---
_id: '1490'
abstract:
- lang: eng
text: To induce adaptive immunity, dendritic cells (DCs) migrate through afferent
lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in
several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively
crawl into downstream collecting vessels. From there, they are next passively
and rapidly transported to the dLN by lymph flow. Here, we describe a role for
the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging
in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely
abolished DC migration from capillaries toward collecting vessels and reduced
the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that
in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial
monolayers, thereby inducing downstream-directed DC migration. These findings
reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through
the formation of a flow-induced gradient.
author:
- first_name: Erica
full_name: Russo, Erica
last_name: Russo
- first_name: Alvaro
full_name: Teijeira, Alvaro
last_name: Teijeira
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Ann
full_name: Willrodt, Ann
last_name: Willrodt
- first_name: Joël
full_name: Bloch, Joël
last_name: Bloch
- first_name: Maximilian
full_name: Nitschké, Maximilian
last_name: Nitschké
- first_name: Laura
full_name: Santambrogio, Laura
last_name: Santambrogio
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- 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: Cornelia
full_name: Halin, Cornelia
last_name: Halin
citation:
ama: Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue
egress of dendritic cells through afferent lymphatic vessels. Cell Reports.
2016;14(7):1723-1734. doi:10.1016/j.celrep.2016.01.048
apa: Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké,
M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic
cells through afferent lymphatic vessels. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.01.048
chicago: Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch,
Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt,
and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic
Cells through Afferent Lymphatic Vessels.” Cell Reports. Cell Press, 2016.
https://doi.org/10.1016/j.celrep.2016.01.048.
ieee: E. Russo et al., “Intralymphatic CCL21 promotes tissue egress of dendritic
cells through afferent lymphatic vessels,” Cell Reports, vol. 14, no. 7.
Cell Press, pp. 1723–1734, 2016.
ista: Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio
L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue
egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7),
1723–1734.
mla: Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic
Cells through Afferent Lymphatic Vessels.” Cell Reports, vol. 14, no. 7,
Cell Press, 2016, pp. 1723–34, doi:10.1016/j.celrep.2016.01.048.
short: E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké,
L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.
date_created: 2018-12-11T11:52:19Z
date_published: 2016-02-23T00:00:00Z
date_updated: 2021-01-12T06:51:07Z
day: '23'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1016/j.celrep.2016.01.048
file:
- access_level: open_access
checksum: c98c1151d5f1e5ce1643a83d8d7f3c29
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:30Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4948'
file_name: IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf
file_size: 5489897
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1723 - 1734
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5697'
pubrep_id: '515'
quality_controlled: '1'
scopus_import: 1
status: public
title: Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent
lymphatic vessels
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1491'
abstract:
- lang: eng
text: We study the ground state of a trapped Bose gas, starting from the full many-body
Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional
in the limit of a large particle number, when the interaction potential converges
slowly to a Dirac delta function. Our method is based on quantitative estimates
on the discrepancy between the full many-body energy and its mean-field approximation
using Hartree states. These are proved using finite dimensional localization and
a quantitative version of the quantum de Finetti theorem. Our approach covers
the case of attractive interactions in the regime of stability. In particular,
our main new result is a derivation of the 2D attractive non-linear Schrödinger
ground state.
acknowledgement: The authors acknowledge financial support from the European Research
Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project,
ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality
of the Institute for Mathematical Science of the National University of Singapore.
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Nicolas
full_name: Rougerie, Nicolas
last_name: Rougerie
citation:
ama: Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases. Transactions of the American
Mathematical Society. 2016;368(9):6131-6157. doi:10.1090/tran/6537
apa: Lewin, M., Nam, P., & Rougerie, N. (2016). The mean-field approximation
and the non-linear Schrödinger functional for trapped Bose gases. Transactions
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6537
chicago: Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation
and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions
of the American Mathematical Society. American Mathematical Society, 2016.
https://doi.org/10.1090/tran/6537.
ieee: M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases,” Transactions of the American
Mathematical Society, vol. 368, no. 9. American Mathematical Society, pp.
6131–6157, 2016.
ista: Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical
Society. 368(9), 6131–6157.
mla: Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger
Functional for Trapped Bose Gases.” Transactions of the American Mathematical
Society, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57,
doi:10.1090/tran/6537.
short: M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical
Society 368 (2016) 6131–6157.
date_created: 2018-12-11T11:52:20Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:07Z
day: '01'
department:
- _id: RoSe
doi: 10.1090/tran/6537
intvolume: ' 368'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1405.3220
month: '01'
oa: 1
oa_version: Submitted Version
page: 6131 - 6157
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5692'
quality_controlled: '1'
scopus_import: 1
status: public
title: The mean-field approximation and the non-linear Schrödinger functional for
trapped Bose gases
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 368
year: '2016'
...
---
_id: '1492'
abstract:
- lang: eng
text: To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated
cells with a preserved prolif eration capacity. The root pericycle represents
a unique tissue with conditional meristematic activity, and its tight control
determines initiation of lateral organs. Here we show that the meristematic activity
of the pericycle is constrained by the interaction with the adjacent endodermis.
Release of these restraints by elimination of endo dermal cells by single-cell
ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis
removal substitutes for the phytohormone auxin-dependent initiation of the pericycle
meristematic activity. However, auxin is indispensable to steer the cell division
plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally
distinct role for auxin during lateral root initiation. In the endodermis, auxin
releases constraints arising from cell-to-cell interactions that compromise the
pericycle meristematic activity, whereas, in the pericycle, auxin defines the
orientation of the cell division plane to initiate lateral roots.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: 'This work was supported by a European Research Council Starting
Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders
(G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is
indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. '
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Joop
full_name: Vermeer, Joop
last_name: Vermeer
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Hana
full_name: Rakusova, Hana
last_name: Rakusova
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination
reveals an auxin-guided biphasic mode of lateral root initiation. Genes and
Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115
apa: Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer,
J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided
biphasic mode of lateral root initiation. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115
chicago: Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme,
Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination
Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and
Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115.
ieee: P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided
biphasic mode of lateral root initiation,” Genes and Development, vol.
