---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
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. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
record:
- id: '9715'
relation: research_data
status: public
- id: '9772'
relation: research_data
status: public
scopus_import: 1
status: public
title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
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. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
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.s003
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: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9773'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015.
doi:10.1371/journal.pcbi.1004055.s002
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary
simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary
Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation
code.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code,
Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-08-05T12:58:07Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s002
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Evolutionary simulation code
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '981'
abstract:
- lang: eng
text: The tunability of topological surface states and controllable opening of the
Dirac gap are of fundamental and practical interest in the field of topological
materials. In the newly discovered topological crystalline insulators (TCIs),
theory predicts that the Dirac node is protected by a crystalline symmetry and
that the surface state electrons can acquire a mass if this symmetry is broken.
Recent studies have detected signatures of a spontaneously generated Dirac gap
in TCIs; however, the mechanism of mass formation remains elusive. In this work,
we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x
Sn x Se for a wide range of alloy compositions spanning the topological and non-topological
regimes. The STM topographies reveal a symmetry-breaking distortion on the surface,
which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous
to the long sought-after Higgs mechanism in particle physics. Interestingly, the
measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude
of the distortion remains nearly constant. Our data and calculations reveal that
the penetration depth of Dirac surface states controls the magnitude of the Dirac
mass. At the limit of the critical composition, the penetration depth is predicted
to go to infinity, resulting in zero mass, consistent with our measurements. Finally,
we discover the existence of surface states in the non-topological regime, which
have the characteristics of gapped, double-branched Dirac fermions and could be
exploited in realizing superconductivity in these materials.
acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny,
A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon
for help with EDS measurements. V.M. gratefully acknowledges funding from the US
Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880
for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported
by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University
is supported by the US Department of Energy grant number DE-FG02-07ER46352, and
benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work
at Princeton University is supported by the US National Science Foundation Grant,
NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project
number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Junwei
full_name: Liu, Junwei
last_name: Liu
- first_name: Guoqing
full_name: Chang, Guoqing
last_name: Chang
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry
breaking on the surfaces of topological crystalline insulators. Nature Materials.
2015;14(3):318-324. doi:10.1038/nmat4215
apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces
of topological crystalline insulators. Nature Materials. Nature Publishing
Group. https://doi.org/10.1038/nmat4215
chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry
Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials.
Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.
ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking
on the surfaces of topological crystalline insulators,” Nature Materials,
vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.
ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G,
Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation
from crystal symmetry breaking on the surfaces of topological crystalline insulators.
Nature Materials. 14(3), 318–324.
mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking
on the Surfaces of Topological Crystalline Insulators.” Nature Materials,
vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.
short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu,
G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature
Materials 14 (2015) 318–324.
date_created: 2018-12-11T11:49:31Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '01'
doi: 10.1038/nmat4215
extern: 1
intvolume: ' 14'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.4906
month: '03'
oa: 1
page: 318 - 324
publication: Nature Materials
publication_status: published
publisher: Nature Publishing Group
publist_id: '6419'
quality_controlled: 0
status: public
title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological
crystalline insulators
type: journal_article
volume: 14
year: '2015'
...
---
_id: '982'
abstract:
- lang: eng
text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional
quantum manybody systems based on their response to a local perturbation. We study
the distribution of matrix elements of a local operator between the system's eigenstates,
finding a qualitatively different behavior in the manybody localized (MBL) and
ergodic phases. To characterize how strongly a local perturbation modifies the
eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the
disorder-averaged ratio of a typical matrix element of a local operator V to energy
level spacing δ this parameter is reminiscent of the Thouless conductance in the
single-particle localization. We show that the parameter g(L) decreases with system
size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization
transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate
our approach by studying the many-body localization transition and resolving the
many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using
exact diagonalization and time-evolving block-decimation methods. Our criterion
for the MBL transition gives insights into microscopic details of transition.
