---
_id: '2918'
abstract:
- lang: eng
text: "Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar
cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems,
including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during
zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however,
unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a
(Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic
A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms
an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2.
Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts
with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically,
Antxr2a functions as a Wnt-dependent polarized determinant, which, through the
action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V
axis.\r\n"
acknowledgement: This work was supported by the SNSF, the Swiss SystemsX.ch initiative
and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au
Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers
in Genetics and Chemical Biology programmes and the Polish–Swiss research program
(M.G-G.).
article_processing_charge: No
author:
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Laurence
full_name: Abrami, Laurence
last_name: Abrami
- first_name: Laurent
full_name: Holtzer, Laurent
last_name: Holtzer
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Françoise
full_name: Van Der Goot, Françoise
last_name: Van Der Goot
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
citation:
ama: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González
Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature
Cell Biology. 2013;15(1):28-39. doi:10.1038/ncb2632
apa: Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot,
F., & González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic
spindle positioning. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2632
chicago: Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg,
Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a
Controls Mitotic Spindle Positioning.” Nature Cell Biology. Nature Publishing
Group, 2013. https://doi.org/10.1038/ncb2632.
ieee: I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot,
and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,”
Nature Cell Biology, vol. 15, no. 1. Nature Publishing Group, pp. 28–39,
2013.
ista: Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González
Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning.
Nature Cell Biology. 15(1), 28–39.
mla: Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle
Positioning.” Nature Cell Biology, vol. 15, no. 1, Nature Publishing Group,
2013, pp. 28–39, doi:10.1038/ncb2632.
short: I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot,
M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2025-09-30T08:16:16Z
day: '01'
department:
- _id: CaHe
doi: 10.1038/ncb2632
external_id:
isi:
- '000312841300007'
fulldoi: https://doi.org/10.1038/ncb2632
intvolume: ' 15'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 28 - 39
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3819'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anthrax toxin receptor 2a controls mitotic spindle positioning
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2013'
...
---
_id: '2919'
abstract:
- lang: eng
text: The distribution of the phytohormone auxin regulates many aspects of plant
development including growth response to gravity. Gravitropic root curvature involves
coordinated and asymmetric cell elongation between the lower and upper side of
the root, mediated by differential cellular auxin levels. The asymmetry in the
auxin distribution is established and maintained by a spatio-temporal regulation
of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights
into the complex regulation of PIN abundance and activity during root gravitropism.
We show that PIN2 turnover is differentially regulated on the upper and lower
side of gravistimulated roots by distinct but partially overlapping auxin feedback
mechanisms. In addition to regulating transcription and clathrin-mediated internalization,
auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar
targeting and degradation. This effect of elevated auxin levels requires the activity
of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also
suboptimal auxin levels mediate PIN degradation utilizing the same signalling
pathway. These feedback mechanisms are functionally important during gravitropic
response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating
asymmetric growth.
article_processing_charge: No
author:
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates
PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal.
2013;32(2):260-274. doi:10.1038/emboj.2012.310
apa: Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald,
W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking
and auxin fluxes during root gravitropism. EMBO Journal. Wiley-Blackwell.
https://doi.org/10.1038/emboj.2012.310
chicago: Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste,
Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1
AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during
Root Gravitropism.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.310.
ieee: P. Baster et al., “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol.
32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.
ista: Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel
B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar
trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.
mla: Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar
Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal, vol.
32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:10.1038/emboj.2012.310.
short: P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald,
B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.
corr_author: '1'
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-23T00:00:00Z
date_updated: 2025-09-29T13:28:19Z
day: '23'
department:
- _id: JiFr
doi: 10.1038/emboj.2012.310
external_id:
isi:
- '000316464500009'
pmid:
- '23211744'
fulldoi: https://doi.org/10.1038/emboj.2012.310
intvolume: ' 32'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/
month: '01'
oa: 1
oa_version: Submitted Version
page: 260 - 274
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3818'
quality_controlled: '1'
scopus_import: '1'
status: public
title: SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin
fluxes during root gravitropism
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2920'
abstract:
- lang: eng
text: Cell polarisation in development is a common and fundamental process underlying
embryo patterning and morphogenesis, and has been extensively studied over the
past years. Our current knowledge of cell polarisation in development is predominantly
based on studies that have analysed polarisation of single cells, such as eggs,
or cellular aggregates with a stable polarising interface, such as cultured epithelial
cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly
of vertebrates, cell polarisation processes often encompass large numbers of cells
that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial
transitions with a highly complex spatiotemporal choreography. How such intricate
cell polarisation processes in embryonic development are achieved has only started
to be analysed. By using live imaging of neurulation in the transparent zebrafish
embryo, Buckley et al (2012) now describe a novel polarisation strategy by which
cells assemble an apical domain in the part of their cell body that intersects
with the midline of the forming neural rod. This mechanism, along with the previously
described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger
formation of both neural rod midline and lumen.