30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.
ista: Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq
J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination
reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development.
30(4), 471–483.
mla: Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic
Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4,
Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115.
short: P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer,
J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes
and Development 30 (2016) 471–483.
date_created: 2018-12-11T11:52:20Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:08Z
day: '01'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1101/gad.276964.115
external_id:
pmid:
- ' 26883363'
file:
- access_level: open_access
checksum: ea394498ee56270e021d1028a29358a0
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T09:56:11Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5883'
file_name: 2016_GeneDev_Marhavy.pdf
file_size: 2757636
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 471 - 483
pmid: 1
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '5691'
quality_controlled: '1'
scopus_import: 1
status: public
title: Targeted cell elimination reveals an auxin-guided biphasic mode of lateral
root initiation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2016'
...
---
_id: '1493'
abstract:
- lang: eng
text: We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock
equations as an effective mean-field dynamics from the microscopic Schrödinger
equation for fermionic many-particle systems in quantum mechanics. The method
is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011)
for bosonic systems to fermionic systems. It is based on a Gronwall type estimate
for a suitable measure of distance between the microscopic solution and an antisymmetrized
product state. We use this method to treat a new mean-field limit for fermions
with long-range interactions in a large volume. Some of our results hold for singular
attractive or repulsive interactions. We can also treat Coulomb interaction assuming
either a mild singularity cutoff or certain regularity conditions on the solutions
to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction
energy are of the same order, while the average force is subleading. For some
interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation
than a simpler dynamics that one would expect from the subleading force. With
our method we also treat the mean-field limit coupled to a semiclassical limit,
which was discussed in the literature before, and we recover some of the previous
results. All results hold for initial data close (but not necessarily equal) to
antisymmetrized product states and we always provide explicit rates of convergence.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_number: '3'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field
dynamics. Mathematical Physics, Analysis and Geometry. 2016;19(1). doi:10.1007/s11040-016-9204-2
apa: Petrat, S. P., & Pickl, P. (2016). A new method and a new scaling for deriving
fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry.
Springer. https://doi.org/10.1007/s11040-016-9204-2
chicago: Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving
Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry.
Springer, 2016. https://doi.org/10.1007/s11040-016-9204-2.
ieee: S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic
mean-field dynamics,” Mathematical Physics, Analysis and Geometry, vol.
19, no. 1. Springer, 2016.
ista: Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic
mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.
mla: Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving
Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry,
vol. 19, no. 1, 3, Springer, 2016, doi:10.1007/s11040-016-9204-2.
short: S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).
date_created: 2018-12-11T11:52:20Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:08Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1007/s11040-016-9204-2
ec_funded: 1
file:
- access_level: open_access
checksum: eb5d2145ef0d377c4f78bf06e18f4529
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:55Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5246'
file_name: IST-2016-514-v1+1_s11040-016-9204-2.pdf
file_size: 911310
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '5690'
pubrep_id: '514'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new method and a new scaling for deriving fermionic mean-field dynamics
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: 19
year: '2016'
...
---
_id: '1494'
abstract:
- lang: eng
text: Turbulence is one of the most frequently encountered non-equilibrium phenomena
in nature, yet characterizing the transition that gives rise to turbulence in
basic shear flows has remained an elusive task. Although, in recent studies, critical
points marking the onset of sustained turbulence have been determined for several
such flows, the physical nature of the transition could not be fully explained.
In extensive experimental and computational studies we show for the example of
Couette flow that the onset of turbulence is a second-order phase transition and
falls into the directed percolation universality class. Consequently, the complex
laminar–turbulent patterns distinctive for the onset of turbulence in shear flows
result from short-range interactions of turbulent domains and are characterized
by universal critical exponents. More generally, our study demonstrates that even
high-dimensional systems far from equilibrium such as turbulence exhibit universality
at onset and that here the collective dynamics obeys simple rules.
acknowledgement: We thank P. Maier for providing valuable ideas and supporting us
in the technical aspects. Discussions with D. Barkley, Y. Duguet, B. Eckhart, N.
Goldenfeld, P. Manneville and K. Takeuchi are gratefully acknowledged. We acknowledge
the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research
Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC
Grant Agreement 306589 for financial support. L.S. and B.H. acknowledge research
funding by Deutsche Forschungsgemeinschaft (DFG) under Grant No. SFB 963/1 (project
A8). Numerical simulations were performed thanks to the CPU time allocations of
JUROPA in Juelich Supercomputing Center (project HGU17) and of the Max Planck Computing
and Data Facility (Garching, Germany). Excellent technical support from M. Rampp
on the hybrid code nsCouette is appreciated.
author:
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Liang
full_name: Shi, Liang
id: 374A3F1A-F248-11E8-B48F-1D18A9856A87
last_name: Shi
- first_name: Kerstin
full_name: Avila, Kerstin
last_name: Avila
- first_name: Shreyas V
full_name: Jalikop, Shreyas V
id: 44A1D772-F248-11E8-B48F-1D18A9856A87
last_name: Jalikop
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. Directed percolation
phase transition to sustained turbulence in Couette flow. Nature Physics.
2016;12(3):254-258. doi:10.1038/nphys3675
apa: Lemoult, G. M., Shi, L., Avila, K., Jalikop, S. V., Avila, M., & Hof, B.
