---
_id: '9017'
abstract:
- lang: eng
text: MCM2 is a subunit of the replicative helicase machinery shown to interact
with histones H3 and H4 during the replication process through its N-terminal
domain. During replication, this interaction has been proposed to assist disassembly
and assembly of nucleosomes on DNA. However, how this interaction participates
in crosstalk with histone chaperones at the replication fork remains to be elucidated.
Here, we solved the crystal structure of the ternary complex between the histone-binding
domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4
assemble as a tetramer in the crystal structure, but MCM2 interacts only with
a single molecule of H3-H4. The latter interaction exploits binding surfaces that
contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome
core particle. Upon binding of the ternary complex with the histone chaperone
ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously
with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis
of the quaternary complex together with structural modeling support that ASF1
and MCM2 could form a chaperoning module for histones H3 and H4 protecting them
from promiscuous interactions. This suggests an additional function for MCM2 outside
its helicase function as a proper histone chaperone connected to the replication
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Danni
full_name: Liu, Danni
last_name: Liu
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Christophe
full_name: Velours, Christophe
last_name: Velours
- first_name: Armelle
full_name: Corpet, Armelle
last_name: Corpet
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Gwenaelle
full_name: Moal-Raisin, Gwenaelle
last_name: Moal-Raisin
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Christel
full_name: Compper, Christel
last_name: Compper
- first_name: Arthur
full_name: Besle, Arthur
last_name: Besle
- first_name: Berengère
full_name: Guichard, Berengère
last_name: Guichard
- first_name: Genevieve
full_name: Almouzni, Genevieve
last_name: Almouzni
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase
subunit MCM2 may act as a histone chaperone together with ASF1 at the replication
fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021
apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein,
F. (2015). Structural insight into how the human helicase subunit MCM2 may act
as a histone chaperone together with ASF1 at the replication fork. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021
chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle
Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the
Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1
at the Replication Fork.” Nucleic Acids Research. Oxford University Press,
2015. https://doi.org/10.1093/nar/gkv021.
ieee: N. Richet et al., “Structural insight into how the human helicase subunit
MCM2 may act as a histone chaperone together with ASF1 at the replication fork,”
Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917,
2015.
ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin
G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015.
Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork. Nucleic Acids Research.
43(3), 1905–1917.
mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit
MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.”
Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015,
pp. 1905–17, doi:10.1093/nar/gkv021.
short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail,
G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F.
Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.
date_created: 2021-01-19T11:01:01Z
date_published: 2015-02-18T00:00:00Z
date_updated: 2023-02-23T13:46:50Z
day: '18'
doi: 10.1093/nar/gkv021
extern: '1'
external_id:
pmid:
- '25618846'
intvolume: ' 43'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1905-1917
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '924'
abstract:
- lang: eng
text: This paper presents a numerical study of a Capillary Pumped Loop evaporator.
A two-dimensional unsteady mathematical model of a flat evaporator is developed
to simulate heat and mass transfer in unsaturated porous wick with phase change.
The liquid-vapor phase change inside the porous wick is described by Langmuir's
law. The governing equations are solved by the Finite Element Method. The results
are presented then for a sintered nickel wick and methanol as a working fluid.
The heat flux required to the transition from the all-liquid wick to the vapor-liquid
wick is calculated. The dynamic and thermodynamic behavior of the working fluid
in the capillary structure are discussed in this paper.
acknowledgement: The work presented in this paper is supported by Alstom Transport,
site de Tarbes (Contract number is 11099).
article_processing_charge: No
author:
- first_name: Riadh
full_name: Boubaker, Riadh
last_name: Boubaker
- first_name: Vincent
full_name: Platel, Vincent
last_name: Platel
- first_name: Alexis
full_name: Bergès, Alexis
last_name: Bergès
- first_name: Mathieu
full_name: Bancelin, Mathieu
last_name: Bancelin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat
and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied
Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009
apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015).
Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009
chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard
B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick
of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015.
https://doi.org/10.1016/j.applthermaleng.2014.10.009.
ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic
model of heat and mass transfer in an unsaturated porous wick of capillary pumped
loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.
ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model
of heat and mass transfer in an unsaturated porous wick of capillary pumped loop.
Applied Thermal Engineering. 76, 1–8.
mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated
Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol.
76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.
short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal
Engineering 76 (2015) 1–8.
date_created: 2018-12-11T11:49:13Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '05'
doi: 10.1016/j.applthermaleng.2014.10.009
extern: '1'
intvolume: ' 76'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 8
publication: Applied Thermal Engineering
publication_status: published
publisher: Elsevier
publist_id: '6514'
status: public
title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2015'
...
---
_id: '929'
abstract:
- lang: eng
text: 'An essential question of morphogenesis is how patterns arise without preexisting
positional information, as inspired by Turing. In the past few years, cytoskeletal
flows in the cell cortex have been identified as a key mechanism of molecular
patterning at the subcellular level. Theoretical and in vitro studies have suggested
that biological polymers such as actomyosin gels have the property to self-organize,
but the applicability of this concept in an in vivo setting remains unclear. Here,
we report that the regular spacing pattern of supracellular actin rings in the
Drosophila tracheal tubule is governed by a self-organizing principle. We propose
a simple biophysical model where pattern formation arises from the interplay of
myosin contractility and actin turnover. We validate the hypotheses of the model
using photobleaching experiments and report that the formation of actin rings
is contractility dependent. Moreover, genetic and pharmacological perturbations
of the physical properties of the actomyosin gel modify the spacing of the pattern,
as the model predicted. In addition, our model posited a role of cortical friction
in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion
of apical extracellular matrix caused strikingly dynamic movements of actin rings,
mirroring our model prediction of a transition from steady to chaotic actin patterns
at low cortical friction. Our results therefore demonstrate quantitatively that
a hydrodynamical instability of the actin cortex can trigger regular pattern formation
and drive morphogenesis in an in vivo setting. '
acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro,
Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto),
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang
for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions
and discussion. This work was supported by the Taishan Scholar Program of Shandong
and the Fundamental Research Funds for the Central Universities in China (3005000-841412019)
(to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry
of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges
support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives
periodic supracellular actin pattern formation in epithelial tubes. PNAS.
2015;112(28):8620-8625. doi:10.1073/pnas.1504762112
apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015).
Cortical instability drives periodic supracellular actin pattern formation in
epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112
chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi.
“Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in
Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.
ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS,
vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.
ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes. PNAS.
112(28), 8620–8625.
mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular
Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National
Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.
short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.
date_created: 2018-12-11T11:49:15Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '14'
doi: 10.1073/pnas.1504762112
extern: '1'
intvolume: ' 112'
issue: '28'
language:
- iso: eng
month: '07'
oa_version: None
page: 8620 - 8625
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6513'
status: public
title: Cortical instability drives periodic supracellular actin pattern formation
in epithelial tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '933'
abstract:
- lang: eng
text: Although collective cell motion plays an important role, for example during
wound healing, embryogenesis, or cancer progression, the fundamental rules governing
this motion are still not well understood, in particular at high cell density.
We study here the motion of human bronchial epithelial cells within a monolayer,
over long times. We observe that, as the monolayer ages, the cells slow down monotonously,
while the velocity correlation length first increases as the cells slow down but
eventually decreases at the slowest motions. By comparing experiments, analytic
model, and detailed particle-based simulations, we shed light on this biological
amorphous solidification process, demonstrating that the observed dynamics can
be explained as a consequence of the combined maturation and strengthening of
cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface
density due to proliferation is only secondary in this process. This analysis
is confirmed with two other cell types. The very general relations between the
mean cell velocity and velocity correlation lengths, which apply for aggregates
of self-propelled particles, as well as motile cells, can possibly be used to
discriminate between various parameter changes in vivo, from noninvasive microscopy
data.
author:
- first_name: Simón
full_name: García, Simón
last_name: García
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Pascal
full_name: Silberzan, Pascal
last_name: Silberzan
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active
jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319.
doi:10.1073/pnas.1510973112
apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov,
N. (2015). Physics of active jamming during collective cellular motion in a monolayer.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112
chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan,
and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a
Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.
ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov,
“Physics of active jamming during collective cellular motion in a monolayer,”
PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319,
2015.
ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics
of active jamming during collective cellular motion in a monolayer. PNAS. 112(50),
15314–15319.
mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular
Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences,
2015, pp. 15314–19, doi:10.1073/pnas.1510973112.
short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS
112 (2015) 15314–15319.
date_created: 2018-12-11T11:49:16Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '15'
doi: 10.1073/pnas.1510973112
extern: '1'
external_id:
pmid:
- '26627719'
intvolume: ' 112'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf
month: '12'
oa: 1
oa_version: None
page: 15314 - 15319
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6511'
quality_controlled: '1'
status: public
title: Physics of active jamming during collective cellular motion in a monolayer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '9684'
abstract:
- lang: eng
text: The size dependence of the strength of nano- and micron-sized crystals is
studied using a new simulation approach in which the dynamics of the density functions
of dislocations are modeled. Since any quantity of dislocations can be represented
by a density, this approach can handle large systems containing large quantities
of dislocations, which may handicap discrete dislocation dynamics schemes due
to the excessive computation time involved. For this reason, pillar sizes spanning
a large range, from the sub-micron to micron regimes, can be simulated. The simulation
results reveal the power-law relationship between strength and specimen size up
to a certain size, beyond which the strength varies much more slowly with size.
For specimens smaller than ~4000b, their strength is found to be controlled by
the dislocation depletion condition, in which the total dislocation density remains
almost constant throughout the loading process. In specimens larger than ~4000b,
the initial dislocation distribution is of critical importance since the presence
of dislocation entanglements is found to obstruct deformation in the neighboring
regions within a distance of ~2000b. This length scale suggests that the effects
of dense dislocation clusters are greater in intermediate-sized specimens (e.g.
4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link
concept.
article_number: '035001'
article_processing_charge: No
article_type: original
author:
- first_name: P S S
full_name: Leung, P S S
last_name: Leung
- first_name: H S
full_name: Leung, H 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 PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated
by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001
apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size
dependence of yield strength simulated by a dislocation-density function dynamics
approach. Modelling and Simulation in Materials Science and Engineering.
IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001
chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence
of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.”
Modelling and Simulation in Materials Science and Engineering. IOP Publishing,
2015. https://doi.org/10.1088/0965-0393/23/3/035001.
ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence
of yield strength simulated by a dislocation-density function dynamics approach,”
Modelling and Simulation in Materials Science and Engineering, vol. 23,
no. 3. IOP Publishing, 2015.
ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength
simulated by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 23(3), 035001.
mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density
Function Dynamics Approach.” Modelling and Simulation in Materials Science
and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.
short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation
in Materials Science and Engineering 23 (2015).
date_created: 2021-07-19T09:11:12Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:54Z
day: '01'
doi: 10.1088/0965-0393/23/3/035001
extern: '1'
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
publication: Modelling and Simulation in Materials Science and Engineering
publication_identifier:
eissn:
- 1361-651X
issn:
- 0965-0393
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Size dependence of yield strength simulated by a dislocation-density function
dynamics approach
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 23
year: '2015'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T14:05:55Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: 1
status: public
title: An exploration of the universe of polyglutamine structures
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: 11
year: '2015'
...
