislocations based on the Hirth–Lothe formulation.
Other features considered include (i) the continuity nature of the movements of
dislocation densities, (ii) forest hardening, (iii) generation according to high
spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation
by the finite-volume method, which is well suited for flow problems with high
gradients, is discussed. Numerical examples performed for a single-crystal aluminum
model show typical strength anisotropy behavior comparable to experimental observations.
Furthermore, a detailed case study on small-scale crystal plasticity successfully
captures a number of key experimental features, including power-law relation between
strength and size, low dislocation storage and jerky deformation.
article_processing_charge: No
article_type: original
author:
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: P.S.S.
full_name: Leung, P.S.S.
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity.
2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009
apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new
dislocation-density-function dynamics scheme for computational crystal plasticity
by explicit consideration of dislocation elastic interactions. International
Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009
chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function
Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration
of Dislocation Elastic Interactions.” International Journal of Plasticity.
Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.
ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions,” International Journal of Plasticity,
vol. 67. Elsevier, pp. 1–25, 2015.
ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity. 67,
1–25.
mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for
Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic
Interactions.” International Journal of Plasticity, vol. 67, Elsevier,
2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.
short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of
Plasticity 67 (2015) 1–25.
date_created: 2021-07-15T14:09:32Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:28Z
day: '01'
doi: 10.1016/j.ijplas.2014.09.009
extern: '1'
intvolume: ' 67'
language:
- iso: eng
month: '04'
oa_version: None
page: 1-25
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
scopus_import: '1'
status: public
title: A new dislocation-density-function dynamics scheme for computational crystal
plasticity by explicit consideration of dislocation elastic interactions
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 67
year: '2015'
...
---
_id: '9688'
abstract:
- lang: eng
text: The properties of the interface between solid and melt are key to solidification
and melting, as the interfacial free energy introduces a kinetic barrier to phase
transitions. This makes solidification happen below the melting temperature, in
out-of-equilibrium conditions at which the interfacial free energy is ill defined.
Here we draw a connection between the atomistic description of a diffuse solid-liquid
interface and its thermodynamic characterization. This framework resolves the
ambiguities in defining the solid-liquid interfacial free energy above and below
the melting temperature. In addition, we introduce a simulation protocol that
allows solid-liquid interfaces to be reversibly created and destroyed at conditions
relevant for experiments. We directly evaluate the value of the interfacial free
energy away from the melting point for a simple but realistic atomic potential,
and find a more complex temperature dependence than the constant positive slope
that has been generally assumed based on phenomenological considerations and that
has been used to interpret experiments. This methodology could be easily extended
to the study of other phase transitions, from condensation to precipitation. Our
analysis can help reconcile the textbook picture of classical nucleation theory
with the growing body of atomistic studies and mesoscale models of solidification.
article_number: '180102'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out
of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
2015;92(18). doi:10.1103/physrevb.92.180102
apa: Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial
free energy out of equilibrium. Physical Review B - Condensed Matter and Materials
Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102
chicago: Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid
Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.
ieee: B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free
energy out of equilibrium,” Physical Review B - Condensed Matter and Materials
Physics, vol. 92, no. 18. American Physical Society, 2015.
ista: Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy
out of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
92(18), 180102.
mla: Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.”
Physical Review B - Condensed Matter and Materials Physics, vol. 92, no.
18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.
short: B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter
and Materials Physics 92 (2015).
date_created: 2021-07-19T10:07:22Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2021-08-09T12:38:49Z
day: '01'
doi: 10.1103/physrevb.92.180102
extern: '1'
external_id:
arxiv:
- '1511.08668'
intvolume: ' 92'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.08668
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
eissn:
- 1550-235X
issn:
- 1098-0121
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solid-liquid interfacial free energy out of equilibrium
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 92
year: '2015'
...
---
_id: '9711'
article_processing_charge: No
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay Hazal
full_name: Ayhan, Dilay Hazal
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw
data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all
figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing
the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.
ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.”
Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Excel file containing the raw data for all figures, Public Library of
Science, 10.1371/journal.pbio.1002299.s001.
mla: Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All
Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-07-23T11:53:50Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-02-23T10:07:02Z
day: '18'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1619'
relation: used_in_publication
status: public
status: public
title: Excel file containing the raw data for all figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1855'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
acknowledgement: We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying
qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This
work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1
and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological
Sciences Research Council, the Department for Environment, Food and Rural Affairs,
the Natural Environment Research Council, The Scottish Government and The Wellcome
Trust, under the Living with Environmental Change Partnership.
article_processing_charge: No
article_type: original
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the
spit: Widespread cross-infection of multiple RNA viruses across wild and managed
bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses
across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology.
Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A
sting in the spit: Widespread cross-infection of multiple RNA viruses across wild
and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp.
615–624, 2015.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting
in the spit: Widespread cross-infection of multiple RNA viruses across wild and
managed bees. Journal of Animal Ecology. 84(3), 615–624.'
mla: 'Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology,
vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal
of Animal Ecology 84 (2015) 615–624.
date_created: 2018-12-11T11:54:23Z
date_published: 2015-03-03T00:00:00Z
date_updated: 2023-02-23T14:06:09Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1111/1365-2656.12345
external_id:
pmid:
- '25646973'
file:
- access_level: open_access
checksum: 542a0b9b07e78050a81b35f26f0b82da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:29Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5350'
file_name: IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf
file_size: 1823045
relation: main_file
file_date_updated: 2020-07-14T12:45:19Z
has_accepted_license: '1'
intvolume: ' 84'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 615 - 624
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley
publist_id: '5245'
pubrep_id: '460'
quality_controlled: '1'
related_material:
record:
- id: '9720'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'A sting in the spit: Widespread cross-infection of multiple RNA viruses across
wild and managed bees'
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 84
year: '2015'
...
---
_id: '1830'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
acknowledgement: We thank Meghan L. Vyleta for the genetical fungal strain characterization
and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D.
Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers
and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments
on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on
disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108
apa: Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects
of allogrooming on disease transmission in ant societies. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2014.0108
chicago: Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing
Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.
ieee: F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming
on disease transmission in ant societies,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669.
Royal Society, The, 2015.
ista: Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming
on disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 370(1669).
mla: Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission
in Ant Societies.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015,
doi:10.1098/rstb.2014.0108.
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of
the Royal Society of London. Series B, Biological Sciences 370 (2015).
date_created: 2018-12-11T11:54:15Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2023-02-23T14:06:12Z
day: '26'
department:
- _id: SyCr
doi: 10.1098/rstb.2014.0108
ec_funded: 1
external_id:
pmid:
- '25870394'
intvolume: ' 370'
issue: '1669'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities
in ant societies: a chemo-neuro-immunological approach'
- _id: 25E0E184-B435-11E9-9278-68D0E5697425
name: Antnet
- _id: 25E24DB2-B435-11E9-9278-68D0E5697425
name: Fellowship of Wissenschaftskolleg zu Berlin
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society, The
publist_id: '5273'
quality_controlled: '1'
related_material:
record:
- id: '9721'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Opposing effects of allogrooming on disease transmission in ant societies
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 370
year: '2015'
...
---
_id: '9721'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming
on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf'
apa: 'Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing
effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf'
chicago: 'Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data
from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.”
Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.'
ieee: 'F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects
of allogrooming on disease transmission in ant societies.” Dryad, 2015.'
ista: 'Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects
of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.'
mla: 'Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease
Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.'
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).
date_created: 2021-07-26T09:38:36Z
date_published: 2015-12-29T00:00:00Z
date_updated: 2023-02-23T10:16:22Z
day: '29'
department:
- _id: SyCr
doi: 10.5061/dryad.dj2bf
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.dj2bf
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1830'
relation: used_in_publication
status: public
status: public
title: 'Data from: Opposing effects of allogrooming on disease transmission in ant
societies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9718'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015.
doi:10.1371/journal.pcbi.1004055.s001
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting
information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting
Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information
text.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text,
Public Library of Science, 10.1371/journal.pcbi.1004055.s001.