(2016). Directed percolation phase transition to sustained turbulence in Couette
flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3675
chicago: Lemoult, Grégoire M, Liang Shi, Kerstin Avila, Shreyas V Jalikop, Marc
Avila, and Björn Hof. “Directed Percolation Phase Transition to Sustained Turbulence
in Couette Flow.” Nature Physics. Nature Publishing Group, 2016. https://doi.org/10.1038/nphys3675.
ieee: G. M. Lemoult, L. Shi, K. Avila, S. V. Jalikop, M. Avila, and B. Hof, “Directed
percolation phase transition to sustained turbulence in Couette flow,” Nature
Physics, vol. 12, no. 3. Nature Publishing Group, pp. 254–258, 2016.
ista: Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. 2016. Directed percolation
phase transition to sustained turbulence in Couette flow. Nature Physics. 12(3),
254–258.
mla: Lemoult, Grégoire M., et al. “Directed Percolation Phase Transition to Sustained
Turbulence in Couette Flow.” Nature Physics, vol. 12, no. 3, Nature Publishing
Group, 2016, pp. 254–58, doi:10.1038/nphys3675.
short: G.M. Lemoult, L. Shi, K. Avila, S.V. Jalikop, M. Avila, B. Hof, Nature Physics
12 (2016) 254–258.
date_created: 2018-12-11T11:52:21Z
date_published: 2016-02-15T00:00:00Z
date_updated: 2021-01-12T06:51:08Z
day: '15'
department:
- _id: BjHo
doi: 10.1038/nphys3675
ec_funded: 1
intvolume: ' 12'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 254 - 258
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '5685'
quality_controlled: '1'
scopus_import: 1
status: public
title: Directed percolation phase transition to sustained turbulence in Couette flow
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '1496'
abstract:
- lang: eng
text: The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is
theoretically investigated within a fully relativistic framework and a second-order
perturbation theory. We focus our analysis on how electron correlation, as well
as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For
this purpose, we include the electronic correlation via an effective local potential
and within a single configuration-state model. Due to its experimental interest,
evaluations of decay rates are performed for berylliumlike xenon and uranium.
We find that the negative-energy contribution can be neglected at the present
level of accuracy in the evaluation of the decay rate. On the other hand, if contributions
of electronic correlation are not carefully taken into account, it may change
the lifetime of the metastable state by up to 20%. By performing a full-relativistic
jj-coupling calculation, we found a decrease of the decay rate by two orders of
magnitude compared to non-relativistic LS-coupling calculations, for the selected
heavy ions.
acknowledgement: 'This research was supported in part by FCT, Portugal, through
Project No. PTDC/FIS/117606/2010, financed by the European Community Fund FEDER through the COMPETE. '
article_number: '032502'
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Jorge
full_name: Machado, Jorge
last_name: Machado
- first_name: Mauro
full_name: Guerra, Mauro
last_name: Guerra
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon
decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3).
doi:10.1103/PhysRevA.93.032502
apa: Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P.,
& Santos, J. (2016). Relativistic evaluation of the two-photon decay of the
metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model. Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society. https://doi.org/10.1103/PhysRevA.93.032502
chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra,
Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay
of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
Model.” Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.032502.
ieee: P. Amaro et al., “Relativistic evaluation of the two-photon decay of
the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model,” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
93, no. 3. American Physical Society, 2016.
ista: Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J.
2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
state in berylliumlike ions with an effective-potential model. Physical Review
A - Atomic, Molecular, and Optical Physics. 93(3), 032502.
mla: Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the
Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
Model.” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
93, no. 3, 032502, American Physical Society, 2016, doi:10.1103/PhysRevA.93.032502.
short: P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J.
Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).
date_created: 2018-12-11T11:52:21Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.93.032502
ec_funded: 1
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.06169
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5683'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
state in berylliumlike ions with an effective-potential model
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1518'
abstract:
- lang: eng
text: The inference of demographic history from genome data is hindered by a lack
of efficient computational approaches. In particular, it has proved difficult
to exploit the information contained in the distribution of genealogies across
the genome. We have previously shown that the generating function (GF) of genealogies
can be used to analytically compute likelihoods of demographic models from configurations
of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
a simple, recursive form, the size of such likelihood calculations explodes quickly
with the number of individuals and applications of this framework have so far
been mainly limited to small samples (pairs and triplets) for which the GF can
be written by hand. Here we investigate several strategies for exploiting the
inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
can be decomposed into a set of equivalence classes that allows likelihood calculations
from nontrivial samples. Using this strategy, we automated blockwise likelihood
calculations for a general set of demographic scenarios in Mathematica. These
histories may involve population size changes, continuous migration, discrete
divergence, and admixture between multiple populations. To give a concrete example,
we calculate the likelihood for a model of isolation with migration (IM), assuming
two diploid samples without phase and outgroup information. We demonstrate the
new inference scheme with an analysis of two individual butterfly genomes from
the sister species Heliconius melpomene rosina and H. cydno.
acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project
and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on
an earlier version of this manuscript. This work was supported by funding from the\r\nUnited
Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant
from the European\r\nResearch Council (250152) (to N.H.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Simon
full_name: Martin, Simon
last_name: Martin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786.
doi:10.1534/genetics.115.183814
apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies
for calculating blockwise likelihoods under the coalescent. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.115.183814
chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient
Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics.
Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.
ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for
calculating blockwise likelihoods under the coalescent,” Genetics, vol.
202, no. 2. Genetics Society of America, pp. 775–786, 2016.
ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.
mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods
under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America,
2016, pp. 775–86, doi:10.1534/genetics.115.183814.
short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.
date_created: 2018-12-11T11:52:29Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2025-05-28T11:42:48Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
- _id: NiBa
doi: 10.1534/genetics.115.183814
ec_funded: 1
external_id:
pmid:
- '26715666'
file:
- access_level: open_access
checksum: 41c9b5d72e7fe4624dd22dfe622337d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:51Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5241'
file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf
file_size: 957466
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
page: 775 - 786
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5658'
pubrep_id: '561'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient strategies for calculating blockwise likelihoods under the coalescent
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1521'
abstract:
- lang: eng
text: Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular
energy production, coupling electron transfer between NADH and quinone to proton
translocation. It is the largest protein assembly of respiratory chains and one
of the most elaborate redox membrane proteins known. Bacterial enzyme is about
half the size of mitochondrial and thus provides its important "minimal"
model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative
diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer
occurs, and a membrane arm, where proton translocation takes place. We have solved
the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus,
the membrane domain from Escherichia coli and recently of the intact, entire complex
I from T. thermophilus (536. kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane
helices). The 95. Å long electron transfer pathway through the enzyme proceeds
from the primary electron acceptor flavin mononucleotide through seven conserved
Fe-S clusters to the unusual elongated quinone-binding site at the interface with
the membrane domain. Four putative proton translocation channels are found in
the membrane domain, all linked by the central flexible axis containing charged
residues. The redox energy of electron transfer is coupled to proton translocation
by the as yet undefined mechanism proposed to involve long-range conformational
changes. This article is part of a Special Issue entitled Respiratory complex
I, edited by Volker Zickermann and Ulrich Brandt.
acknowledgement: funded by the Medical Research Council (Grant number MC_U105674180)
author:
- first_name: John
full_name: Berrisford, John
last_name: Berrisford
- first_name: Rozbeh
full_name: Baradaran, Rozbeh
last_name: Baradaran
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Berrisford J, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex
I. Biochimica et Biophysica Acta - Bioenergetics. 2016;1857(7):892-901.
doi:10.1016/j.bbabio.2016.01.012
apa: Berrisford, J., Baradaran, R., & Sazanov, L. A. (2016). Structure of bacterial
respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. Elsevier.
https://doi.org/10.1016/j.bbabio.2016.01.012
chicago: Berrisford, John, Rozbeh Baradaran, and Leonid A Sazanov. “Structure of
Bacterial Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics.
Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.01.012.
ieee: J. Berrisford, R. Baradaran, and L. A. Sazanov, “Structure of bacterial respiratory
complex I,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no.
7. Elsevier, pp. 892–901, 2016.
ista: Berrisford J, Baradaran R, Sazanov LA. 2016. Structure of bacterial respiratory
complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(7), 892–901.
mla: Berrisford, John, et al. “Structure of Bacterial Respiratory Complex I.” Biochimica
et Biophysica Acta - Bioenergetics, vol. 1857, no. 7, Elsevier, 2016, pp.
892–901, doi:10.1016/j.bbabio.2016.01.012.
short: J. Berrisford, R. Baradaran, L.A. Sazanov, Biochimica et Biophysica Acta
- Bioenergetics 1857 (2016) 892–901.
date_created: 2018-12-11T11:52:30Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:51:21Z
day: '01'
department:
- _id: LeSa
doi: 10.1016/j.bbabio.2016.01.012
intvolume: ' 1857'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 892 - 901
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '5654'
quality_controlled: '1'
scopus_import: 1
status: public
title: Structure of bacterial respiratory complex I
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1857
year: '2016'
...
---
_id: '1522'
abstract:
- lang: eng
text: 'We classify smooth Brunnian (i.e., unknotted on both components) embeddings
(S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to
an explicitly constructed embedding fk,m,n for some integers k, m, n such that
m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if
k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification
of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2
× S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show
that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such
that the componentwise embedded connected sum f # g is isotopic to f # g′ but
g is not isotopic to g′.'
acknowledgement: "I thank A. Skopenkov for telling me about the problem and for his
useful remarks. I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev,
and an anonymous referee for their feedback. Author was partially\r\nsupported
by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Serhii
full_name: Avvakumov, Serhii
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
citation:
ama: Avvakumov S. The classification of certain linked 3-manifolds in 6-space. Moscow
Mathematical Journal. 2016;16(1):1-25. doi:10.17323/1609-4514-2016-16-1-1-25
apa: Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space.
Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2016-16-1-1-25
chicago: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in
6-Space.” Moscow Mathematical Journal. Independent University of Moscow,
2016. https://doi.org/10.17323/1609-4514-2016-16-1-1-25.
ieee: S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,”
Moscow Mathematical Journal, vol. 16, no. 1. Independent University of
Moscow, pp. 1–25, 2016.
ista: Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space.
Moscow Mathematical Journal. 16(1), 1–25.
mla: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.”
Moscow Mathematical Journal, vol. 16, no. 1, Independent University of
Moscow, 2016, pp. 1–25, doi:10.17323/1609-4514-2016-16-1-1-25.
short: S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.
date_created: 2018-12-11T11:52:30Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2022-02-25T10:15:57Z
day: '01'
department:
- _id: UlWa
doi: 10.17323/1609-4514-2016-16-1-1-25
external_id:
arxiv:
- '1408.3918'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.3918
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 25
publication: Moscow Mathematical Journal
publication_identifier:
eissn:
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
publist_id: '5652'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The classification of certain linked 3-manifolds in 6-space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1523'
abstract:
- lang: eng
text: For random graphs, the containment problem considers the probability that
a binomial random graph G(n, p) contains a given graph as a substructure. When
asking for the graph as a topological minor, i.e., for a copy of a subdivision
of the given graph, it is well known that the (sharp) threshold is at p = 1/n.
We consider a natural analogue of this question for higher-dimensional random
complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k =
2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold
for containing a subdivision of any fixed complete 2-complex. For higher dimensions
k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability
of containing a subdivision of a fixed k-dimensional complex.
acknowledgement: This research was supported by the Swiss National Science Foundation
(SNF Projects 200021-125309 and 200020-138230
author:
- first_name: Anna
full_name: Gundert, Anna
last_name: Gundert
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Gundert A, Wagner U. On topological minors in random simplicial complexes.