article_processing_charge: No
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and
lumen formation. EMBO Journal. 2013;32(1):1-3. doi:10.1038/emboj.2012.325
apa: Compagnon, J., & Heisenberg, C.-P. J. (2013). Neurulation coordinating
cell polarisation and lumen formation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.325
chicago: Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.325.
ieee: J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation
and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp.
1–3, 2013.
ista: Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation
and lumen formation. EMBO Journal. 32(1), 1–3.
mla: Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating
Cell Polarisation and Lumen Formation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 1–3, doi:10.1038/emboj.2012.325.
short: J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.
corr_author: '1'
date_created: 2018-12-11T12:00:20Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2025-09-29T13:27:27Z
day: '09'
department:
- _id: CaHe
doi: 10.1038/emboj.2012.325
external_id:
isi:
- '000314141900001'
pmid:
- '23211745'
fulldoi: https://doi.org/10.1038/emboj.2012.325
intvolume: ' 32'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/
month: '01'
oa: 1
oa_version: Submitted Version
page: 1 - 3
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3817'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neurulation coordinating cell polarisation and lumen formation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2926'
abstract:
- lang: eng
text: To fight infectious diseases, host immune defenses are employed at multiple
levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first
line of defense to prevent infection [1] before activation of the physiological
immune system. Insect societies have evolved a wide range of collective hygiene
measures and intensive health care toward pathogen-exposed group members [2].
One of the most common behaviors is allogrooming, in which nestmates remove infectious
particles from the body surfaces of exposed individuals [3]. Here we show that,
in invasive garden ants, grooming of fungus-exposed brood is effective beyond
the sheer mechanical removal of fungal conidiospores; it also includes chemical
disinfection through the application of poison produced by the ants themselves.
Formic acid is the main active component of the poison. It inhibits fungal growth
of conidiospores remaining on the brood surface after grooming and also those
collected in the mouth of the grooming ant. This dual function is achieved by
uptake of the poison droplet into the mouth through acidopore self-grooming and
subsequent application onto the infectious brood via brood grooming. This extraordinary
behavior extends the current understanding of grooming and the establishment of
social immunity in insect societies.
acknowledgement: "Funding for this project was obtained by the German Research Foundation
(DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant
to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen
Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal
strain and its characterization; Volker Witte for chemical information; Eva Sixt
for ant drawings; and Robert Hauschild for help with image analysis. We further
thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion
and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript.
\r\n"
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Barbara
full_name: Mitteregger, Barbara
id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1
last_name: Mitteregger
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- 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: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect
fungus-exposed brood by oral uptake and spread of their poison. Current Biology.
2013;23(1):76-82. doi:10.1016/j.cub.2012.11.034
apa: Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &
Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread
of their poison. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.11.034
chicago: Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line
V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake
and Spread of Their Poison.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2012.11.034.
ieee: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer,
“Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,”
Current Biology, vol. 23, no. 1. Cell Press, pp. 76–82, 2013.
ista: Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013.
Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.
Current Biology. 23(1), 76–82.
mla: Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake
and Spread of Their Poison.” Current Biology, vol. 23, no. 1, Cell Press,
2013, pp. 76–82, doi:10.1016/j.cub.2012.11.034.
short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer,
Current Biology 23 (2013) 76–82.
corr_author: '1'
date_created: 2018-12-11T12:00:23Z
date_published: 2013-01-07T00:00:00Z
date_updated: 2026-04-08T14:22:39Z
day: '07'
department:
- _id: SyCr
- _id: CaHe
doi: 10.1016/j.cub.2012.11.034
ec_funded: 1
external_id:
isi:
- '000313383700026'
fulldoi: https://doi.org/10.1016/j.cub.2012.11.034
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 76 - 82
project:
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Collective disease defence and pathogen detection abilities in ant societies:
a chemo-neuro-immunological approach'
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3811'
quality_controlled: '1'
related_material:
record:
- id: '9757'
relation: research_data
status: public
- id: '961'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2013'
...