Its direct physical consequences, in particular, logarithmically slow transport
at the transition and extensive entanglement entropy of the eigenstates, are consistent
with recent renormalization-group predictions.
acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew
Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and
David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor
library. Research at Perimeter Institute is supported by the Government of Canada
through Industry Canada and by the Province of Ontario through the Ministry of Economic
Development & Innovation. This research was supported by Gordon and Betty Moore
Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation,
NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the
facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium
and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities
of Leeds and Manchester.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047
apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization
phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body
Localization-Delocalization Phase Transition.” Physical Review X. American
Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization
phase transition,” Physical Review X, vol. 5, no. 4. American Physical
Society, 2015.
ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 5(4).
mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization
Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical
Society, 2015, doi:10.1103/PhysRevX.5.041047.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).
date_created: 2018-12-11T11:49:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:25Z
day: '01'
doi: 10.1103/PhysRevX.5.041047
extern: 1
intvolume: ' 5'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.01635
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '6418'
quality_controlled: 0
status: public
title: Criterion for many-body localization-delocalization phase transition
type: journal_article
volume: 5
year: '2015'
...
---
_id: '99'
abstract:
- lang: eng
text: Quasiparticle excitations can compromise the performance of superconducting
devices, causing high-frequency dissipation, decoherence in Josephson qubits,
and braiding errors in proposed Majorana-based topological quantum computers.
Quasiparticle dynamics have been studied in detail in metallic superconductors
but remain relatively unexplored in semiconductor-superconductor structures, which
are now being intensely pursued in the context of topological superconductivity.
To this end, we use a system comprising a gate-confined semiconductor nanowire
with an epitaxially grown superconductor layer, yielding an isolated, proximitized
nanowire segment. We identify bound states in the semiconductor by means of bias
spectroscopy, determine the characteristic temperatures and magnetic fields for
quasiparticle excitations, and extract a parity lifetime (poisoning time) of the
bound state in the semiconductor exceeding 10 ms.
acknowledgement: Research support by Microsoft Project Q, the Danish National Research
Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European
Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M.
acknowledges support from the Villum Foundation.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Gediminas
full_name: Kiršanskas, Gediminas
last_name: Kiršanskas
- first_name: W
full_name: Chang, W
last_name: Chang
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021.
doi:10.1038/nphys3461
apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth,
F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized
semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461
chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand
Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg,
and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor
Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.
ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized
semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing
Group, pp. 1017–1021, 2015.
ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup
P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.
mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized
Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing
Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.
short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P.
Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11
(2015) 1017–1021.
date_created: 2018-12-11T11:44:37Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:22:28Z
day: '14'
doi: 10.1038/nphys3461
extern: '1'
external_id:
arxiv:
- '1501.05155'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.05155
month: '09'
oa: 1
oa_version: Preprint
page: 1017 - 1021
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7955'
quality_controlled: '1'
status: public
title: Parity lifetime of bound states in a proximitized semiconductor nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '8495'
abstract:
- lang: eng
text: 'In this note, we consider the dynamics associated to a perturbation of an
integrable Hamiltonian system in action-angle coordinates in any number of degrees
of freedom and we prove the following result of ``micro-diffusion'''': under generic
assumptions on $ h$ and $ f$, there exists an orbit of the system for which the
drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after
a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially
minimal, are that there exists a resonant point for $ h$ and that the corresponding
averaged perturbation is non-constant. The conclusions, although very weak when
compared to usual instability phenomena, are also essentially optimal within this
setting.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems
close to integrable. Proceedings of the American Mathematical Society.
2015;144(4):1553-1560. doi:10.1090/proc/12796
apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for
Hamiltonian systems close to integrable. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12796
chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for
Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical
Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.
ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian
systems close to integrable,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.
ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian
systems close to integrable. Proceedings of the American Mathematical Society.