Proceedings of the American Mathematical Society. 2016;144(4):1815-1828.
doi:10.1090/proc/12824
apa: Gundert, A., & Wagner, U. (2016). On topological minors in random simplicial
complexes. Proceedings of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/proc/12824
chicago: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
Complexes.” Proceedings of the American Mathematical Society. American
Mathematical Society, 2016. https://doi.org/10.1090/proc/12824.
ieee: A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,”
Proceedings of the American Mathematical Society, vol. 144, no. 4. American
Mathematical Society, pp. 1815–1828, 2016.
ista: Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes.
Proceedings of the American Mathematical Society. 144(4), 1815–1828.
mla: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
Complexes.” Proceedings of the American Mathematical Society, vol. 144,
no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:10.1090/proc/12824.
short: A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144
(2016) 1815–1828.
date_created: 2018-12-11T11:52:30Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '01'
department:
- _id: UlWa
doi: 10.1090/proc/12824
intvolume: ' 144'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.2106
month: '04'
oa: 1
oa_version: Preprint
page: 1815 - 1828
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5650'
quality_controlled: '1'
scopus_import: 1
status: public
title: On topological minors in random simplicial complexes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1524'
abstract:
- lang: eng
text: "When designing genetic circuits, the typical primitives used in major existing
modelling formalisms are gene interaction graphs, where edges between genes denote
either an activation or inhibition relation. However, when designing experiments,
it is important to be precise about the low-level mechanistic details as to how
each such relation is implemented. The rule-based modelling language Kappa allows
to unambiguously specify mechanistic details such as DNA binding sites, dimerisation
of transcription factors, or co-operative interactions. Such a detailed description
comes with complexity and computationally costly executions. We propose a general
method for automatically transforming a rule-based program, by eliminating intermediate
species and adjusting the rate constants accordingly. To the best of our knowledge,
we show the first automated reduction of rule-based models based on equilibrium
approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which
was designed for reducing reaction-based programs; our version of the algorithm
scans the rule-based Kappa model in search for those interaction patterns known
to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional
checks are then performed in order to verify if the reduction is meaningful in
the context of the full model. The reduced model is efficiently obtained by static
inspection over the rule-set. The tool is tested on a detailed rule-based model
of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has
11 rules and 5 agents, and provides a dramatic reduction in simulation time of
several orders of magnitude."
acknowledgement: This research was supported by the People Programme (Marie Curie
Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship,
the grant number P2EZP2_148797.
alternative_title:
- LNCS
author:
- first_name: Andreea
full_name: Beica, Andreea
last_name: Beica
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static
inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10'
apa: 'Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa
models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented
at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10'
chicago: Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction
of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer,
2016. https://doi.org/10.1007/978-3-319-26916-0_10.
ieee: 'A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models
by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology,
Madrid, Spain, 2016, vol. 9271, pp. 173–191.'
ista: 'Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by
static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271,
173–191.'
mla: Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection
of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.
short: A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.
conference:
end_date: 2015-09-05
location: Madrid, Spain
name: 'HSB: Hybrid Systems Biology'
start_date: 2015-09-04
date_created: 2018-12-11T11:52:31Z
date_published: 2016-01-10T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '10'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-319-26916-0_10
ec_funded: 1
intvolume: ' 9271'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00440
month: '01'
oa: 1
oa_version: Preprint
page: 173 - 191
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5649'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient reduction of kappa models by static inspection of the rule-set
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9271
year: '2016'
...
---
_id: '1526'
abstract:
- lang: eng
text: 'We present the first study of robustness of systems that are both timed as
well as reactive (I/O). We study the behavior of such timed I/O systems in the
presence of uncertain inputs and formalize their robustness using the analytic
notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if
the perturbation in its output is at most K times the perturbation in its input.
We quantify input and output perturbation using similarity functions over timed
words such as the timed version of the Manhattan distance and the Skorokhod distance.
We consider two models of timed I/O systems — timed transducers and asynchronous
sequential circuits. We show that K-robustness of timed transducers can be decided
in polynomial space under certain conditions. For asynchronous sequential circuits,
we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete
letter-to-letter transducers and show PSpace-completeness of the problem.'
acknowledgement: This research was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants
S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
Centre (NCN), Poland under grant 2014/15/D/ST6/04543.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
citation:
ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems.
In: Vol 9583. Springer; 2016:250-267. doi:10.1007/978-3-662-49122-5_12'
apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2016). Lipschitz robustness
of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification,
Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer.
https://doi.org/10.1007/978-3-662-49122-5_12'
chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness
of Timed I/O Systems,” 9583:250–67. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_12.
ieee: 'T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed
I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract
Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.'
ista: 'Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O
systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS,
vol. 9583, 250–267.'
mla: Henzinger, Thomas A., et al. Lipschitz Robustness of Timed I/O Systems.
Vol. 9583, Springer, 2016, pp. 250–67, doi:10.1007/978-3-662-49122-5_12.
short: T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:52:32Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:23Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_12
ec_funded: 1
intvolume: ' 9583'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1506.01233
month: '01'
oa: 1
oa_version: Preprint
page: 250 - 267
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5647'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lipschitz robustness of timed I/O systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9583
year: '2016'
...