---
_id: '2939'
abstract:
- lang: eng
text: In this paper, we present the first output-sensitive algorithm to compute
the persistence diagram of a filtered simplicial complex. For any Γ > 0, it
returns only those homology classes with persistence at least Γ. Instead of the
classical reduction via column operations, our algorithm performs rank computations
on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the
running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number
of homology classes with persistence at least (1 - δ) Γ, n is the total number
of simplices in the complex, d its dimension, and R d (n) is the complexity of
computing the rank of an n × n matrix with O (d n) nonzero entries. Depending
on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ)
Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C
(1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} >
0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n
log n).
acknowledgement: The authors thank Herbert Edelsbrunner for many helpful discussions
and suggestions. Moreover, they are grateful for the careful reviews that helped
to improve the quality of the paper.
article_processing_charge: No
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Chen C, Kerber M. An output sensitive algorithm for persistent homology. Computational
Geometry: Theory and Applications. 2013;46(4):435-447. doi:10.1016/j.comgeo.2012.02.010'
apa: 'Chen, C., & Kerber, M. (2013). An output sensitive algorithm for persistent
homology. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2012.02.010'
chicago: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent
Homology.” Computational Geometry: Theory and Applications. Elsevier, 2013.
https://doi.org/10.1016/j.comgeo.2012.02.010.'
ieee: 'C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,”
Computational Geometry: Theory and Applications, vol. 46, no. 4. Elsevier,
pp. 435–447, 2013.'
ista: 'Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology.
Computational Geometry: Theory and Applications. 46(4), 435–447.'
mla: 'Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent
Homology.” Computational Geometry: Theory and Applications, vol. 46, no.
4, Elsevier, 2013, pp. 435–47, doi:10.1016/j.comgeo.2012.02.010.'
short: 'C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013)
435–447.'
corr_author: '1'
date_created: 2018-12-11T12:00:27Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2025-09-29T13:26:21Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2012.02.010
external_id:
isi:
- '000314437000004'
fulldoi: https://doi.org/10.1016/j.comgeo.2012.02.010
intvolume: ' 46'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 435 - 447
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '3796'
quality_controlled: '1'
related_material:
record:
- id: '3367'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: An output sensitive algorithm for persistent homology
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2013'
...
---
_id: '2940'
abstract:
- lang: eng
text: "A chain rule for an entropy notion H(.) states that the entropy H(X) of a
variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)>=
H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)>=
H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware
of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional
entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability
entropy and several variants of HILL entropy) satisfy the chain rule for conditional
entropy, though here not only the quantity decreases by l, but also the quality
of the entropy decreases exponentially in l. However, for \r\nthe standard notion
of conditional HILL entropy (the computational equivalent of min-entropy) the
existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that
for conditional HILL entropy no meaningful chain rule exists, assuming the existence
of one-way permutations: there exist distributions X,Y,A, where A is a distribution
over a single bit, but $H(X|Y)>>H(X|Y,A)$, even if we simultaneously allow
for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying
our construction is based on a surprising connection between the chain rule for
HILL entropy and deniable encryption. "
alternative_title:
- LNCS
author:
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Akshay
full_name: Wadia, Akshay
last_name: Wadia
citation:
ama: 'Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional
HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed.
Vol 7785. Springer; 2013:23-39. doi:10.1007/978-3-642-36594-2_2'
apa: 'Krenn, S., Pietrzak, K. Z., & Wadia, A. (2013). A counterexample to the
chain rule for conditional HILL entropy, and what deniable encryption has to do
with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory
of Cryptography Conference, Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-642-36594-2_2'
chicago: Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample
to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has
to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. https://doi.org/10.1007/978-3-642-36594-2_2.
ieee: 'S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule
for conditional HILL entropy, and what deniable encryption has to do with it,”
presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol.
7785, pp. 23–39.'
ista: 'Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for
conditional HILL entropy, and what deniable encryption has to do with it. TCC:
Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.'
mla: Krenn, Stephan, et al. A Counterexample to the Chain Rule for Conditional
HILL Entropy, and What Deniable Encryption Has to Do with It. Edited by Amit
Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:10.1007/978-3-642-36594-2_2.
short: S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp.