144(4), 1553–1560.
mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian
Systems Close to Integrable.” Proceedings of the American Mathematical Society,
vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.
short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society
144 (2015) 1553–1560.
date_created: 2020-09-18T10:46:14Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '21'
doi: 10.1090/proc/12796
extern: '1'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 1553-1560
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 0002-9939
- 1088-6826
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A note on micro-instability for Hamiltonian systems close to integrable
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2015'
...
---
_id: '866'
abstract:
- lang: eng
text: Proteases play important roles in many biologic processes and are key mediators
of cancer, inflammation, and thrombosis. However, comprehensive and quantitative
techniques to define the substrate specificity profile of proteases are lacking.
The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand
factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage
display library based on a 73-amino acid fragment of VWF was constructed, and
the ADAMTS13-dependent change in library complexity was evaluated over reaction
time points, using high-throughput sequencing. Reaction rate constants (kcat/KM)
were calculated for nearly every possible single amino acid substitution within
this fragment. This massively parallel enzyme kinetics analysis detailed the specificity
of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues
while defining exosite binding domains. These data provided empirical evidence
for the propensity for epistasis within VWF and showed strong correlation to conservation
across orthologs, highlighting evolutionary selective pressures for VWF.
acknowledgement: |
We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Colin
full_name: Kretz, Colin A
last_name: Kretz
- first_name: Manhong
full_name: Dai, Manhong
last_name: Dai
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Andrew
full_name: Yee, Andrew
last_name: Yee
- first_name: Karl
full_name: Desch, Karl C
last_name: Desch
- first_name: David
full_name: Siemieniak, David R
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Fan
full_name: Meng, Fan
last_name: Meng
- first_name: David
full_name: Ginsburg, David B
last_name: Ginsburg
citation:
ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals
the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS.
2015;112(30):9328-9333. doi:10.1073/pnas.1511328112
apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg,
D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition
landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1511328112
chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David
Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively
Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease
ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.
ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112,
no. 30. National Academy of Sciences, pp. 9328–9333, 2015.
ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov
F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate
Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112,
no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg,
F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
date_created: 2018-12-11T11:48:55Z
date_published: 2015-07-28T00:00:00Z
date_updated: 2021-01-12T08:20:26Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: 1
intvolume: ' 112'
issue: '30'
month: '07'
page: 9328 - 9333
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: 0
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
volume: 112
year: '2015'
...
---
_id: '886'
abstract:
- lang: eng
text: The factors that determine the tempo and mode of protein evolution continue
to be a central question in molecular evolution. Traditionally, studies of protein
evolution focused on the rates of amino acid substitutions. More recently, with
the availability of sequence data and advanced experimental techniques, the focus
of attention has shifted toward the study of evolutionary trajectories and the
overall layout of protein fitness landscapes. In this review we describe the effect
of epistasis on the topology of evolutionary pathways that are likely to be found
in fitness landscapes and develop a simple theory to connect the number of maladapted
genotypes to the topology of fitness landscapes with epistatic interactions. Finally,
we review recent studies that have probed the extent of epistatic interactions
and have begun to chart the fitness landscapes in protein sequence space.
acknowledgement: 'This work has been supported by a grant from the HHMI International
Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants
from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo
Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional
Development Fund (ERDF), the European Union, and the European Research Council under
grant agreement no 335980_EinME.'
author:
- first_name: Dmitry
full_name: Kondrashov, Dmitry A
last_name: Kondrashov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009
apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged
fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009
chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015.
https://doi.org/10.1016/j.tig.2014.09.009.
ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes
in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33,
2015.
ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 31(1), 24–33.
mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no.
1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
date_created: 2018-12-11T11:49:01Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1016/j.tig.2014.09.009
extern: 1
intvolume: ' 31'
issue: '1'
month: '01'
page: 24 - 33
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6764'
quality_controlled: 0
status: public
title: Topological features of rugged fitness landscapes in sequence space
type: journal_article
volume: 31
year: '2015'
...
---
_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
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language:
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main_file_link:
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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
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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'
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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:
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- id: '1709'
relation: part_of_dissertation
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- 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
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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:
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status: public
- id: '1792'
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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'
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