---
_id: '1529'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and an integer cost associated with every transition. The
optimization objective we study asks to minimize the expected total cost of reaching
a state in the target set, while ensuring that the target set is reached almost
surely (with probability 1). We show that for integer costs approximating the
optimal cost is undecidable. For positive costs, our results are as follows: (i)
we establish matching lower and upper bounds for the optimal cost, both double
exponential in the POMDP state space size; (ii) we show that the problem of approximating
the optimal cost is decidable and present approximation algorithms developing
on the existing algorithms for POMDPs with finite-horizon objectives. While the
worst-case running time of our algorithm is double exponential, we also present
efficient stopping criteria for the algorithm and show experimentally that it
performs well in many examples of interest.'
acknowledgement: 'We thank Blai Bonet for helping us with RTDP-Bel. The research was
partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant
No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty
fellows award.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost
almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier.
https://doi.org/10.1016/j.artint.2016.01.007
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence.
Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp.
26–48, 2016.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure
reachability in POMDPs. Artificial Intelligence. 234, 26–48.
mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence
234 (2016) 26–48.
date_created: 2018-12-11T11:52:33Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-23T12:25:49Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2016.01.007
ec_funded: 1
external_id:
arxiv:
- '1411.3880'
intvolume: ' 234'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.3880
month: '05'
oa: 1
oa_version: Preprint
page: 26 - 48
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5642'
quality_controlled: '1'
related_material:
record:
- id: '1820'
relation: earlier_version
status: public
- id: '5425'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 234
year: '2016'
...
---
_id: '1545'
abstract:
- lang: eng
text: We provide general conditions for which bosonic quadratic Hamiltonians on
Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover
the case when quantum systems have infinite degrees of freedom and the associated
one-body kinetic and paring operators are unbounded. Our sufficient conditions
are optimal in the sense that they become necessary when the relevant one-body
operators commute.
acknowledgement: We thank Jan Dereziński for several inspiring discussions and useful
remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger
Institute for the hospitality during the thematic programme “Quantum many-body systems,
random matrices, and disorder”. We gratefully acknowledge the financial supports
by the European Union's Seventh Framework Programme under the ERC Advanced Grant
ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as
well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185
and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians
by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368.
doi:10.1016/j.jfa.2015.12.007
apa: Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of
bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional
Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007
chicago: Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of
Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional
Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.
ieee: P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis,
vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.
ista: Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11),
4340–4368.
mla: Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov
Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic
Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.
short: P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270
(2016) 4340–4368.
date_created: 2018-12-11T11:52:38Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '01'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2015.12.007
ec_funded: 1
intvolume: ' 270'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.07321
month: '06'
oa: 1
oa_version: Submitted Version
page: 4340 - 4368
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5626'
quality_controlled: '1'
scopus_import: 1
status: public
title: Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2016'
...
---
_id: '1552'
abstract:
- lang: eng
text: Antibiotic resistance carries a fitness cost that must be overcome in order
for resistance to persist over the long term. Compensatory mutations that recover
the functional defects associated with resistance mutations have been argued to
play a key role in overcoming the cost of resistance, but compensatory mutations
are expected to be rare relative to generally beneficial mutations that increase
fitness, irrespective of antibiotic resistance. Given this asymmetry, population
genetics theory predicts that populations should adapt by compensatory mutations
when the cost of resistance is large, whereas generally beneficial mutations should
drive adaptation when the cost of resistance is small. We tested this prediction
by determining the genomic mechanisms underpinning adaptation to antibiotic-free
conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that
carry costly antibiotic resistance mutations. Whole-genome sequencing revealed
that populations founded by high-cost rifampicin-resistant mutants adapted via
compensatory mutations in three genes of the RNA polymerase core enzyme, whereas
populations founded by low-cost mutants adapted by generally beneficial mutations,
predominantly in the quorum-sensing transcriptional regulator gene lasR. Even
though the importance of compensatory evolution in maintaining resistance has
been widely recognized, our study shows that the roles of general adaptation in
maintaining resistance should not be underestimated and highlights the need to
understand how selection at other sites in the genome influences the dynamics
of resistance alleles in clinical settings.
acknowledgement: "We thank the High-Throughput Genomics Group at the Wellcome Trust
Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z
and Medical Research Council Hub grant no. G0900747 91070 for generation of the
high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for
their constructive feedback on previous versions of our manuscript."
article_number: '20152452'
author:
- first_name: Qin
full_name: Qi, Qin
id: 3B22D412-F248-11E8-B48F-1D18A9856A87
last_name: Qi
orcid: 0000-0002-6148-2416
- first_name: Macarena
full_name: Toll Riera, Macarena
last_name: Toll Riera
- first_name: Karl
full_name: Heilbron, Karl
last_name: Heilbron
- first_name: Gail
full_name: Preston, Gail
last_name: Preston
- first_name: R Craig
full_name: Maclean, R Craig
last_name: Maclean
citation:
ama: Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of
adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa.
Proceedings of the Royal Society of London Series B Biological Sciences.
2016;283(1822). doi:10.1098/rspb.2015.2452
apa: Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., & Maclean, R. C. (2016).
The genomic basis of adaptation to the fitness cost of rifampicin resistance in
Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2015.2452
chicago: Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig
Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance
in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2015.2452.
ieee: Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic
basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas
aeruginosa,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 283, no. 1822. Royal Society, The, 2016.
ista: Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis
of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa.
Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822),
20152452.
mla: Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin
Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of
London Series B Biological Sciences, vol. 283, no. 1822, 20152452, Royal Society,
The, 2016, doi:10.1098/rspb.2015.2452.
short: Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings
of the Royal Society of London Series B Biological Sciences 283 (2016).
date_created: 2018-12-11T11:52:40Z
date_published: 2016-01-13T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '13'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1098/rspb.2015.2452
file:
- access_level: open_access
checksum: 78ffe70c1c88af3856d31ca6b7195a27
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:43Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4899'
file_name: IST-2016-488-v1+1_20152452.full.pdf
file_size: 626804
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 283'
issue: '1822'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '5619'
pubrep_id: '488'
quality_controlled: '1'
scopus_import: 1
status: public
title: The genomic basis of adaptation to the fitness cost of rifampicin resistance
in Pseudomonas aeruginosa
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 283
year: '2016'
...