23–39.
conference:
end_date: 2013-03-06
location: Tokyo, Japan
name: 'TCC: Theory of Cryptography Conference'
start_date: 2013-03-03
date_created: 2018-12-11T12:00:27Z
date_published: 2013-01-29T00:00:00Z
date_updated: 2025-09-18T11:37:22Z
day: '29'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-642-36594-2_2
ec_funded: 1
editor:
- first_name: Amit
full_name: Sahai, Amit
last_name: Sahai
file:
- access_level: open_access
checksum: beb0cc1c0579da2d2e84394230a5da78
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:11:11Z
date_updated: 2020-07-14T12:45:54Z
file_id: '5875'
file_name: 2013_LNCS_Krenn.pdf
file_size: 414823
relation: main_file
file_date_updated: 2020-07-14T12:45:54Z
fulldoi: https://doi.org/10.1007/978-3-642-36594-2_2
has_accepted_license: '1'
intvolume: ' 7785'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 23 - 39
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '3795'
quality_controlled: '1'
related_material:
record:
- id: '1479'
relation: later_version
status: public
scopus_import: 1
status: public
title: A counterexample to the chain rule for conditional HILL entropy, and what deniable
encryption has to do with it
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7785
year: '2013'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
corr_author: '1'
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2025-09-29T13:25:36Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
external_id:
isi:
- '000314220900008'
fulldoi: https://doi.org/10.1111/mec.12165
intvolume: ' 22'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 22
year: '2013'
...
---
_id: '2948'
abstract:
- lang: eng
text: 'Many visual datasets are traditionally used to analyze the performance of
different learning techniques. The evaluation is usually done within each dataset,
therefore it is questionable if such results are a reliable indicator of true
generalization ability. We propose here an algorithm to exploit the existing data
resources when learning on a new multiclass problem. Our main idea is to identify
an image representation that decomposes orthogonally into two subspaces: a part
specific to each dataset, and a part generic to, and therefore shared between,
all the considered source sets. This allows us to use the generic representation
as un-biased reference knowledge for a novel classification task. By casting the
method in the multi-view setting, we also make it possible to use different features
for different databases. We call the algorithm MUST, Multitask Unaligned Shared
knowledge Transfer. Through extensive experiments on five public datasets, we
show that MUST consistently improves the cross-datasets generalization performance.'
acknowledgement: This work was supported by the PASCAL 2 Network of Excellence (TT)
and by the Newton International Fellowship (NQ)
alternative_title:
- LNCS
author:
- first_name: Tatiana
full_name: Tommasi, Tatiana
last_name: Tommasi
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Barbara
full_name: Caputo, Barbara
last_name: Caputo
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task
unaligned shared knowledge transfer. 2013;7724:1-15. doi:10.1007/978-3-642-37331-2_1'
apa: 'Tommasi, T., Quadrianto, N., Caputo, B., & Lampert, C. (2013). Beyond
dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the
ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. https://doi.org/10.1007/978-3-642-37331-2_1'
chicago: 'Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert.
“Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-37331-2_1.'
ieee: 'T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias:
Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15,
2013.'
ista: 'Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias:
Multi-task unaligned shared knowledge transfer. 7724, 1–15.'
mla: 'Tommasi, Tatiana, et al. Beyond Dataset Bias: Multi-Task Unaligned Shared
Knowledge Transfer. Vol. 7724, Springer, 2013, pp. 1–15, doi:10.1007/978-3-642-37331-2_1.'
short: T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.
conference:
end_date: 2012-11-09
location: Daejeon, Korea
name: 'ACCV: Asian Conference on Computer Vision'
start_date: 2012-11-05
date_created: 2018-12-11T12:00:30Z
date_published: 2013-04-04T00:00:00Z
date_updated: 2020-08-11T10:09:54Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-37331-2_1
file:
- access_level: open_access
checksum: a0a7234a89e2192af655b0d0ae3bf445
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T14:03:11Z
date_updated: 2020-07-14T12:45:55Z
file_id: '5874'
file_name: 2012_ACCV_Tommasi.pdf
file_size: 1513620
relation: main_file
file_date_updated: 2020-07-14T12:45:55Z
fulldoi: https://doi.org/10.1007/978-3-642-37331-2_1
has_accepted_license: '1'
intvolume: ' 7724'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 1 - 15
publication_status: published
publisher: Springer
publist_id: '3784'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: 'Beyond dataset bias: Multi-task unaligned shared knowledge transfer'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7724
year: '2013'
...