---
_id: '9712'
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison
& for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness
models for comparison & for interacting TFBSs. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1005639.s001
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other
Fitness Models for Comparison & for Interacting TFBSs.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for
comparison & for interacting TFBSs.” Public Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison
& for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting
TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
date_created: 2021-07-23T12:00:37Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-23T10:09:08Z
day: '06'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1666'
relation: used_in_publication
status: public
status: public
title: Other fitness models for comparison & for interacting TFBSs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9714'
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures - submission to PLOS journals. 2015.
doi:10.1371/journal.pcbi.1004541.s001
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures - submission to PLOS
journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission
to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures - submission to PLOS journals.” Public
Library of Science , 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures - submission to PLOS journals, Public
Library of Science , 10.1371/journal.pcbi.1004541.s001.
mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine
Structures - Submission to PLOS Journals. Public Library of Science , 2015,
doi:10.1371/journal.pcbi.1004541.s001.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).
date_created: 2021-07-23T12:05:28Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T10:04:35Z
day: '23'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541.s001
month: '10'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '1566'
relation: used_in_publication
status: public
status: public
title: An exploration of the universe of polyglutamine structures - submission to
PLOS journals
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9715'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015.
doi:10.1371/journal.pone.0126907.s001
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of
the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference
of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.
ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results,
Public Library of Science, 10.1371/journal.pone.0126907.s001.
mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public
Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-07-23T12:11:30Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s001
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Mathematical inference of the results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2023-02-23T14:06:41Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
pmid:
- '25473011'
intvolume: ' 282'
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
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: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '9742'
abstract:
- lang: eng
text: 'Repeated pathogen exposure is a common threat in colonies of social insects,
posing selection pressures on colony members to respond with improved disease-defense
performance. We here tested whether experience gained by repeated tending of low-level
fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary
brood care in the clonal ant, Platythyrea punctata. We trained ants individually
over nine consecutive trials to either sham-treated or fungus-exposed larvae.
We then compared the larval grooming behavior of naive and trained ants and measured
how effectively they removed infectious fungal conidiospores from the fungus-exposed
larvae. We found that the ants changed the duration of larval grooming in response
to both, larval treatment and their level of experience: (1) sham-treated larvae
received longer grooming than the fungus-exposed larvae and (2) trained ants performed
less self-grooming but longer larval grooming than naive ants, which was true
for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants
that groomed the fungus-exposed larvae for longer periods removed a higher number
of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced
ants performed longer larval grooming, they were more effective in fungal removal,
thus making them better caretakers under pathogen attack of the colony. By studying
this clonal ant, we can thus conclude that even in the absence of genetic variation
between colony members, differences in experience levels of brood care may affect
performance of sanitary brood care in social insects.'
article_processing_charge: No
author:
- first_name: Claudia
full_name: Westhus, Claudia
last_name: Westhus
- 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: Edouard
full_name: Tourdot, Edouard
last_name: Tourdot
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Claudie
full_name: Doums, Claudie
last_name: Doums
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from:
Increased grooming after repeated brood care provides sanitary benefits in a clonal
ant. 2015. doi:10.5061/dryad.7kc79'
apa: 'Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer,
S. (2015). Data from: Increased grooming after repeated brood care provides sanitary
benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79'
chicago: 'Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie
Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood
Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.'
ieee: 'C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer,
“Data from: Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant.” Dryad, 2015.'
ista: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data
from: Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant, Dryad, 10.5061/dryad.7kc79.'
mla: 'Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood
Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.'
short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).
date_created: 2021-07-28T08:52:53Z
date_published: 2015-07-09T00:00:00Z
date_updated: 2023-02-23T10:30:52Z
day: '09'
department:
- _id: SyCr
doi: 10.5061/dryad.7kc79
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.7kc79
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2161'
relation: used_in_publication
status: public
status: public
title: 'Data from: Increased grooming after repeated brood care provides sanitary
benefits in a clonal ant'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9765'
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. Gene ontology enrichment analysis
for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the
most sensitive gene deletion strains for all drugs. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299.s008
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment
Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library
of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008.
ieee: G. Chevereau et al., “Gene ontology enrichment analysis for the most
sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion
strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008.
mla: Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most
Sensitive Gene Deletion Strains for All Drugs. Public Library of Science,
2015, doi:10.1371/journal.pbio.1002299.s008.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-08-03T07:05:16Z
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.s008
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: Gene ontology enrichment analysis for the most sensitive gene deletion strains
for all drugs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '12630'
abstract:
- lang: eng
text: "The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region
(HKH) is poorly known. The correct representation of internal states and process
dynamics in glacio-hydrological models can often not be verified due to missing
in situ measurements. We use a new set of detailed ground data from the upper
Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological
model through a parameter assigning process with the aim to understand the hydrology
of the catchment and contribution of snow and ice processes to runoff. 14 parameters
are directly calculated on the basis of local data, and 13 parameters are calibrated
against 5 different datasets of in situ or remote sensing data. Spatial fields
of debris thickness are reconstructed through a novel approach that employs data
from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical
techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe
efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The
advanced representation of processes allowed assessing the role played by avalanching
for runoff for the first time for a Himalayan catchment (5% of annual water inputs
to the hydrological system are due to snow redistribution) and to quantify the
hydrological significance of sub-debris ice melt (9% of annual water inputs).
Snowmelt is the most important contributor to total runoff during the hydrological
year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and
ice melt (26%). A sensitivity analysis is used to assess the efficiency of the
monitoring network and identify the timing and location of field measurements
that constrain model uncertainty. The methodology to set up a glacio-hydrological
model in high-elevation regions presented in this study can be regarded as a benchmark
for modelers in the HKH seeking to evaluate their calibration approach, their
experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: E.S.
full_name: Miles, E.S.
last_name: Miles
- first_name: L.
full_name: Petersen, L.
last_name: Petersen
- first_name: M.
full_name: Heynen, M.
last_name: Heynen
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: D.
full_name: Stumm, D.
last_name: Stumm
- first_name: S.
full_name: Joshi, S.
last_name: Joshi
- first_name: A.
full_name: Shrestha, A.
last_name: Shrestha
citation:
ama: Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of
a Himalayan catchment through integration of high resolution in situ data and
remote sensing with an advanced simulation model. Advances in Water Resources.
2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013
apa: Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L.,
Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment
through integration of high resolution in situ data and remote sensing with an
advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013
chicago: Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen,
M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology
of a Himalayan Catchment through Integration of High Resolution in Situ Data and
Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources.
Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013.
ieee: S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment
through integration of high resolution in situ data and remote sensing with an
advanced simulation model,” Advances in Water Resources, vol. 78, no. 4.
Elsevier, pp. 94–111, 2015.
ista: Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M,
Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan
catchment through integration of high resolution in situ data and remote sensing
with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.
mla: Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through
Integration of High Resolution in Situ Data and Remote Sensing with an Advanced
Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier,
2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013.
short: S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M.
Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources
78 (2015) 94–111.
date_created: 2023-02-20T08:16:21Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-24T09:28:04Z
day: '01'
doi: 10.1016/j.advwatres.2015.01.013
extern: '1'
intvolume: ' 78'
issue: '4'
keyword:
- Water Science and Technology
language:
- iso: eng
month: '04'
oa_version: None
page: 94-111
publication: Advances in Water Resources
publication_identifier:
issn:
- 0309-1708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unraveling the hydrology of a Himalayan catchment through integration of high
resolution in situ data and remote sensing with an advanced simulation model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2015'
...
---
_id: '12628'
abstract:
- lang: eng
text: Thick debris cover on glaciers can significantly reduce ice melt. However,
several studies have suggested that debris-covered glaciers in the Himalaya might
have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation
and mass changes for the debris-covered glaciers of the upper Langtang valley,
Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon
satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties
are high in the accumulation areas, due to data gaps in the SRTM and difficulties
with delineation of the glacier borders. Even with these uncertainties, we obtain
thinning rates comparable to those of several other studies in the Himalaya. In
particular, we obtain a total mass balance for the investigated debris-covered
glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However,
there are major spatial differences both between glaciers and within any single
glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation.
Through analysis of surface velocities derived from Landsat ETM+ imagery, we show
that thinning occurs in areas of low velocity and low slope. These areas are prone
to a general, dynamic decay of surface features and to the development of supraglacial
lakes and ice cliffs, which may be responsible for a considerable increase in
overall glacier ablation.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Christa
full_name: Stephan, Christa
last_name: Stephan
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Sam
full_name: Herreid, Sam
last_name: Herreid
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Tobias
full_name: Bolch, Tobias
last_name: Bolch
citation:
ama: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance
changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974
to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237
apa: Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., &
Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang
Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological
Society. https://doi.org/10.3189/2015jog13j237
chicago: Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter
W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers
in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology.
International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237.
ieee: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T.
Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal,
Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International
Glaciological Society, pp. 373–386, 2015.
ista: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015.
Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal,
from 1974 to 1999. Journal of Glaciology. 61(226), 373–386.
mla: Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered
Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology,
vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237.
short: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch,
Journal of Glaciology 61 (2015) 373–386.
date_created: 2023-02-20T08:16:11Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2023-02-24T09:35:21Z
day: '01'
doi: 10.3189/2015jog13j237
extern: '1'
intvolume: ' 61'
issue: '226'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG13J237
month: '03'
oa: 1
oa_version: Published Version
page: 373-386
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mass-balance changes of the debris-covered glaciers in the Langtang Himal,
Nepal, from 1974 to 1999
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '12631'
abstract:
- lang: eng
text: Air temperature is one of the most relevant input variables for snow and ice
melt calculations. However, local meteorological conditions, complex topography,
and logistical concerns in glacierized regions make the measuring and modeling
of air temperature a difficult task. In this study, we investigate the spatial
distribution of 2 m air temperature over mountain glaciers and propose a modification
to an existing model to improve its representation. Spatially distributed meteorological
data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte
(Chile) Glaciers are used to examine approximate flow line temperatures during
their respective ablation seasons. During warm conditions (off-glacier temperatures
well above 0°C), observed air temperatures in the upper reaches of Place Glacier
and Haut Glacier d'Arolla decrease down glacier along the approximate flow line.
At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed
over the glacier tongue. While the temperature behavior over the upper part can
be explained by the cooling effect of the glacier surface, the temperature increase
over the glacier tongue may be caused by several processes induced by the surrounding
warm atmosphere. In order to capture the latter effect, we add an additional term
to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier
temperatures, the modified GB model reduces root-mean-square error up to 32% and
provides a new approach for distributing air temperature over mountain glaciers
as a function of off-glacier temperatures and approximate glacier flow lines.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Ayala, A.
last_name: Ayala
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: J. M.
full_name: Shea, J. M.
last_name: Shea
citation:
ama: 'Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain
glaciers: Exploring the influence of katabatic cooling and external warming. Journal
of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137'
apa: 'Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures
over mountain glaciers: Exploring the influence of katabatic cooling and external
warming. Journal of Geophysical Research: Atmospheres. American Geophysical
Union. https://doi.org/10.1002/2015jd023137'
chicago: 'Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures
over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External
Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical
Union, 2015. https://doi.org/10.1002/2015jd023137.'
ieee: 'A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures
over mountain glaciers: Exploring the influence of katabatic cooling and external
warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8.