---
_id: '1592'
abstract:
- lang: eng
text: A modular approach to constructing cryptographic protocols leads to simple
designs but often inefficient instantiations. On the other hand, ad hoc constructions
may yield efficient protocols at the cost of losing conceptual simplicity. We
suggest a new design paradigm, structure-preserving cryptography, that provides
a way to construct modular protocols with reasonable efficiency while retaining
conceptual simplicity. A cryptographic scheme over a bilinear group is called
structure-preserving if its public inputs and outputs consist of elements from
the bilinear groups and their consistency can be verified by evaluating pairing-product
equations. As structure-preserving schemes smoothly interoperate with each other,
they are useful as building blocks in modular design of cryptographic applications.
This paper introduces structure-preserving commitment and signature schemes over
bilinear groups with several desirable properties. The commitment schemes include
homomorphic, trapdoor and length-reducing commitments to group elements, and the
structure-preserving signature schemes are the first ones that yield constant-size
signatures on multiple group elements. A structure-preserving signature scheme
is called automorphic if the public keys lie in the message space, which cannot
be achieved by compressing inputs via a cryptographic hash function, as this would
destroy the mathematical structure we are trying to preserve. Automorphic signatures
can be used for building certification chains underlying privacy-preserving protocols.
Among a vast number of applications of structure-preserving protocols, we present
an efficient round-optimal blind-signature scheme and a group signature scheme
with an efficient and concurrently secure protocol for enrolling new members.
acknowledgement: The authors would like to thank the anonymous reviewers of this paper.
We also would like to express our appreciation to the program committee and the
anonymous reviewers for CRYPTO 2010. The first author thanks Sherman S. M. Chow
for his comment on group signatures in Sect. 7.1.
author:
- first_name: Masayuki
full_name: Abe, Masayuki
last_name: Abe
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Jens
full_name: Groth, Jens
last_name: Groth
- first_name: Kristiyan
full_name: Haralambiev, Kristiyan
last_name: Haralambiev
- first_name: Miyako
full_name: Ohkubo, Miyako
last_name: Ohkubo
citation:
ama: Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. Structure preserving
signatures and commitments to group elements. Journal of Cryptology. 2016;29(2):363-421.
doi:10.1007/s00145-014-9196-7
apa: Abe, M., Fuchsbauer, G., Groth, J., Haralambiev, K., & Ohkubo, M. (2016).
Structure preserving signatures and commitments to group elements. Journal
of Cryptology. Springer. https://doi.org/10.1007/s00145-014-9196-7
chicago: Abe, Masayuki, Georg Fuchsbauer, Jens Groth, Kristiyan Haralambiev, and
Miyako Ohkubo. “Structure Preserving Signatures and Commitments to Group Elements.”
Journal of Cryptology. Springer, 2016. https://doi.org/10.1007/s00145-014-9196-7.
ieee: M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, and M. Ohkubo, “Structure
preserving signatures and commitments to group elements,” Journal of Cryptology,
vol. 29, no. 2. Springer, pp. 363–421, 2016.
ista: Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. 2016. Structure preserving
signatures and commitments to group elements. Journal of Cryptology. 29(2), 363–421.
mla: Abe, Masayuki, et al. “Structure Preserving Signatures and Commitments to Group
Elements.” Journal of Cryptology, vol. 29, no. 2, Springer, 2016, pp. 363–421,
doi:10.1007/s00145-014-9196-7.
short: M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, M. Ohkubo, Journal of Cryptology
29 (2016) 363–421.
date_created: 2018-12-11T11:52:54Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:51:49Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00145-014-9196-7
intvolume: ' 29'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 363 - 421
publication: Journal of Cryptology
publication_status: published
publisher: Springer
publist_id: '5579'
quality_controlled: '1'
scopus_import: 1
status: public
title: Structure preserving signatures and commitments to group elements
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1597'
abstract:
- lang: eng
text: Chemokines are the main guidance cues directing leukocyte migration. Opposed
to early assumptions, chemokines do not necessarily act as soluble cues but are
often immobilized within tissues, e.g., dendritic cell migration toward lymphatic
vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled
assay systems to quantitatively study haptotaxis in vitro are still missing. In
this chapter, we describe an in vitro haptotaxis assay optimized for the unique
properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive
state, using laser-assisted protein adsorption by photobleaching. The cells follow
this immobilized CCL21 gradient in a haptotaxis chamber, which provides three
dimensionally confined migration conditions.
acknowledged_ssus:
- _id: Bio
acknowledgement: This work was supported by the Boehringer Ingelheim Fonds, the European
Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation
(FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input
and the Imaging Facility of IST Austria for excellent support.
article_processing_charge: No
article_type: original
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. Methods
in Enzymology. 2016;570:567-581. doi:10.1016/bs.mie.2015.11.004
apa: Schwarz, J., & Sixt, M. K. (2016). Quantitative analysis of dendritic cell
haptotaxis. Methods in Enzymology. Elsevier. https://doi.org/10.1016/bs.mie.2015.11.004
chicago: Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell
Haptotaxis.” Methods in Enzymology. Elsevier, 2016. https://doi.org/10.1016/bs.mie.2015.11.004.
ieee: J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,”
Methods in Enzymology, vol. 570. Elsevier, pp. 567–581, 2016.
ista: Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis.