mla: Friedlander, Tamar, et al. Supporting Information Text. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-07-26T08:35:23Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Supporting information text
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1793'
abstract:
- lang: eng
text: We present a software platform for reconstructing and analyzing the growth
of a plant root system from a time-series of 3D voxelized shapes. It aligns the
shapes with each other, constructs a geometric graph representation together with
the function that records the time of growth, and organizes the branches into
a hierarchy that reflects the order of creation. The software includes the automatic
computation of structural and dynamic traits for each root in the system enabling
the quantification of growth on fine-scale. These are important advances in plant
phenotyping with applications to the study of genetic and environmental influences
on growth.
article_number: e0127657
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for
the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6).
doi:10.1371/journal.pone.0127657'
apa: 'Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software
platform for the reconstruction and analysis of growing plant roots. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0127657'
chicago: 'Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots:
A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.”
PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.'
ieee: 'O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots,” PLoS One,
vol. 10, no. 6. Public Library of Science, 2015.'
ista: 'Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.'
mla: 'Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction
and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657,
Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.'
short: O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:02Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T14:06:33Z
day: '01'
ddc:
- '000'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657
file:
- access_level: open_access
checksum: d20f26461ca575276ad3ed9ce4bfc787
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5150'
file_name: IST-2016-454-v1+1_journal.pone.0127657.pdf
file_size: 1850825
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5318'
pubrep_id: '454'
quality_controlled: '1'
related_material:
record:
- id: '9737'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'DynamicRoots: A software platform for the reconstruction and analysis of growing
plant roots'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9737'
article_processing_charge: No
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for
the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001
apa: Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed
by DynamicRoots for the maize root shown in fig 2. Public Library of Science.
https://doi.org/10.1371/journal.pone.0127657.s001
chicago: Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits
Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.
ieee: O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots
for the maize root shown in fig 2.” Public Library of Science, 2015.
ista: Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots
for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.
mla: Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize
Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.
short: O. Symonova, C. Topp, H. Edelsbrunner, (2015).
date_created: 2021-07-28T06:20:13Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:14:42Z
day: '01'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1793'
relation: used_in_publication
status: public
status: public
title: Root traits computed by DynamicRoots for the maize root shown in fig 2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1827'
abstract:
- lang: eng
text: Bow-tie or hourglass structure is a common architectural feature found in
many biological systems. A bow-tie in a multi-layered structure occurs when intermediate
layers have much fewer components than the input and output layers. Examples include
metabolism where a handful of building blocks mediate between multiple input nutrients
and multiple output biomass components, and signaling networks where information
from numerous receptor types passes through a small set of signaling pathways
to regulate multiple output genes. Little is known, however, about how bow-tie
architectures evolve. Here, we address the evolution of bow-tie architectures
using simulations of multi-layered systems evolving to fulfill a given input-output
goal. We find that bow-ties spontaneously evolve when the information in the evolutionary
goal can be compressed. Mathematically speaking, bow-ties evolve when the rank
of the input-output matrix describing the evolutionary goal is deficient. The
maximal compression possible (the rank of the goal) determines the size of the
narrowest part of the network—that is the bow-tie. A further requirement is that
a process is active to reduce the number of links in the network, such as product-rule
mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations.
This offers a mechanism to understand a common architectural principle of biological
systems, and a way to quantitate the effective rank of the goals under which they
evolved.
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham
full_name: Mayo, Avraham
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055
apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of
bow-tie architectures in biology. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1004055
chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution
of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.
ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures
in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library
of Science, 2015.
ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 11(3).
mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.”
PLoS Computational Biology, vol. 11, no. 3, Public Library of Science,
2015, doi:10.1371/journal.pcbi.1004055.
short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11
(2015).
date_created: 2018-12-11T11:54:14Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T14:07:51Z
day: '23'
ddc:
- '576'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055
ec_funded: 1
file:
- access_level: open_access
checksum: b8aa66f450ff8de393014b87ec7d2efb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:39Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5161'
file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf
file_size: 1811647
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5278'
pubrep_id: '452'
quality_controlled: '1'
related_material:
record:
- id: '9718'
relation: research_data
status: public
- id: '9773'
relation: research_data
status: public
scopus_import: 1
status: public
title: Evolution of bow-tie architectures in biology
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...