American Geophysical Union, pp. 3139–3157, 2015.'
ista: 'Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over
mountain glaciers: Exploring the influence of katabatic cooling and external warming.
Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.'
mla: 'Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring
the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical
Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015,
pp. 3139–57, doi:10.1002/2015jd023137.'
short: 'A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres
120 (2015) 3139–3157.'
date_created: 2023-02-20T08:16:28Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2023-02-24T09:16:26Z
day: '18'
doi: 10.1002/2015jd023137
extern: '1'
intvolume: ' 120'
issue: '8'
keyword:
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Geophysics
language:
- iso: eng
month: '04'
oa_version: Published Version
page: 3139-3157
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
eissn:
- 2169-8996
issn:
- 2169-897X
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Modeling 2 m air temperatures over mountain glaciers: Exploring the influence
of katabatic cooling and external warming'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2015'
...
---
_id: '12629'
abstract:
- lang: eng
text: Meteorological studies in high-mountain environments form the basis of our
understanding of catchment hydrology and glacier accumulation and melt processes,
yet high-altitude (>4000 m above sea level, asl) observatories are rare. This
research presents meteorological data recorded between December 2012 and November
2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl.
Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave
and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation
are compared between sites. Solar radiation strongly affects diurnal temperature
and vapour pressure cycles, but local topography and valley-scale circulations
alter wind speed and precipitation cycles. The observed diurnal variability in
vertical temperature gradients in all seasons highlights the importance of in
situ measurements for melt modelling. The monsoon signal (progressive onset and
sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon
Phailin in mid-October 2013 provides an interesting case study on the possible
effects of such storms on glaciers in the region.
article_processing_charge: No
article_type: original
author:
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: P.
full_name: Wagnon, P.
last_name: Wagnon
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: R.
full_name: Biron, R.
last_name: Biron
- first_name: F.
full_name: Brun, F.
last_name: Brun
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative
high-altitude meteorological analysis from three catchments in the Nepalese Himalaya.
International Journal of Water Resources Development. 2015;31(2):174-200.
doi:10.1080/07900627.2015.1020417
apa: Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti,
F. (2015). A comparative high-altitude meteorological analysis from three catchments
in the Nepalese Himalaya. International Journal of Water Resources Development.
Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417
chicago: Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca
Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three
Catchments in the Nepalese Himalaya.” International Journal of Water Resources
Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.
ieee: J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti,
“A comparative high-altitude meteorological analysis from three catchments in
the Nepalese Himalaya,” International Journal of Water Resources Development,
vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.
ista: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A
comparative high-altitude meteorological analysis from three catchments in the
Nepalese Himalaya. International Journal of Water Resources Development. 31(2),
174–200.
mla: Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from
Three Catchments in the Nepalese Himalaya.” International Journal of Water
Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200,
doi:10.1080/07900627.2015.1020417.
short: J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti,
International Journal of Water Resources Development 31 (2015) 174–200.
date_created: 2023-02-20T08:16:17Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2023-02-24T09:30:42Z
day: '18'
doi: 10.1080/07900627.2015.1020417
extern: '1'
intvolume: ' 31'
issue: '2'
keyword:
- Water Science and Technology
- Development
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/07900627.2015.1020417
month: '04'
oa: 1
oa_version: Published Version
page: 174-200
publication: International Journal of Water Resources Development
publication_identifier:
eissn:
- 1360-0648
issn:
- 0790-0627
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparative high-altitude meteorological analysis from three catchments in
the Nepalese Himalaya
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '12626'
abstract:
- lang: eng
text: Ice cliffs have been identified as a reason for higher ablation rates on debris-covered
glaciers than are implied by the insulation effects of the debris. This study
aims to improve our understanding of cliff backwasting, and the role of radiative
fluxes in particular. An energy-balance model is forced with new data gathered
in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show
substantial variability in melt between cliffs, between locations on any cliff
and between seasons. Using a high-resolution digital elevation model we calculate
longwave fluxes incident to the cliff from surrounding terrain and include the
effect of local shading on shortwave radiation. This is an advance over previous
studies, that made simplified assumptions on cliff geometry and radiative fluxes.
Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34
cm d−1 in October. Model results reproduce the strong variability in space and
time, suggesting considerable differences in radiative fluxes over one cliff.
In October the model fails to reproduce stake readings, probably due to the lack
of a refreezing component. Disregarding local topography can lead to overestimation
of melt at the point scale by up to ∼9%.
article_processing_charge: No
article_type: original
author:
- first_name: Jakob F.
full_name: Steiner, Jakob F.
last_name: Steiner
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Tim D.
full_name: Reid, Tim D.
last_name: Reid
citation:
ama: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling
ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal
of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194
apa: Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W.,
& Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered
glacier in the Nepalese Himalaya. Journal of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2015jog14j194
chicago: Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles,
Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered
Glacier in the Nepalese Himalaya.” Journal of Glaciology. International
Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194.
ieee: J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and
T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the
Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International
Glaciological Society, pp. 889–907, 2015.
ista: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015.
Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya.
Journal of Glaciology. 61(229), 889–907.
mla: Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered
Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no.
229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.
short: J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D.
Reid, Journal of Glaciology 61 (2015) 889–907.
date_created: 2023-02-20T08:16:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-24T09:43:14Z
day: '01'
doi: 10.3189/2015jog14j194
extern: '1'
intvolume: ' 61'
issue: '229'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG14J194
month: '07'
oa: 1
oa_version: Published Version
page: 889-907
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese
Himalaya
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '12627'
abstract:
- lang: eng
text: Spatial evolution of supraglacial debris cover on mountain glaciers is a largely
unmonitored and poorly understood phenomenon that directly affects glacier melt.
Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan,
was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type
glaciers occupy 41% of the study area and were considered separately. The time
series of debris-covered surface area change shows a mean value of zero or near-zero
change for both surging and non-surging glaciers. An increase in debris-covered
area is often associated with negative regional mass balances. We extend this
logic to suggest that the stable regional mass balances in the Karakoram explain
the zero or near-zero change in debris-covered area. This coupling of trends combined
with our 37 year time series of data suggests the Karakoram anomaly extends further
back in time than previously known.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Herreid, Sam
last_name: Herreid
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Alvaro
full_name: Ayala, Alvaro
last_name: Ayala
- first_name: Anna
full_name: Chesnokova, Anna
last_name: Chesnokova
- first_name: Christian
full_name: Kienholz, Christian
last_name: Kienholz
- first_name: Joseph
full_name: Shea, Joseph
last_name: Shea
- first_name: Arun
full_name: Shrestha, Arun
last_name: Shrestha
citation:
ama: Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net
change in the percentage of supraglacial debris-covered area in northern Pakistan
from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227
apa: Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea,
J., & Shrestha, A. (2015). Satellite observations show no net change in the
percentage of supraglacial debris-covered area in northern Pakistan from 1977
to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227
chicago: Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian
Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net
Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan
from 1977 to 2014.” Journal of Glaciology. International Glaciological
Society, 2015. https://doi.org/10.3189/2015jog14j227.
ieee: S. Herreid et al., “Satellite observations show no net change in the
percentage of supraglacial debris-covered area in northern Pakistan from 1977
to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological
Society, pp. 524–536, 2015.
ista: Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha
A. 2015. Satellite observations show no net change in the percentage of supraglacial
debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology.
61(227), 524–536.
mla: Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage
of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal
of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015,
pp. 524–36, doi:10.3189/2015jog14j227.
short: S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea,
A. Shrestha, Journal of Glaciology 61 (2015) 524–536.
date_created: 2023-02-20T08:16:06Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-24T09:40:30Z
day: '01'
doi: 10.3189/2015jog14j227
extern: '1'
intvolume: ' 61'
issue: '227'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG14J227
month: '05'
oa: 1
oa_version: Published Version
page: 524-536
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Satellite observations show no net change in the percentage of supraglacial
debris-covered area in northern Pakistan from 1977 to 2014
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '1618'
abstract:
- lang: eng
text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells,
particularly within the lymphatic system, through activation of CCR7. Concurrent
expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells
to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of
CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping
shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19
and binding is competitive. Implications for the mechanism of PSGL-1's enhancement
of resting T-cell recruitment are discussed.
article_processing_charge: No
author:
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Skylar
full_name: Gabel Eissens, Skylar
last_name: Gabel Eissens
- first_name: Miranda
full_name: Gillitzer, Miranda
last_name: Gillitzer
- first_name: David
full_name: Lippner, David
last_name: Lippner
- first_name: Frank
full_name: Disilvio, Frank
last_name: Disilvio
- first_name: Casey
full_name: Mueller, Casey
last_name: Mueller
- first_name: Paeton
full_name: Wantuch, Paeton
last_name: Wantuch
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Michael
full_name: Famiglietti, Michael
last_name: Famiglietti
- first_name: Danielle
full_name: Zgoba, Danielle
last_name: Zgoba
- first_name: Asha
full_name: Bailey, Asha
last_name: Bailey
- first_name: Yaya
full_name: Bah, Yaya
last_name: Bah
- first_name: Samantha
full_name: Engebretson, Samantha
last_name: Engebretson
- first_name: David
full_name: Graupner, David
last_name: Graupner
- first_name: Emily
full_name: Lackner, Emily
last_name: Lackner
- first_name: Vincent
full_name: Larosa, Vincent
last_name: Larosa
- first_name: Tysha
full_name: Medeiros, Tysha
last_name: Medeiros
- first_name: Michael
full_name: Olson, Michael
last_name: Olson
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Harley
full_name: Pyles, Harley
last_name: Pyles
- first_name: Amanda
full_name: Richard, Amanda
last_name: Richard
- first_name: Scott
full_name: Schoeller, Scott
last_name: Schoeller
- first_name: Boris
full_name: Touzeau, Boris
last_name: Touzeau
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Francis
full_name: Peterson, Francis
last_name: Peterson
citation:
ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19
and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry.
2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560
apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D.,
Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical
Society. https://doi.org/10.1021/acs.biochem.5b00560
chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer,
David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19
and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry.
American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.
ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no.
27. American Chemical Society, pp. 4163–4166, 2015.
ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio
F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson
S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H,
Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution
structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites.
Biochemistry. 54(27), 4163–4166.
mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification
of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no.
27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.
short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F.
Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey,
Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson,
A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K.
Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.
date_created: 2018-12-11T11:53:03Z
date_published: 2015-06-26T00:00:00Z
date_updated: 2023-03-30T11:32:57Z
day: '26'
department:
- _id: MiSi
doi: 10.1021/acs.biochem.5b00560
ec_funded: 1
external_id:
pmid:
- '26115234'
intvolume: ' 54'
issue: '27'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/
month: '06'
oa: 1
oa_version: Submitted Version
page: 4163 - 4166
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Biochemistry
publication_status: published
publisher: American Chemical Society
publist_id: '5548'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1
binding sites
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '12881'
acknowledgement: This work was supported by the DFG (SPP 1527) and the EU (FP7, REA
grant no 291734).