Methods in Enzymology. 570, 567–581.
mla: Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell
Haptotaxis.” Methods in Enzymology, vol. 570, Elsevier, 2016, pp. 567–81,
doi:10.1016/bs.mie.2015.11.004.
short: J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.
date_created: 2018-12-11T11:52:56Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:51Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/bs.mie.2015.11.004
ec_funded: 1
external_id:
pmid:
- '26921962'
intvolume: ' 570'
language:
- iso: eng
month: '01'
oa_version: None
page: 567 - 581
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)
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Methods in Enzymology
publication_status: published
publisher: Elsevier
publist_id: '5573'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative analysis of dendritic cell haptotaxis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 570
year: '2016'
...
---
_id: '1599'
abstract:
- lang: eng
text: "The addition of polysialic acid to N- and/or O-linked glycans, referred to
as polysialylation, is a rare posttranslational modification that is mainly known
to control the developmental plasticity of the nervous system. Here we show that
CCR7, the central chemokine receptor controlling immune cell trafficking to secondary
lymphatic organs, carries polysialic acid. This modification is essential for
the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking
is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed
lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function
analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited
conformation, which is released upon interaction with polysialic acid. Thus, we
describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic
basis.\r\n"
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We thank S. Schüchner and E. Ogris for kindly providing the antibody
to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific
Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for
critically reading the manuscript. '
article_processing_charge: No
article_type: original
author:
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Rita
full_name: Gerardy Schahn, Rita
last_name: Gerardy Schahn
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Friedrich
full_name: Freiberger, Friedrich
last_name: Freiberger
- first_name: Richard
full_name: Imre, Richard
last_name: Imre
- first_name: Deni
full_name: Taleski, Deni
last_name: Taleski
- first_name: Richard
full_name: Payne, Richard
last_name: Payne
- first_name: Asolina
full_name: Braun, Asolina
last_name: Braun
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Martina
full_name: Mühlenhoff, Martina
last_name: Mühlenhoff
- first_name: Brian
full_name: Volkman, Brian
last_name: Volkman
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic
cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190.
doi:10.1126/science.aad0512
apa: Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I.,
Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aad0512
chicago: Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy
Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation
Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.
ieee: E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition,” Science, vol. 351, no. 6269. American
Association for the Advancement of Science, pp. 186–190, 2016.
ista: Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams
L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster
R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls
dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269),
186–190.
mla: Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking
by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American
Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.
short: E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries,
L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne,
A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science
351 (2016) 186–190.
date_created: 2018-12-11T11:52:57Z
date_published: 2016-01-08T00:00:00Z
date_updated: 2021-01-12T06:51:52Z
day: '08'
department:
- _id: MiSi
doi: 10.1126/science.aad0512
ec_funded: 1
external_id:
pmid:
- '26657283'
intvolume: ' 351'
issue: '6269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 190
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)
- _id: 25A76F58-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '289720'
name: Stromal Cell-immune Cell Interactions in Health and Disease
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5570'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polysialylation controls dendritic cell trafficking by regulating chemokine
recognition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 351
year: '2016'
...
---
_id: '1608'
abstract:
- lang: eng
text: 'We show that the Anderson model has a transition from localization to delocalization
at exactly 2 dimensional growth rate on antitrees with normalized edge weights
which are certain discrete graphs. The kinetic part has a one-dimensional structure
allowing a description through transfer matrices which involve some Schur complement.
For such operators we introduce the notion of having one propagating channel and
extend theorems from the theory of one-dimensional Jacobi operators that relate
the behavior of transfer matrices with the spectrum. These theorems are then applied
to the considered model. In essence, in a certain energy region the kinetic part
averages the random potentials along shells and the transfer matrices behave similar
as for a one-dimensional operator with random potential of decaying variance.
At d dimensional growth for d>2 this effective decay is strong enough to obtain
absolutely continuous spectrum, whereas for some uniform d dimensional growth
with d<2 one has pure point spectrum in this energy region. At exactly uniform
2 dimensional growth also some singular continuous spectrum appears, at least
at small disorder. As a corollary we also obtain a change from singular spectrum
(d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type
rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete
adjacency operator (Laplacian) on ℤd and λ a random potential. '
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
citation:
ama: Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel. Annales Henri Poincare.
2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3
apa: Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3
chicago: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on
Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales
Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.
ieee: C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel,” Annales Henri
Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016.
ista: Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. 17(7), 1631–1675.
mla: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees
and Spectral Theory for Operators with One Propagating Channel.” Annales Henri
Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3.
short: C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.
date_created: 2018-12-11T11:53:00Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:51:58Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00023-015-0456-3
ec_funded: 1
intvolume: ' 17'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04287
month: '07'
oa: 1
oa_version: Preprint
page: 1631 - 1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '5558'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anderson transition at 2 dimensional growth rate on antitrees and spectral
theory for operators with one propagating channel
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1612'
abstract:
- lang: eng
text: We prove that whenever A is a 3-conservative relational structure with only
binary and unary relations,then the algebra of polymorphisms of A either has no
Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety
(i.e.,CSP(A)has bounded width).
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
citation:
ama: Kazda A. CSP for binary conservative relational structures. Algebra Universalis.
2016;75(1):75-84. doi:10.1007/s00012-015-0358-8
apa: Kazda, A. (2016). CSP for binary conservative relational structures. Algebra
Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8
chicago: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.
ieee: A. Kazda, “CSP for binary conservative relational structures,” Algebra
Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.
ista: Kazda A. 2016. CSP for binary conservative relational structures. Algebra
Universalis. 75(1), 75–84.
mla: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8.
short: A. Kazda, Algebra Universalis 75 (2016) 75–84.
date_created: 2018-12-11T11:53:01Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00012-015-0358-8
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1112.1099
month: '02'
oa: 1
oa_version: Preprint
page: 75 - 84
publication: Algebra Universalis
publication_status: published
publisher: Springer
publist_id: '5554'
quality_controlled: '1'
scopus_import: 1
status: public
title: CSP for binary conservative relational structures
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2016'
...