---
_id: '2182'
abstract:
- lang: eng
text: We propose a general framework for abstraction with respect to quantitative
properties, such as worst-case execution time, or power consumption. Our framework
provides a systematic way for counter-example guided abstraction refinement for
quantitative properties. The salient aspect of the framework is that it allows
anytime verification, that is, verification algorithms that can be stopped at
any time (for example, due to exhaustion of memory), and report approximations
that improve monotonically when the algorithms are given more time. We instantiate
the framework with a number of quantitative abstractions and refinement schemes,
which differ in terms of how much quantitative information they keep from the
original system. We introduce both state-based and trace-based quantitative abstractions,
and we describe conditions that define classes of quantitative properties for
which the abstractions provide over-approximations. We give algorithms for evaluating
the quantitative properties on the abstract systems. We present algorithms for
counter-example based refinements for quantitative properties for both state-based
and segment-based abstractions. We perform a case study on worst-case execution
time of executables to evaluate the anytime verification aspect and the quantitative
abstractions we proposed.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A. Quantitative abstraction refinement.
In: Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles
of Programming Language. ACM; 2013:115-128. doi:10.1145/2429069.2429085'
apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2013). Quantitative abstraction
refinement. In Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium
on Principles of programming language (pp. 115–128). Rome, Italy: ACM. https://doi.org/10.1145/2429069.2429085'
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative
Abstraction Refinement.” In Proceedings of the 40th Annual ACM SIGPLAN-SIGACT
Symposium on Principles of Programming Language, 115–28. ACM, 2013. https://doi.org/10.1145/2429069.2429085.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative abstraction
refinement,” in Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium
on Principles of programming language, Rome, Italy, 2013, pp. 115–128.
ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2013. Quantitative abstraction refinement.
Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming
language. POPL: Principles of Programming Languages, 115–128.'
mla: Cerny, Pavol, et al. “Quantitative Abstraction Refinement.” Proceedings
of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language,
ACM, 2013, pp. 115–28, doi:10.1145/2429069.2429085.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Proceedings of the 40th Annual
ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013,
pp. 115–128.
conference:
end_date: 2013-01-25
location: Rome, Italy
name: 'POPL: Principles of Programming Languages'
start_date: 2013-07-23
corr_author: '1'
date_created: 2018-12-11T11:56:11Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2024-10-09T20:55:21Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2429069.2429085
ec_funded: 1
fulldoi: https://doi.org/10.1145/2429069.2429085
language:
- iso: eng
month: '01'
oa_version: None
page: 115 - 128
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles
of programming language
publication_status: published
publisher: ACM
publist_id: '4800'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantitative abstraction refinement
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '1374'
abstract:
- lang: eng
text: 'We study two-player zero-sum games over infinite-state graphs equipped with
ωB and finitary conditions. Our first contribution is about the strategy complexity,
i.e the memory required for winning strategies: we prove that over general infinite-state
graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory
suffices for finitary parity games. We then study pushdown games with boundedness
conditions, with two contributions. First we prove a collapse result for pushdown
games with ωB-conditions, implying the decidability of solving these games. Second
we consider pushdown games with finitary parity along with stack boundedness conditions,
and show that solving these games is EXPTIME-complete.'
alternative_title:
- LIPIcs
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: 'Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In:
22nd EACSL Annual Conference on Computer Science Logic. Vol 23. Leibniz
International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2013:181-196. doi:10.4230/LIPIcs.CSL.2013.181'
apa: 'Chatterjee, K., & Fijalkow, N. (2013). Infinite-state games with finitary
conditions. In 22nd EACSL Annual Conference on Computer Science Logic (Vol.
23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CSL.2013.181'
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with
Finitary Conditions.” In 22nd EACSL Annual Conference on Computer Science Logic,
23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.181.
ieee: K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,”
in 22nd EACSL Annual Conference on Computer Science Logic, Torino, Italy,
2013, vol. 23, pp. 181–196.
ista: 'Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions.
22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science
LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196.'