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Eckehard
full_name: Olbrich, Eckehard
last_name: Olbrich
citation:
ama: 'Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous
robots. In: Proceedings of the 13th European Conference on Artificial Life.
MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018'
apa: 'Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior
of autonomous robots. In Proceedings of the 13th European Conference on Artificial
Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018'
chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior
of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial
Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018.
ieee: G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous
robots,” in Proceedings of the 13th European Conference on Artificial Life,
York, United Kingdom, 2015, p. 78.
ista: 'Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous
robots. Proceedings of the 13th European Conference on Artificial Life. ECAL:
European Conference on Artificial Life, 78.'
mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior
of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial
Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.
short: G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference
on Artificial Life, MIT Press, 2015, p. 78.
conference:
end_date: 2015-07-24
location: York, United Kingdom
name: 'ECAL: European Conference on Artificial Life'
start_date: 2015-07-20
date_created: 2023-04-30T22:01:07Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-05-02T07:06:21Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.7551/978-0-262-33027-5-ch018
ec_funded: 1
file:
- access_level: open_access
checksum: 880eabe59c9df12f06a882aa1bc4e600
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:02:59Z
date_updated: 2023-05-02T07:02:59Z
file_id: '12882'
file_name: 2015_ECAL_Martius.pdf
file_size: 1674241
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:02:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '78'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the 13th European Conference on Artificial Life
publication_identifier:
isbn:
- '9780262330275'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying self-organizing behavior of autonomous robots
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '12196'
abstract:
- lang: eng
text: SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular
Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in
the induction of defense responses. However, the molecular mechanisms underlying
NLR activation and the subsequent provocation of immune responses are only partially
characterized. To identify negative regulators of NLR-mediated immunity, a forward
genetic screen was undertaken to search for enhancers of the dwarf, autoimmune
gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism,
the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display
wild-type-like morphology and resistance. M2 progeny were screened for mutant,
snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes.
The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated
expression of the pPR2-GUS defense marker reporter gene and enhanced resistance
to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning
and Illumina sequencing, it was determined that the muse9 mutation is in the gene
encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10.
The syd-10 single mutant has no observable alteration from wild-type-like resistance,
although the syd-4 T-DNA insertion allele displays enhanced resistance to the
bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of
SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays
a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated
immunity. SYD may work with other proteins at the chromatin level to repress SNC1
transcription; such regulation is important for fine-tuning the expression of
NLR-encoding genes to prevent unpropitious autoimmunity.
acknowledgement: "This work was supported by the National Sciences and Engineering
Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery
Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the
Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang
and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles
Copeland for critical reading of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Kaeli C.M.
full_name: Johnson, Kaeli C.M.
last_name: Johnson
- first_name: Shitou
full_name: Xia, Shitou
last_name: Xia
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xin
full_name: Li, Xin
last_name: Li
citation:
ama: Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623.
doi:10.1093/pcp/pcv087
apa: Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler
SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcv087
chicago: Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin
Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell
Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.
ieee: K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED
negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology,
vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.
ista: Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.
mla: Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates
SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford
University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.
short: K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015)
1616–1623.
date_created: 2023-01-16T09:20:22Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-05-08T11:03:23Z
department:
- _id: XiFe
doi: 10.1093/pcp/pcv087
extern: '1'
external_id:
pmid:
- '26063389'
intvolume: ' 56'
issue: '8'
keyword:
- Cell Biology
- Plant Science
- Physiology
- General Medicine
language:
- iso: eng
month: '08'
oa_version: None
page: 1616-1623
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- 0032-0781
- 1471-9053
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2015'
...
---
_id: '13392'
abstract:
- lang: eng
text: The chemical behaviour of molecules can be significantly modified by confinement
to volumes comparable to the dimensions of the molecules. Although such confined
spaces can be found in various nanostructured materials, such as zeolites, nanoporous
organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of
molecules in and out of these materials has greatly hampered studying the effect
of confinement on their physicochemical properties. Here, we show that this diffusion
limitation can be overcome by reversibly creating and destroying confined environments
by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals
functionalized with light-responsive ligands that readily self-assemble and trap
various molecules from the surrounding bulk solution. Once trapped, these molecules
can undergo chemical reactions with increased rates and with stereoselectivities
significantly different from those in bulk solution. Illumination with visible
light disassembles these nanoflasks, releasing the product in solution and thereby
establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying
chemical reactivities in confined environments and for synthesizing molecules
that are otherwise hard to achieve in bulk solution.
article_processing_charge: No
article_type: original
author:
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Soumyo
full_name: Sen, Soumyo
last_name: Sen
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Michał
full_name: Sawczyk, Michał
last_name: Sawczyk
- first_name: Kristina
full_name: Kučanda, Kristina
last_name: Kučanda
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction
acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology.
2015;11:82-88. doi:10.1038/nnano.2015.256
apa: Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D.,
… Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically
self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256
chicago: Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda,
Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible
Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.”
Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256.
ieee: H. Zhao et al., “Reversible trapping and reaction acceleration within
dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11.
Springer Nature, pp. 82–88, 2015.
ista: Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK,
Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration
within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.
mla: Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically
Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature,
2015, pp. 82–88, doi:10.1038/nnano.2015.256.
short: H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K.
Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.
date_created: 2023-08-01T09:44:04Z
date_published: 2015-11-23T00:00:00Z
date_updated: 2023-08-07T12:55:46Z
day: '23'
doi: 10.1038/nnano.2015.256
extern: '1'
external_id:
pmid:
- '26595335'
intvolume: ' 11'
keyword:
- Electrical and Electronic Engineering
- Condensed Matter Physics
- General Materials Science
- Biomedical Engineering
- Atomic and Molecular Physics
- and Optics
- Bioengineering
language:
- iso: eng
month: '11'
oa_version: None
page: 82-88
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible trapping and reaction acceleration within dynamically self-assembling
nanoflasks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '13394'
abstract:
- lang: eng
text: The ability to guide the assembly of nanosized objects reversibly with external
stimuli, in particular light, is of fundamental importance, and it contributes
to the development of applications as diverse as nanofabrication and controlled
drug delivery. However, all the systems described to date are based on nanoparticles
(NPs) that are inherently photoresponsive, which makes their preparation cumbersome
and can markedly hamper their performance. Here we describe a conceptually new
methodology to assemble NPs reversibly using light that does not require the particles
to be functionalized with light-responsive ligands. Our strategy is based on the
use of a photoswitchable medium that responds to light in such a way that it modulates
the interparticle interactions. NP assembly proceeds quantitatively and without
apparent fatigue, both in solution and in gels. Exposing the gels to light in
a spatially controlled manner allowed us to draw images that spontaneously disappeared
after a specific period of time.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Ron
full_name: Leizrowice, Ron
last_name: Leizrowice
- first_name: Baruch
full_name: Margulis, Baruch
last_name: Margulis
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Martin
full_name: Börner, Martin
last_name: Börner
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of
non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303
apa: Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner,
M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303
chicago: Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao,
Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled
Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry.
Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.
ieee: P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive
nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652,
2015.
ista: Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao
T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. 7, 646–652.
mla: Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive
Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52,
doi:10.1038/nchem.2303.
short: P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T.
Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.
date_created: 2023-08-01T09:44:33Z
date_published: 2015-07-20T00:00:00Z
date_updated: 2023-08-07T13:00:15Z
day: '20'
doi: 10.1038/nchem.2303
extern: '1'
external_id:
pmid:
- '26201741'
intvolume: ' 7'
keyword:
- General Chemical Engineering
- General Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 646-652
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-controlled self-assembly of non-photoresponsive nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '13393'
abstract:
- lang: eng
text: Precise control of the self-assembly of selected components within complex
mixtures is a challenging goal whose realization is important for fabricating
novel nanomaterials. Herein we show that by decorating the surfaces of metallic
nanoparticles with differently substituted azobenzenes, it is possible to modulate
the wavelength of light at which the self-assembly of these nanoparticles is induced.
Exposing a mixture of two types of nanoparticles, each functionalized with a different
azobenzene, to UV or blue light induces the selective self-assembly of only one
type of nanoparticles. Irradiation with the other wavelength triggers the disassembly
of the aggregates, and the simultaneous self-assembly of nanoparticles of the
other type. By placing both types of azobenzenes on the same nanoparticles, we
created unique materials (“frustrated” nanoparticles) whose self-assembly is induced
irrespective of the wavelength of the incident light.
article_processing_charge: No
article_type: original
author:
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly
of nanoparticles using differently substituted azobenzenes. Angewandte Chemie
International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419
apa: Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal
light-induced self-assembly of nanoparticles using differently substituted azobenzenes.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419
chicago: Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal
Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.”
Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419.
ieee: D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte
Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.
ista: Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte
Chemie International Edition. 54(42), 12394–12397.
mla: Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles
Using Differently Substituted Azobenzenes.” Angewandte Chemie International
Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.
short: D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International
Edition 54 (2015) 12394–12397.
date_created: 2023-08-01T09:44:19Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-08-07T12:58:29Z
day: '01'
doi: 10.1002/anie.201502419
extern: '1'
external_id:
pmid:
- '25959725'
intvolume: ' 54'
issue: '42'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '10'
oa_version: None
page: 12394-12397
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orthogonal light-induced self-assembly of nanoparticles using differently substituted
azobenzenes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '13395'
abstract:
- lang: eng
text: Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive
ligands were prepared and shown to respond to these two types of stimuli reversibly
and in an orthogonal fashion. The composition of the coating could be tailored
to yield nanoparticles capable of aggregating exclusively when both UV and CO2
were applied at the same time, analogously to the behaviour of an AND logic gate.
article_processing_charge: No
article_type: original
author:
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous
action of light and CO2. Chemical Communications. 2015;51(11):2036-2039.
doi:10.1039/c4cc08541h
apa: Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate
under the simultaneous action of light and CO2. Chemical Communications.
Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h
chicago: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.
ieee: J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2,” Chemical Communications, vol.
51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.
ista: Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.
mla: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications,
vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h.
short: J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.
date_created: 2023-08-01T09:44:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-08-07T13:01:53Z
day: '18'
doi: 10.1039/c4cc08541h
extern: '1'
external_id:
pmid:
- '25417754'
intvolume: ' 51'
issue: '11'
keyword:
- Materials Chemistry
- Metals and Alloys
- Surfaces
- Coatings and Films
- General Chemistry
- Ceramics and Composites
- Electronic
- Optical and Magnetic Materials
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4CC08541H
month: '11'
oa: 1
oa_version: Published Version
page: 2036-2039
pmid: 1
publication: Chemical Communications
publication_identifier:
eissn:
- 1364-548X
issn:
- 1359-7345
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual-responsive nanoparticles that aggregate under the simultaneous action
of light and CO2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2015'
...