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with
Finitary Conditions.” 22nd EACSL Annual Conference on Computer Science Logic,
vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96,
doi:10.4230/LIPIcs.CSL.2013.181.
short: K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer
Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.
conference:
end_date: 2013-09-05
location: Torino, Italy
name: 'CSL: Computer Science Logic'
start_date: 203-09-02
corr_author: '1'
date_created: 2018-12-11T11:51:39Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2024-10-09T20:55:23Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CSL.2013.181
ec_funded: 1
file:
- access_level: open_access
checksum: b7091a3866db573c0db5ec486952255e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:38Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5023'
file_name: IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf
file_size: 547296
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
fulldoi: https://doi.org/10.4230/LIPIcs.CSL.2013.181
has_accepted_license: '1'
intvolume: ' 23'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 181 - 196
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 22nd EACSL Annual Conference on Computer Science Logic
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5837'
pubrep_id: '624'
quality_controlled: '1'
scopus_import: 1
series_title: Leibniz International Proceedings in Informatics
status: public
title: Infinite-state games with finitary conditions
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
volume: 23
year: '2013'
...
---
OA_place: repository
OA_type: green
_id: '1376'
abstract:
- lang: eng
text: 'We consider the distributed synthesis problem for temporal logic specifications.
Traditionally, the problem has been studied for LTL, and the previous results
show that the problem is decidable iff there is no information fork in the architecture.
We consider the problem for fragments of LTL and our main results are as follows:
(1) We show that the problem is undecidable for architectures with information
forks even for the fragment of LTL with temporal operators restricted to next
and eventually. (2) For specifications restricted to globally along with non-nested
next operators, we establish decidability (in EXPSPACE) for star architectures
where the processes receive disjoint inputs, whereas we establish undecidability
for architectures containing an information fork-meet structure. (3) Finally,
we consider LTL without the next operator, and establish decidability (NEXPTIME-complete)
for all architectures for a fragment that consists of a set of safety assumptions,
and a set of guarantees where each guarantee is a safety, reachability, or liveness
condition.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: 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: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis
for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided
Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386'
apa: 'Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013).
Distributed synthesis for LTL fragments. In 13th International Conference on
Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United
States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis.
“Distributed Synthesis for LTL Fragments.” In 13th International Conference
on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed
synthesis for LTL fragments,” in 13th International Conference on Formal Methods
in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25.
ista: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis
for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided
Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.'
mla: Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th
International Conference on Formal Methods in Computer-Aided Design, IEEE,
2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386.
short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International
Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.
conference:
end_date: 2013-10-23
location: Portland, OR, United States
name: 'FMCAD: Formal Methods in Computer-Aided Design'
start_date: 2013-10-20
corr_author: '1'
date_created: 2018-12-11T11:51:40Z
date_published: 2013-12-11T00:00:00Z
date_updated: 2025-06-26T08:33:43Z
day: '11'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/FMCAD.2013.6679386
ec_funded: 1
fulldoi: https://doi.org/10.1109/FMCAD.2013.6679386
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15479/AT:IST-2013-130-v1-1
month: '12'
oa: 1
oa_version: Preprint
page: 18 - 25
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: 13th International Conference on Formal Methods in Computer-Aided Design
publication_status: published
publisher: IEEE
publist_id: '5835'
quality_controlled: '1'
related_material:
record:
- id: '5406'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Distributed synthesis for LTL fragments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
OA_place: publisher
_id: '1405'
abstract:
- lang: eng
text: "Motivated by the analysis of highly dynamic message-passing systems, i.e.
unbounded thread creation, mobility, etc. we present a framework for the analysis
of depth-bounded systems. Depth-bounded systems are one of the most expressive
known fragment of the π-calculus for which interesting verification problems are
still decidable. Even though they are infinite state systems depth-bounded systems
are well-structured, thus can be analyzed algorithmically. We give an interpretation
of depth-bounded systems as graph-rewriting systems. This gives more flexibility
and ease of use to apply depth-bounded systems to other type of systems like shared
memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for
depth-bounded systems, a prerequisite for the effective representation of downward-closed
sets. Downward-closed sets are needed by forward saturation-based algorithms to
represent potentially infinite sets of states. Then, we present an abstract interpretation
framework to compute the covering set of well-structured transition systems. Because,
in general, the covering set is not computable, our abstraction over-approximates
the actual covering set. Our abstraction captures the essence of acceleration
based-algorithms while giving up enough precision to ensure convergence. We have
implemented the analysis in the PICASSO tool and show that it is accurate in practice.