---
_id: '13396'
abstract:
- lang: eng
text: 'Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs)
is strongly affected by steric constraints and excitonic coupling between neighboring
chromophores. Therefore, control of the chromophore density is essential for enhancing
and manipulating the photoisomerization yield. We systematically compare two methods
to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate
SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates
and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual
decrease of the chromophore density and enable efficient photoswitching with low-power
light sources. X-ray spectroscopy reveals that coadsorption from solution yields
mixtures with tunable composition. The orientation of the chromophores with respect
to the surface normal changes from a tilted to an upright position with increasing
azobenzene density. For both systems, optical spectroscopy reveals a pronounced
excitonic shift that increases with the chromophore density. In spite of exciting
the optical transition of the monomer, the main spectral change in mixed SAMs
occurs in the excitonic band. In addition, the photoisomerization yield decreases
only slightly by increasing the azobenzene–alkanethiolate density, and we observed
photoswitching even with minor dilutions. Unlike in solution, azobenzene in the
planar SAM can be switched back almost completely by optical excitation from the
cis to the original trans state within a short time scale. These observations
indicate cooperativity in the photoswitching process of mixed SAMs.'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Moldt, Thomas
last_name: Moldt
- first_name: Daniel
full_name: Brete, Daniel
last_name: Brete
- first_name: Daniel
full_name: Przyrembel, Daniel
last_name: Przyrembel
- first_name: Sanjib
full_name: Das, Sanjib
last_name: Das
- first_name: Joel R.
full_name: Goldman, Joel R.
last_name: Goldman
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Cornelius
full_name: Gahl, Cornelius
last_name: Gahl
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Martin
full_name: Weinelt, Martin
last_name: Weinelt
citation:
ama: Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized
azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057.
doi:10.1021/la504291n
apa: Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K.,
… Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. American Chemical
Society. https://doi.org/10.1021/la504291n
chicago: Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman,
Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the
Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface
Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.
ieee: T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3.
American Chemical Society, pp. 1048–1057, 2015.
ista: Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn
R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.
mla: Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes
by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3,
American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.
short: T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl,
R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.
date_created: 2023-08-01T09:45:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2023-08-07T13:05:04Z
day: '27'
doi: 10.1021/la504291n
extern: '1'
external_id:
pmid:
- '25544061'
intvolume: ' 31'
issue: '3'
keyword:
- Electrochemistry
- Spectroscopy
- Surfaces and Interfaces
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '01'
oa_version: None
page: 1048-1057
pmid: 1
publication: Langmuir
publication_identifier:
eissn:
- 1520-5827
issn:
- 0743-7463
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution
and surface curvature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '13397'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been studied extensively for
particles having different sizes and compositions. However, relatively little
attention has been devoted to how the shape and surface chemistry of magnetic
nanoparticles affects their self-assembly properties. Here, we undertook a combined
experiment–theory study aimed at better understanding of the self-assembly of
cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental
parameters, such as the direction of the magnetic field and nanoparticle density,
a variety of superstructures can be obtained, including one-dimensional filaments
and helices, as well as C-shaped assemblies described here for the first time.
Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive
ligands. Using these modified nanoparticles, we were able to achieve orthogonal
control of self-assembly using a magnetic field and light.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Davide
full_name: Peddis, Davide
last_name: Peddis
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Gregory
full_name: Leitus, Gregory
last_name: Leitus
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly
of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b
apa: Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin,
A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b
chicago: Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide
Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced
Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society
of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.
ieee: G. Singh et al., “Magnetic field-induced self-assembly of iron oxide
nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry,
pp. 403–421, 2015.
ista: Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus
G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. 181, 403–421.
mla: Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide
Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry,
2015, pp. 403–21, doi:10.1039/c4fd00265b.
short: G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin,
G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.
date_created: 2023-08-01T09:45:17Z
date_published: 2015-01-02T00:00:00Z
date_updated: 2023-08-07T13:06:23Z
day: '02'
doi: 10.1039/c4fd00265b
extern: '1'
external_id:
pmid:
- '25920522'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4FD00265B
month: '01'
oa: 1
oa_version: Published Version
page: 403-421
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic field-induced self-assembly of iron oxide nanocubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '13398'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yugang
full_name: Sun, Yugang
last_name: Sun
- first_name: Leonardo
full_name: Scarabelli, Leonardo
last_name: Scarabelli
- first_name: Nicholas
full_name: Kotov, Nicholas
last_name: Kotov
- first_name: Moritz
full_name: Tebbe, Moritz
last_name: Tebbe
- first_name: Xiao-Min
full_name: Lin, Xiao-Min
last_name: Lin
- first_name: Ward
full_name: Brullot, Ward
last_name: Brullot
- first_name: Lucio
full_name: Isa, Lucio
last_name: Isa
- first_name: Peter
full_name: Schurtenberger, Peter
last_name: Schurtenberger
- first_name: Helmuth
full_name: Moehwald, Helmuth
last_name: Moehwald
- first_name: Igor
full_name: Fedin, Igor
last_name: Fedin
- first_name: Orlin
full_name: Velev, Orlin
last_name: Velev
- first_name: Damien
full_name: Faivre, Damien
last_name: Faivre
- first_name: Christopher
full_name: Sorensen, Christopher
last_name: Sorensen
- first_name: Régine
full_name: Perzynski, Régine
last_name: Perzynski
- first_name: Munish
full_name: Chanana, Munish
last_name: Chanana
- first_name: Zhihai
full_name: Li, Zhihai
last_name: Li
- first_name: Fernando
full_name: Bresme, Fernando
last_name: Bresme
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Emre
full_name: Firlar, Emre
last_name: Firlar
- first_name: David
full_name: Schiffrin, David
last_name: Schiffrin
- first_name: Joao Batista
full_name: Souza Junior, Joao Batista
last_name: Souza Junior
- first_name: Andreas
full_name: Fery, Andreas
last_name: Fery
- first_name: Elena
full_name: Shevchenko, Elena
last_name: Shevchenko
- first_name: Ozgur
full_name: Tarhan, Ozgur
last_name: Tarhan
- first_name: Armand Paul
full_name: Alivisatos, Armand Paul
last_name: Alivisatos
- first_name: Sabrina
full_name: Disch, Sabrina
last_name: Disch
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Suvojit
full_name: Ghosh, Suvojit
last_name: Ghosh
citation:
ama: 'Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process:
General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g'
apa: 'Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., …
Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday
Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g'
chicago: 'Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min
Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General
Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.'
ieee: 'Y. Sun et al., “Field-assisted self-assembly process: General discussion,”
Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479,
2015.'
ista: 'Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger
P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M,
Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko
E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly
process: General discussion. Faraday Discussions. 181, 463–479.'
mla: 'Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.”
Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79,
doi:10.1039/c5fd90041g.'
short: Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa,
P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R.
Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B.
Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R.
Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.
date_created: 2023-08-01T09:45:29Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2023-08-08T07:16:20Z
day: '07'
doi: 10.1039/c5fd90041g
extern: '1'
external_id:
pmid:
- '26149295'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 463-479
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Field-assisted self-assembly process: General discussion'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '14017'
abstract:
- lang: eng
text: The detection of electron motion and electronic wave-packet dynamics is one
of the core goals of attosecond science. Recently, choosing the nitric oxide molecule
as an example, we have introduced and demonstrated an experimental approach to
measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation
(HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short
outline of the theory to describe the combination of the pump and HHG probe process
was published together with an extensive discussion of experimental results [Baykusheva
et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment
showed good agreement on a quantitative level. Here, we present the theory in
detail, which is based on a generalized density-matrix approach that describes
the pump process and the subsequent probing of the wave packets by a semiclassical
quantitative rescattering approach. An in-depth analysis of the different Raman
scattering contributions to the creation of the coupled rotational and electronic
spin-orbit wave packets is made. We present results for parallel and perpendicular
linear polarizations of the pump and probe laser pulses. Furthermore, an analysis
of the combined rotational-electronic density matrix in terms of irreducible components
is presented that facilitates interpretation of the results.
article_number: '023421'
article_processing_charge: No
article_type: original
author:
- first_name: Song Bin
full_name: Zhang, Song Bin
last_name: Zhang
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Peter M.
full_name: Kraus, Peter M.
last_name: Kraus
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
- first_name: Nina
full_name: Rohringer, Nina
last_name: Rohringer
citation:
ama: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study
of molecular electronic and rotational coherences by high-order-harmonic generation.
Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421
apa: Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer,
N. (2015). Theoretical study of molecular electronic and rotational coherences
by high-order-harmonic generation. Physical Review A. American Physical
Society. https://doi.org/10.1103/physreva.91.023421
chicago: Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob
Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational
Coherences by High-Order-Harmonic Generation.” Physical Review A. American
Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.
ieee: S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer,
“Theoretical study of molecular electronic and rotational coherences by high-order-harmonic
generation,” Physical Review A, vol. 91, no. 2. American Physical Society,
2015.
ista: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical
study of molecular electronic and rotational coherences by high-order-harmonic
generation. Physical Review A. 91(2), 023421.
mla: Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational
Coherences by High-Order-Harmonic Generation.” Physical Review A, vol.
91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421.
short: S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical
Review A 91 (2015).
date_created: 2023-08-10T06:38:10Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2023-08-22T08:56:34Z
day: '19'
doi: 10.1103/physreva.91.023421
extern: '1'
external_id:
arxiv:
- '1504.03933'
intvolume: ' 91'
issue: '2'
keyword:
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.03933
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 1094-1622
issn:
- 1050-2947
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theoretical study of molecular electronic and rotational coherences by high-order-harmonic
generation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '14016'
abstract:
- lang: eng
text: All attosecond time-resolved measurements have so far relied on the use of
intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced
electron diffraction and high-harmonic generation all make use of non-perturbative
light–matter interactions. Remarkably, the effect of the strong laser field on
the studied sample has often been neglected in previous studies. Here we use high-harmonic
spectroscopy to measure laser-induced modifications of the electronic structure
of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br
as generic examples of polar polyatomic molecules. We accurately measure intensity
ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned
molecules. We show that these robust observables reveal a substantial modification
of the molecular electronic structure by the external laser field. Our insights
offer new challenges and opportunities for a range of emerging strong-field attosecond
spectroscopies.
article_number: '7039'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: C. Z.
full_name: Bisgaard, C. Z.
last_name: Bisgaard
- first_name: T.
full_name: Morishita, T.
last_name: Morishita
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
2015;6. doi:10.1038/ncomms8039
apa: Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider,
J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic
structure in oriented polyatomic molecules. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms8039
chicago: Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan,
J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J.
Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic
Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.
ieee: P. M. Kraus et al., “Observation of laser-induced electronic structure
in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer
Nature, 2015.
ista: Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard
CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
6, 7039.
mla: Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in
Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer
Nature, 2015, doi:10.1038/ncomms8039.
short: P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider,
C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications
6 (2015).
date_created: 2023-08-10T06:38:01Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-08-22T08:52:56Z
day: '05'
doi: 10.1038/ncomms8039
extern: '1'
external_id:
pmid:
- '25940229'
intvolume: ' 6'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms8039
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of laser-induced electronic structure in oriented polyatomic molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '14013'
abstract:
- lang: eng
text: The ultrafast motion of electrons and holes after light-matter interaction
is fundamental to a broad range of chemical and biophysical processes. We advanced
high-harmonic spectroscopy to resolve spatially and temporally the migration of
an electron hole immediately after ionization of iodoacetylene while simultaneously
demonstrating extensive control over the process. A multidimensional approach,
based on the measurement and accurate theoretical description of both even and
odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases
of the electronic states with a resolution of ~100 attoseconds. We separately
reconstructed quasi-field-free and laser-controlled charge migration as a function
of the spatial orientation of the molecule and determined the shape of the hole
created by ionization. Our technique opens the prospect of laser control over
electronic primary processes.
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: B.
full_name: Mignolet, B.
last_name: Mignolet
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: L.
full_name: Horný, L.
last_name: Horný
- first_name: E. F.
full_name: Penka, E. F.
last_name: Penka
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: A. D.
full_name: Bandrauk, A. D.
last_name: Bandrauk
- first_name: F.
full_name: Remacle, F.
last_name: Remacle
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of
attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795.
doi:10.1126/science.aab2160
apa: Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka,
E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge
migration in ionized iodoacetylene. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aab2160
chicago: Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L.
Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond
Charge Migration in Ionized Iodoacetylene.” Science. American Association
for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160.
ieee: P. M. Kraus et al., “Measurement and laser control of attosecond charge
migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American
Association for the Advancement of Science, pp. 790–795, 2015.
ista: Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi
G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner
HJ. 2015. Measurement and laser control of attosecond charge migration in ionized
iodoacetylene. Science. 350(6262), 790–795.
mla: Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration
in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association
for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.
short: P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka,
G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk,
F. Remacle, H.J. Wörner, Science 350 (2015) 790–795.
date_created: 2023-08-10T06:37:35Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2023-08-22T08:47:39Z
day: '22'
doi: 10.1126/science.aab2160
extern: '1'
external_id:
pmid:
- '26494175'
intvolume: ' 350'
issue: '6262'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '10'
oa_version: None
page: 790-795
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measurement and laser control of attosecond charge migration in ionized iodoacetylene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 350
year: '2015'
...
---
_id: '14015'
abstract:
- lang: eng
text: We advance high-harmonic spectroscopy to resolve molecular charge migration
in time and space and simultaneously demonstrate extensive control over the process.
A multidimensional approach enables us to reconstruct both quantum amplitudes
and phases with a resolution of better than 100 attoseconds and to separately
reconstruct field-free and laser- driven charge migration. Our techniques make
charge migration in molecules measurable on the attosecond time scale and open
new avenues for laser control of electronic primary processes.
article_number: '112136'
article_processing_charge: No
article_type: original
author:
- first_name: P M
full_name: Kraus, P M
last_name: Kraus
- first_name: B
full_name: Mignolet, B
last_name: Mignolet
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A
full_name: Rupenyan, A
last_name: Rupenyan
- first_name: L
full_name: Horný, L
last_name: Horný
- first_name: E F
full_name: Penka, E F
last_name: Penka
- first_name: O I
full_name: Tolstikhin, O I
last_name: Tolstikhin
- first_name: J
full_name: Schneider, J
last_name: Schneider
- first_name: F
full_name: Jensen, F
last_name: Jensen
- first_name: L B
full_name: Madsen, L B
last_name: Madsen
- first_name: A D
full_name: Bandrauk, A D
last_name: Bandrauk
- first_name: F
full_name: Remacle, F
last_name: Remacle
- first_name: H J
full_name: Wörner, H J
last_name: Wörner
citation:
ama: 'Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and
its laser control. Journal of Physics: Conference Series. 2015;635(11).
doi:10.1088/1742-6596/635/11/112136'
apa: 'Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka,
E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control.
Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112136'
chicago: 'Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný,
E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.”
Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112136.'
ieee: 'P. M. Kraus et al., “Attosecond charge migration and its laser control,”
Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing,
2015.'
ista: 'Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin
OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015.
Attosecond charge migration and its laser control. Journal of Physics: Conference
Series. 635(11), 112136.'
mla: 'Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.”
Journal of Physics: Conference Series, vol. 635, no. 11, 112136, IOP Publishing,
2015, doi:10.1088/1742-6596/635/11/112136.'
short: 'P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka,
O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle,
H.J. Wörner, Journal of Physics: Conference Series 635 (2015).'
date_created: 2023-08-10T06:37:53Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-08-22T08:49:14Z
day: '01'
doi: 10.1088/1742-6596/635/11/112136
extern: '1'
intvolume: ' 635'
issue: '11'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1742-6596/635/11/112136
month: '07'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Conference Series'
publication_identifier:
eissn:
- 1742-6596
issn:
- 1742-6588
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attosecond charge migration and its laser control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 635
year: '2015'
...
---
_id: '14014'
abstract:
- lang: eng
text: We have studied a coupled electronic-nuclear wave packet in nitric oxide using
time-resolved strong-field photoelectron holography and rescattering. We show
that the electronic dynamics mainly appears in the holographic structures whereas
nuclear motion strongly modulates the angular distribution of the rescattered
photoelectrons.
article_number: '112135'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G
full_name: Walt, Samuel G
last_name: Walt
- first_name: N Bhargava
full_name: Ram, N Bhargava
last_name: Ram
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving
the dynamics of valence-shell electrons and nuclei through laser-induced diffraction
and holography. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112135'
apa: 'Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., &
Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei
through laser-induced diffraction and holography. Journal of Physics: Conference
Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112135'
chicago: 'Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva,
Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell
Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal
of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112135.'
ieee: 'S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J.
Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through
laser-induced diffraction and holography,” Journal of Physics: Conference Series,
vol. 635, no. 11. IOP Publishing, 2015.'
ista: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving
the dynamics of valence-shell electrons and nuclei through laser-induced diffraction
and holography. Journal of Physics: Conference Series. 635(11), 112135.'
mla: 'Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons
and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics:
Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135.'
short: 'S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner,
Journal of Physics: Conference Series 635 (2015).'
date_created: 2023-08-10T06:37:44Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-08-22T08:51:33Z
day: '01'
doi: 10.1088/1742-6596/635/11/112135
extern: '1'
intvolume: ' 635'
issue: '11'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1742-6596/635/11/112135
month: '11'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Conference Series'
publication_identifier:
eissn:
- 1742-6596
issn:
- 1742-6588
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resolving the dynamics of valence-shell electrons and nuclei through laser-induced
diffraction and holography
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 635
year: '2015'
...
---
_id: '9719'
abstract:
- lang: eng
text: Parasitism creates selection for resistance mechanisms in host populations
and is hypothesized to promote increased host evolvability. However, the influence
of these traits on host evolution when parasites are no longer present is unclear.
We used experimental evolution and whole-genome sequencing of Escherichia coli
to determine the effects of past and present exposure to parasitic viruses (phages)
on the spread of mutator alleles, resistance, and bacterial competitive fitness.
We found that mutator alleles spread rapidly during adaptation to any of four
different phage species, and this pattern was even more pronounced with multiple
phages present simultaneously. However, hypermutability did not detectably accelerate
adaptation in the absence of phages and recovery of fitness costs associated with
resistance. Several lineages evolved phage resistance through elevated mucoidy,
and during subsequent evolution in phage-free conditions they rapidly reverted
to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this
phenotypic reversion was achieved by additional genetic changes rather than by
genotypic reversion of the initial resistance mutations. Insertion sequence (IS)
elements played a key role in both the acquisition of resistance and adaptation
in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions
were not more frequent in mutator lineages. Our results provide a genetic explanation
for rapid reversion of mucoidy, a phenotype observed in other bacterial species
including human pathogens. Moreover, this demonstrates that the types of genetic
change underlying adaptation to fitness costs, and consequently the impact of
evolvability mechanisms such as increased point-mutation rates, depend critically
on the mechanism of resistance.
article_processing_charge: No
author:
- first_name: Sébastien
full_name: Wielgoss, Sébastien
last_name: Wielgoss
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M.
full_name: Bischofberger, Anna M.
last_name: Bischofberger
- first_name: Alex R.
full_name: Hall, Alex R.
last_name: Hall
citation:
ama: 'Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation
to parasites and costs of parasite resistance in mutator and non-mutator bacteria.
2015. doi:10.5061/dryad.cj910'
apa: 'Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2015).
Data from: Adaptation to parasites and costs of parasite resistance in mutator
and non-mutator bacteria. Dryad. https://doi.org/10.5061/dryad.cj910'
chicago: 'Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex
R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance
in Mutator and Non-Mutator Bacteria.” Dryad, 2015. https://doi.org/10.5061/dryad.cj910.'
ieee: 'S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from:
Adaptation to parasites and costs of parasite resistance in mutator and non-mutator
bacteria.” Dryad, 2015.'
ista: 'Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation
to parasites and costs of parasite resistance in mutator and non-mutator bacteria,
Dryad, 10.5061/dryad.cj910.'
mla: 'Wielgoss, Sébastien, et al. Data from: Adaptation to Parasites and Costs
of Parasite Resistance in Mutator and Non-Mutator Bacteria. Dryad, 2015, doi:10.5061/dryad.cj910.'
short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).
date_created: 2021-07-26T08:44:04Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2023-09-05T13:46:04Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.cj910
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cj910
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '5749'
relation: used_in_publication
status: public
status: public
title: 'Data from: Adaptation to parasites and costs of parasite resistance in mutator
and non-mutator bacteria'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1401'
abstract:
- lang: eng
text: 'The human ability to recognize objects in complex scenes has driven research
in the computer vision field over couple of decades. This thesis focuses on the
object recognition task in images. That is, given the image, we want the computer
system to be able to predict the class of the object that appears in the image.
A recent successful attempt to bridge semantic understanding of the image perceived
by humans and by computers uses attribute-based models. Attributes are semantic
properties of the objects shared across different categories, which humans and
computers can decide on. To explore the attribute-based models we take a statistical
machine learning approach, and address two key learning challenges in view of
object recognition task: learning augmented attributes as mid-level discriminative
feature representation, and learning with attributes as privileged information.
Our main contributions are parametric and non-parametric models and algorithms
to solve these frameworks. In the parametric approach, we explore an autoencoder
model combined with the large margin nearest neighbor principle for mid-level
feature learning, and linear support vector machines for learning with privileged
information. In the non-parametric approach, we propose a supervised Indian Buffet
Process for automatic augmentation of semantic attributes, and explore the Gaussian
Processes classification framework for learning with privileged information. A
thorough experimental analysis shows the effectiveness of the proposed models
in both parametric and non-parametric views.'
acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance
throughout my studies and for patience in transforming me into a scientist, and
my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice.
\r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative
needs and was always nice and friendly to me, and the campus team for making the
IST Austria campus my second home. \r\nI was honored to collaborate with brilliant
researchers and to learn from their experience. Undoubtedly, I learned most of all
from Novi Quadrianto: brainstorming our projects and getting exciting results was
the most enjoyable part of my work – thank you! I am also grateful to David Knowles,
Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina
for the fantastic projects we worked on together, and to Kristen Grauman and Adriana
Kovashka for the exceptional experience working with user studies. I would like
to thank my colleagues at IST Austria and my office mates who shared their happy
moods, scientific breakthroughs and thought-provoking conversations with me: Chao,
Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina,
Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael,
Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games
of table soccer we played together and the tournaments we teamed up for: we will
definitely win next time:) A very warm hug to Asya for always being so inspiring
and supportive to me, and for helping me to increase the proportion of female computer
scientists in our group. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
citation:
ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric
and non-parametrics views. 2015. doi:10.15479/at:ista:1401'
apa: 'Sharmanska, V. (2015). Learning with attributes for object recognition:
Parametric and non-parametrics views. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:1401'
chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria,
2015. https://doi.org/10.15479/at:ista:1401.'
ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric
and non-parametrics views,” Institute of Science and Technology Austria, 2015.'
ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric
and non-parametrics views. Institute of Science and Technology Austria.'
mla: 'Sharmanska, Viktoriia. Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views. Institute of Science and Technology
Austria, 2015, doi:10.15479/at:ista:1401.'
short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric
and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:11Z
day: '01'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
- _id: GradSch
doi: 10.15479/at:ista:1401
file:
- access_level: open_access
checksum: 3605b402bb6934e09ae4cf672c84baf7
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:33:17Z
date_updated: 2021-02-22T11:33:17Z
file_id: '9177'
file_name: 2015_Thesis_Sharmanska.pdf
file_size: 7964342
relation: main_file
success: 1
- access_level: closed
checksum: e37593b3ee75bf3180629df2d6ca8f4e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:40:45Z
date_updated: 2021-11-17T13:47:24Z
file_id: '10297'
file_name: 2015_Thesis_Sharmanska_pdfa.pdf
file_size: 7372241
relation: main_file
file_date_updated: 2021-11-17T13:47:24Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5806'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: 'Learning with attributes for object recognition: Parametric and non-parametrics
views'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1709'
abstract:
- lang: eng
text: The competition for resources among cells, individuals or species is a fundamental
characteristic of evolution. Biological all-pay auctions have been used to model
situations where multiple individuals compete for a single resource. However,
in many situations multiple resources with various values exist and single reward
auctions are not applicable. We generalize the model to multiple rewards and study
the evolution of strategies. In biological all-pay auctions the bid of an individual
corresponds to its strategy and is equivalent to its payment in the auction. The
decreasingly ordered rewards are distributed according to the decreasingly ordered
bids of the participating individuals. The reproductive success of an individual
is proportional to its fitness given by the sum of the rewards won minus its payments.
Hence, successful bidding strategies spread in the population. We find that the
results for the multiple reward case are very different from the single reward
case. While the mixed strategy equilibrium in the single reward case with more
than two players consists of mostly low-bidding individuals, we show that the
equilibrium can convert to many high-bidding individuals and a few low-bidding
individuals in the multiple reward case. Some reward values lead to a specialization
among the individuals where one subpopulation competes for the rewards and the
other subpopulation largely avoids costly competitions. Whether the mixed strategy
equilibrium is an evolutionarily stable strategy (ESS) depends on the specific
values of the rewards.
acknowledgement: 'This work was supported by grants from the John Templeton Foundation,
ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE),
FWF Grant (No P23499N23) and a Microsoft faculty fellows award.'
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with
multiple rewards. Proceedings of the Royal Society of London Series B Biological
Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041
apa: Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015).
Biological auctions with multiple rewards. Proceedings of the Royal Society
of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041
chicago: Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu
Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the
Royal Society of London Series B Biological Sciences. Royal Society, 2015.
https://doi.org/10.1098/rspb.2015.1041.
ieee: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological
auctions with multiple rewards,” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.
ista: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions
with multiple rewards. Proceedings of the Royal Society of London Series B Biological
Sciences. 282(1812).
mla: Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.
short: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of
the Royal Society of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:53:35Z
date_published: 2015-07-15T00:00:00Z
date_updated: 2023-09-07T11:40:43Z
day: '15'
department:
- _id: KrCh
doi: 10.1098/rspb.2015.1041
external_id:
pmid:
- '26180069'
intvolume: ' 282'
issue: '1812'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '5425'
quality_controlled: '1'
related_material:
record:
- id: '1400'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Biological auctions with multiple rewards
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '1400'
abstract:
- lang: eng
text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially
accumulated genetic and epigenetic alterations decrease cell death and increase
cell replication. We used mathematical models to quantify the effect of driver
gene mutations. The recently developed targeted therapies can lead to dramatic
regressions. However, in solid cancers, clinical responses are often short-lived
because resistant cancer cells evolve. We estimated that approximately 50 different
mutations can confer resistance to a typical targeted therapeutic agent. We find
that resistant cells are likely to be present in expanded subclones before the
start of the treatment. The dominant strategy to prevent the evolution of resistance
is combination therapy. Our analytical results suggest that in most patients,
dual therapy, but not monotherapy, can result in long-term disease control. However,
long-term control can only occur if there are no possible mutations in the genome
that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous
therapy with two drugs is much more likely to result in long-term disease control
than sequential therapy with the same drugs. To improve our understanding of the
underlying subclonal evolution we reconstruct the evolutionary history of a patient's
cancer from next-generation sequencing data of spatially-distinct DNA samples.
Using a quantitative measure of genetic relatedness, we found that pancreatic
cancers and their metastases demonstrated a higher level of relatedness than that
expected for any two cells randomly taken from a normal tissue. This minimal amount
of genetic divergence among advanced lesions indicates that genetic heterogeneity,
when quantitatively defined, is not a fundamental feature of the natural history
of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics
finds evidence for seeding patterns of metastases and can directly be used to
discover rules governing the evolution of solid malignancies to transform cancer
into a more predictable disease.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
citation:
ama: Reiter J. The subclonal evolution of cancer. 2015.
apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science
and Technology Austria.
chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science
and Technology Austria, 2015.
ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology
Austria, 2015.
ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and
Technology Austria.
mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science
and Technology Austria, 2015.
short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:44Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '04'
oa_version: None
page: '183'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5807'
related_material:
record:
- id: '1709'
relation: part_of_dissertation
status: public
- id: '2000'
relation: part_of_dissertation
status: public
- id: '2247'
relation: part_of_dissertation
status: public
- id: '2816'
relation: part_of_dissertation
status: public
- id: '2858'
relation: part_of_dissertation
status: public
- id: '3157'
relation: part_of_dissertation
status: public
- id: '3260'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: The subclonal evolution of cancer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1792'
abstract:
- lang: eng
text: Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop
a new concept of variation of multivariate functions on a compact Hausdorff space
with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka
theorem that holds for this notion of variation and discrepancy with respect to
D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions,
such as extreme or isotropic discrepancy. For extreme discrepancy, our result
coincides with the usual Koksma-Hlawka theorem. We show that the space of functions
of bounded D-variation contains important discontinuous functions and is closed
under natural algebraic operations. Finally, we illustrate the results on concrete
integration problems from integral geometry and stereology.
acknowledgement: F.P. is supported by the Graduate School of IST Austria, A.M.S is
supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by
a grant from the Villum Foundation.
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Anne
full_name: Svane, Anne
last_name: Svane
citation:
ama: Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems.
Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002
apa: Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general
discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002
chicago: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General
Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002.
ieee: F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy
systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797,
2015.
ista: Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy
systems. Journal of Complexity. 31(6), 773–797.
mla: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General
Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press,
2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002.
short: F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.
date_created: 2018-12-11T11:54:02Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jco.2015.06.002
intvolume: ' 31'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 773 - 797
publication: Journal of Complexity
publication_status: published
publisher: Academic Press
publist_id: '5320'
quality_controlled: '1'
related_material:
record:
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A Koksma-Hlawka inequality for general discrepancy systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-09-07T11:53:49Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
file:
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checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Dynamics of transcription factor binding site evolution
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: 11
year: '2015'
...
---
_id: '1502'
abstract:
- lang: eng
text: We extend the theory of input-output conformance with operators for merge
and quotient. The former is useful when testing against multiple requirements
or views. The latter can be used to generate tests for patches of an already tested
system. Both operators can combine systems with different action alphabets, which
is usually the case when constructing complex systems and specifications from
parts, for instance different views as well as newly defined functionality of
a~previous version of the system.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme
(Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373
(nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation,
grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project
No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for
Scientific Excellence."
alternative_title:
- 'Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based
Software Engineering '
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
citation:
ama: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition
operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175'
apa: 'Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015).
Complete composition operators for IOCO-testing theory (pp. 101–110). Presented
at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM.
https://doi.org/10.1145/2737166.2737175'
chicago: Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and
Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10.
ACM, 2015. https://doi.org/10.1145/2737166.2737175.
ieee: 'N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete
composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based
Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.'
ista: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition
operators for IOCO-testing theory. CBSE: Component-Based Software Engineering
, Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based
Software Engineering , , 101–110.'
mla: Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory.
ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.
short: N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015,
pp. 101–110.
conference:
end_date: 2015-05-08
location: Montreal, QC, Canada
name: 'CBSE: Component-Based Software Engineering '
start_date: 2015-05-04
date_created: 2018-12-11T11:52:24Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2737166.2737175
ec_funded: 1
file:
- access_level: open_access
checksum: c6ce681035c163a158751f240cb7d389
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:46Z
date_updated: 2020-07-14T12:44:59Z
file_id: '5303'
file_name: IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf
file_size: 467561
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 101 - 110
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_identifier:
isbn:
- 978-1-4503-3471-6
publication_status: published
publisher: ACM
publist_id: '5676'
pubrep_id: '625'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Complete composition operators for IOCO-testing theory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1501'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems. We focus on qualitative properties for MDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability. We introduce a new simulation relation to capture
the refinement relation of MDPs with respect to qualitative properties, and present
discrete graph algorithms with quadratic complexity to compute the simulation
relation. We present an automated technique for assume-guarantee style reasoning
for compositional analysis of two-player games by giving a counterexample guided
abstraction-refinement approach to compute our new simulation relation. We show
a tight link between two-player games and MDPs, and as a consequence the results
for games are lifted to MDPs with qualitative properties. We have implemented
our algorithms and show that the compositional analysis leads to significant improvements. '
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE),
and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games),
Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive
Modeling).'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative
properties in Markov decision processes. Formal Methods in System Design.
2015;47(2):230-264. doi:10.1007/s10703-015-0235-2
apa: Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional
analysis of qualitative properties in Markov decision processes. Formal Methods
in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for
Compositional Analysis of Qualitative Properties in Markov Decision Processes.”
Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.
ieee: K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis
of qualitative properties in Markov decision processes,” Formal Methods in
System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.
ista: Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of
qualitative properties in Markov decision processes. Formal Methods in System
Design. 47(2), 230–264.
mla: Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative
Properties in Markov Decision Processes.” Formal Methods in System Design,
vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2.
short: K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015)
230–264.
date_created: 2018-12-11T11:52:23Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-09-07T11:58:33Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/s10703-015-0235-2
ec_funded: 1
intvolume: ' 47'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.0835
month: '10'
oa: 1
oa_version: Preprint
page: 230 - 264
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5677'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: CEGAR for compositional analysis of qualitative properties in Markov decision
processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '1602'
abstract:
- lang: eng
text: Interprocedural analysis is at the heart of numerous applications in programming
languages, such as alias analysis, constant propagation, etc. Recursive state
machines (RSMs) are standard models for interprocedural analysis. We consider
a general framework with RSMs where the transitions are labeled from a semiring,
and path properties are algebraic with semiring operations. RSMs with algebraic
path properties can model interprocedural dataflow analysis problems, the shortest
path problem, the most probable path problem, etc. The traditional algorithms
for interprocedural analysis focus on path properties where the starting point
is fixed as the entry point of a specific method. In this work, we consider possible
multiple queries as required in many applications such as in alias analysis. The
study of multiple queries allows us to bring in a very important algorithmic distinction
between the resource usage of the one-time preprocessing vs for each individual
query. The second aspect that we consider is that the control flow graphs for
most programs have constant treewidth. Our main contributions are simple and implementable
algorithms that supportmultiple queries for algebraic path properties for RSMs
that have constant treewidth. Our theoretical results show that our algorithms
have small additional one-time preprocessing, but can answer subsequent queries
significantly faster as compared to the current best-known solutions for several
important problems, such as interprocedural reachability and shortest path. We
provide a prototype implementation for interprocedural reachability and intraprocedural
shortest path that gives a significant speed-up on several benchmarks.
acknowledgement: We thank anonymous reviewers for helpful comments to improve the
presentation of the paper.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Prateesh
full_name: Goyal, Prateesh
last_name: Goyal
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for
algebraic path properties in recursive state machines with constant treewidth.
ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979
apa: 'Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015).
Faster algorithms for algebraic path properties in recursive state machines with
constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and
Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive
State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015.
https://doi.org/10.1145/2676726.2676979.
ieee: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms
for algebraic path properties in recursive state machines with constant treewidth,”
ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms
for algebraic path properties in recursive state machines with constant treewidth.
ACM SIGPLAN Notices. 50(1), 97–109.
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties
in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices,
vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices
50 (2015) 97–109.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'SIGPLAN: Symposium on Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:52:58Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676979
ec_funded: 1
external_id:
arxiv:
- '1410.7724'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1410.7724
month: '01'
oa: 1
oa_version: Preprint
page: 97 - 109
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM SIGPLAN Notices
publication_status: published
publisher: ACM
publist_id: '5565'
quality_controlled: '1'
related_material:
record:
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for algebraic path properties in recursive state machines
with constant treewidth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1604'
abstract:
- lang: eng
text: We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis.
Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551.
doi:10.1145/2676726.2676968
apa: 'Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India:
ACM. https://doi.org/10.1145/2676726.2676968'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative
Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT
. ACM, 2015. https://doi.org/10.1145/2676726.2676968.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural
analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50,
no. 1. ACM, pp. 539–551, 2015.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.
mla: Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings
of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51,
doi:10.1145/2676726.2676968.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual
ACM SIGPLAN-SIGACT 50 (2015) 539–551.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'SIGPLAN: Symposium on Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:52:59Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676968
ec_funded: 1
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 539 - 551
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 'Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT '
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5563'
pubrep_id: '523'
quality_controlled: '1'
related_material:
record:
- id: '5445'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantitative interprocedural analysis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1607'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W
the largest absolute value of the weights. Our main theoretical results are as
follows. First, for constant treewidth graphs we present an algorithm that approximates
the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ))
and linear space, as compared to the classical algorithms that require quadratic
time. Second, for the ratio property we present an algorithm that for constant
treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output
is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)).
Third, for the minimum initial credit problem we show that (i) for general graphs
the problem can be solved in O(n2⋅m) time and the associated decision problem
can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and
O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present
an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W))
bound. We have implemented some of our algorithms and show that they present a
significant speedup on standard benchmarks.
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative
verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157.
doi:10.1007/978-3-319-21690-4_9'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms
for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer.
https://doi.org/10.1007/978-3-319-21690-4_9'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,”
9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for
quantitative verification in constant treewidth graphs,” presented at the CAV:
Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification,
LNCS, vol. 9206, 140–157.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp.
140–157.
conference:
end_date: 2015-07-24
location: San Francisco, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:59Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_9
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07384
month: '07'
oa: 1
oa_version: Preprint
page: 140 - 157
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5560'
quality_controlled: '1'
related_material:
record:
- id: '5430'
relation: earlier_version
status: public
- id: '5437'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1714'
abstract:
- lang: eng
text: 'We present a flexible framework for the automated competitive analysis of
on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective
graphs: Given a task set and an on-line scheduling algorithm specified as a labeled
transition system, along with some optional safety, liveness, and/or limit-average
constraints for the adversary, we automatically compute the competitive ratio
of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility
and power of our approach by comparing the competitive ratio of several on-line
algorithms, including Dover, that have been proposed in the past, for various
task sets. Our experimental results reveal that none of these algorithms is universally
optimal, in the sense that there are task sets where other schedulers provide
better performance. Our framework is hence a very useful design tool for selecting
optimal algorithms for a given application.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Alexander
full_name: Kößler, Alexander
last_name: Kößler
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
citation:
ama: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time
Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9'
apa: 'Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework
for automated competitive analysis of on-line scheduling of firm-deadline tasks.
In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE.
https://doi.org/10.1109/RTSS.2014.9'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich
Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling
of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE,
2015. https://doi.org/10.1109/RTSS.2014.9.
ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for
automated competitive analysis of on-line scheduling of firm-deadline tasks,”
in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January,
pp. 118–127.
ista: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated
competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems
Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.'
mla: Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis
of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium,
vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.
short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems
Symposium, IEEE, 2015, pp. 118–127.
conference:
end_date: 2014-12-05
location: Rome, Italy
name: 'RTSS: Real-Time Systems Symposium'
start_date: 2014-12-02
date_created: 2018-12-11T11:53:37Z
date_published: 2015-01-15T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '15'
department:
- _id: KrCh
doi: 10.1109/RTSS.2014.9
intvolume: ' 2015'
issue: January
language:
- iso: eng
month: '01'
oa_version: None
page: 118 - 127
publication: Real-Time Systems Symposium
publication_status: published
publisher: IEEE
publist_id: '5417'
quality_controlled: '1'
related_material:
record:
- id: '5423'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A framework for automated competitive analysis of on-line scheduling of firm-deadline
tasks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1633'
abstract:
- lang: eng
text: "We present a method for simulating brittle fracture under the assumptions
of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element
method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture
surfaces. The computational cost of the BEM is alleviated by using a low-resolution
mesh and interpolating the resulting stress intensity factors when propagating
the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture
surfaces with high spatial and temporal resolution, taking spatial variation of
material toughness and/or strength into account. It also allows for crack initiation
to be handled separately from crack propagation, which is not only more reasonable
from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating
the resolution of the crack-front from the resolution of the computational mesh
increases the efficiency and therefore the amount of visual detail on the resulting
fracture surfaces. The BEM also allows us to re-use previously computed blocks
of the system matrix."
article_number: '151'
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary
elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896'
apa: 'Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation
with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States: ACM. https://doi.org/10.1145/2766896'
chicago: Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation
with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.
ieee: 'D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with
boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol.
34, no. 4.'
ista: 'Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with
boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques vol. 34, 151.'
mla: Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation
with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896.
short: D. Hahn, C. Wojtan, in:, ACM, 2015.
conference:
end_date: 2015-08-13
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2015-08-09
date_created: 2018-12-11T11:53:09Z
date_published: 2015-07-27T00:00:00Z
date_updated: 2023-09-07T12:02:56Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2766896
ec_funded: 1
file:
- access_level: open_access
checksum: 955aee971983f6b6152bcc1c9b4a7c20
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:13Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5131'
file_name: IST-2016-609-v1+1_FractureBEM.pdf
file_size: 20154270
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5522'
pubrep_id: '609'
quality_controlled: '1'
related_material:
record:
- id: '839'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: High-resolution brittle fracture simulation with boundary elements
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2015'
...
---
_id: '1537'
abstract:
- lang: eng
text: 3D amoeboid cell migration is central to many developmental and disease-related
processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid
cell migration mode in early zebrafish embryos, termed stable-bleb migration.
Stable-bleb cells display an invariant polarized balloon-like shape with exceptional
migration speed and persistence. Progenitor cells can be reversibly transformed
into stable-bleb cells irrespective of their primary fate and motile characteristics
by increasing myosin II activity through biochemical or mechanical stimuli. Using
a combination of theory and experiments, we show that, in stable-bleb cells, cortical
contractility fluctuations trigger a stochastic switch into amoeboid motility,
and a positive feedback between cortical flows and gradients in contractility
maintains stable-bleb cell polarization. We further show that rearward cortical
flows drive stable-bleb cell migration in various adhesive and non-adhesive environments,
unraveling a highly versatile amoeboid migration phenotype.
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We would like to thank R. Hausschild and E. Papusheva for technical
assistance and the service facilities at the IST Austria for continuous support.
The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel
and E. Paluch for exchanging unpublished data. '
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Andrew
full_name: Callan Jones, Andrew
last_name: Callan Jones
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Monika
full_name: Ritsch Marte, Monika
last_name: Ritsch Marte
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers
a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685.
doi:10.1016/j.cell.2015.01.008
apa: Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K.,
… Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch
to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008
chicago: Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi
Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers
a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press,
2015. https://doi.org/10.1016/j.cell.2015.01.008.
ieee: V. Ruprecht et al., “Cortical contractility triggers a stochastic switch
to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp.
673–685, 2015.
ista: Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V,
Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility
triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.
mla: Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch
to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015,
pp. 673–85, doi:10.1016/j.cell.2015.01.008.
short: V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V.
Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160
(2015) 673–685.
date_created: 2018-12-11T11:52:35Z
date_published: 2015-02-12T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
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publication: Cell
publication_status: published
publisher: Cell Press
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relation: dissertation_contains
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scopus_import: 1
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title: Cortical contractility triggers a stochastic switch to fast amoeboid cell motility
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
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year: '2015'
...
---
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abstract:
- lang: eng
text: Auxin participates in a multitude of developmental processes, as well as responses
to environmental cues. Compared with other plant hormones, auxin exhibits a unique
property, as it undergoes directional, cell-to-cell transport facilitated by plasma
membrane-localized transport proteins. Among them, a prominent role has been ascribed
to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin
transport on account of their asymmetric subcellular localizations. In this review,
we provide an overview of the multiple developmental roles of PIN proteins, including
the atypical endoplasmic reticulum-localized members of the family, and look at
the family from an evolutionary perspective. Next, we cover the cell biological
and molecular aspects of PIN function, in particular the establishment of their
polar subcellular localization. Hormonal and environmental inputs into the regulation
of PIN action are summarized as well.
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and
evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874'
apa: 'Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action,
regulation, and evolution. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.114.134874'
chicago: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action,
Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists,
2015. https://doi.org/10.1105/tpc.114.134874.'
ieee: 'M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation,
and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists,
pp. 20–32, 2015.'
ista: 'Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation,
and evolution. Plant Cell. 27(1), 20–32.'
mla: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action,
Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society
of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.'
short: M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.
date_created: 2018-12-11T11:52:54Z
date_published: 2015-01-20T00:00:00Z
date_updated: 2023-09-07T12:06:09Z
day: '20'
department:
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doi: 10.1105/tpc.114.134874
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url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/
month: '01'
oa: 1
oa_version: Submitted Version
page: 20 - 32
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5580'
quality_controlled: '1'
related_material:
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relation: dissertation_contains
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scopus_import: 1
status: public
title: 'PIN-dependent auxin transport: Action, regulation, and evolution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2015'
...