Finally, we build some further analyses like termination using the covering set
as starting point."
acknowledgement: "This work was supported in part by the Austrian Science Fund NFN
RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative
Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger
and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of
Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal
Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint
work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS
2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this
part is mostly related to the implementation. The theory required to understand
the method and its implementation is quickly recalled to make the thesis self-contained,
but should not be considered as a contribution. For the details of the methods,
we refer the reader to the orig- inal publication [13] and the corresponding technical
report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar,
and Thomas Wies. I also would like to thank the people who supported over the past
4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on
projects I was interested in. My collaborators, especially Thomas Wies with whom
I worked since the beginning. The members of my thesis committee, Viktor Kun- cak
and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny,
Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created
an enjoyable environment. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Zufferey D. Analysis of dynamic message passing programs. 2013. doi:10.15479/at:ista:1405
apa: Zufferey, D. (2013). Analysis of dynamic message passing programs. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:1405
chicago: Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute
of Science and Technology Austria, 2013. https://doi.org/10.15479/at:ista:1405.
ieee: D. Zufferey, “Analysis of dynamic message passing programs,” Institute of
Science and Technology Austria, 2013.
ista: Zufferey D. 2013. Analysis of dynamic message passing programs. Institute
of Science and Technology Austria.
mla: Zufferey, Damien. Analysis of Dynamic Message Passing Programs. Institute
of Science and Technology Austria, 2013, doi:10.15479/at:ista:1405.
short: D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science
and Technology Austria, 2013.
corr_author: '1'
date_created: 2018-12-11T11:51:50Z
date_published: 2013-09-05T00:00:00Z
date_updated: 2026-04-09T14:35:24Z
day: '05'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
- _id: GradSch
doi: 10.15479/at:ista:1405
ec_funded: 1
file:
- access_level: open_access
checksum: ed2d7b52933d134e8dc69d569baa284e
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:28:36Z
date_updated: 2021-02-22T11:28:36Z
file_id: '9176'
file_name: 2013_Zufferey_thesis_final.pdf
file_size: 1514906
relation: main_file
success: 1
- access_level: closed
checksum: cecc4c4b14225bee973d32e3dba91a55
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:42:52Z
date_updated: 2021-11-17T13:47:58Z
file_id: '10298'
file_name: 2013_Zufferey_thesis_final_pdfa.pdf
file_size: 1378313
relation: main_file
file_date_updated: 2021-11-17T13:47:58Z
fulldoi: https://doi.org/10.15479/at:ista:1405
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://dzufferey.github.io/files/2013_thesis.pdf
month: '09'
oa: 1
oa_version: Published Version
page: '134'
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5802'
related_material:
record:
- id: '4361'
relation: part_of_dissertation
status: public
- id: '3251'
relation: part_of_dissertation
status: public
- id: '2847'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Analysis of dynamic message passing programs
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2013'
...
---
_id: '476'
abstract:
- lang: eng
text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold
increase in the risk of schizophrenia in the offspring. The critical initiating
factor appears to be the maternal immune activation (MIA) that follows infection.
This process can be induced in rodents by exposure of pregnant dams to the viral
mimic Poly I:C, which triggers an immune response that results in structural,
functional, behavioral, and electrophysiological phenotypes in the adult offspring
that model those seen in schizophrenia. We used this model to explore the role
of synchronization in brain neural networks, a process thought to be dysfunctional
in schizophrenia and previously associated with positive, negative, and cognitive
symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced
an impairment in long-range neural synchrony in adult offspring between two regions
implicated in schizophrenia pathology; the hippocampus and the medial prefrontal
cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the
antipsychotic clozapine. MIA animals have previously been shown to have impaired
pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits
in animal models. Our data showed that deficits in synchrony were positively correlated
with the impairments in PPI. Subsequent analysis of LFP activity during the PPI
response also showed that reduced coupling between the mPFC and the hippocampus
following processing of the pre-pulse was associated with reduced PPI. The ability
of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology
provides a useful platform from which to investigate the ontogeny of aberrant
synchronous processes. Further, the way in which the model expresses translatable
deficits such as aberrant synchrony and reduced PPI will allow researchers to
explore novel intervention strategies targeted to these changes. '
article_processing_charge: No
author:
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: David
full_name: Bilkey, David
last_name: Bilkey
citation:
ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation
model: Using translatable measures to explore targeted interventions. Frontiers
in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217'
apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal
immune activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217'
chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the
Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted
Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.'
ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions,”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research
Foundation, 2013.'
ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. 7(DEC).'
mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal
Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research
Foundation, 2013, doi:10.3389/fnbeh.2013.00217.'
short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).
date_created: 2018-12-11T11:46:41Z
date_published: 2013-12-27T00:00:00Z
date_updated: 2025-09-30T07:30:04Z
day: '27'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.3389/fnbeh.2013.00217
external_id:
isi:
- '000329175600001'
file:
- access_level: open_access
checksum: cd7183121e56251176100ccac165c95c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:10Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5128'
file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf
file_size: 530134
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
fulldoi: https://doi.org/10.3389/fnbeh.2013.00217
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: DEC
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Frontiers in Behavioral Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7346'
pubrep_id: '953'
quality_controlled: '1'
status: public
title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable
measures to explore targeted interventions'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
article_processing_charge: No
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2025-09-30T07:29:30Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
external_id:
isi:
- '000312985800059'
fulldoi: https://doi.org/10.1126/science.1229858
intvolume: ' 339'
isi: 1
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 339
year: '2013'
...
---
_id: '500'
abstract:
- lang: eng
text: 'Background: Reassortment between the RNA segments encoding haemagglutinin
(HA) and neuraminidase (NA), the major antigenic influenza proteins, produces
viruses with novel HA and NA subtype combinations and has preceded the emergence
of pandemic strains. It has been suggested that productive viral infection requires
a balance in the level of functional activity of HA and NA, arising from their
closely interacting roles in the viral life cycle, and that this functional balance
could be mediated by genetic changes in the HA and NA. Here, we investigate how
the selective pressure varies for H7 avian influenza HA on different NA subtype
backgrounds. Results: By extending Bayesian stochastic mutational mapping methods
to calculate the ratio of the rate of non-synonymous change to the rate of synonymous
change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1
region to be significantly greater on an N2 NA subtype background than on an N1,
N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different
NA subtype backgrounds could not be attributed to underlying differences between
avian host species or virus pathogenicity. Examination of d N/d S values for each
subtype on a site-by-site basis indicated that the elevated d N/d S on the N2
NA background was a result of increased selection, rather than a relaxation of
selective constraint. Conclusions: Our results are consistent with the hypothesis
that reassortment exposes influenza HA to significant changes in selective pressure
through genetic interactions with NA. Such epistatic effects might be explicitly
accounted for in future models of influenza evolution.'
acknowledgement: "This work was supported by the Biotechnology and Biological Sciences
Research Council, the Government of the Republic of Panama, the Interdisciplinary
Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the
Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC
BY 2.0\r\n"
article_number: '222'
article_processing_charge: No
author:
- first_name: Melissa
full_name: Ward, Melissa
last_name: Ward
- first_name: Samantha
full_name: Lycett, Samantha
last_name: Lycett
- first_name: Dorita
full_name: Avila, Dorita
last_name: Avila
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Leigh Brown, Andrew
last_name: Leigh Brown
citation:
ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions
between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013).
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and
Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase
in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.
ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza,” BMC
Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza. BMC
Evolutionary Biology. 13(1), 222.
mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and
Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no.
1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:46:49Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2025-09-30T07:28:51Z
day: '09'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-222
external_id:
isi:
- '000326620200001'
file:
- access_level: open_access
checksum: 52cf48a7c1794676ae8b0029573a84a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4722'
file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf
file_size: 1150052
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
fulldoi: https://doi.org/10.1186/1471-2148-13-222
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '7320'
pubrep_id: '941'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interactions between haemagglutinin and neuraminidase in avian
influenza
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
article_processing_charge: No
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2025-09-30T07:28:20Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
external_id:
isi:
- '000329010200015'
file:
- access_level: open_access
checksum: 8007815078dccac21ecd1cf73a269dc6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4980'
file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf
file_size: 1040765
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
fulldoi: https://doi.org/10.1644/12-MAMM-A-169.1
has_accepted_license: '1'
intvolume: ' 94'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1331 - 1345
publication: Journal of Mammalogy
publication_status: published
publisher: Oxford University Press
publist_id: '7319'
pubrep_id: '940'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new species of tapir from the Amazon
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 94
year: '2013'
...
---
_id: '502'
abstract:
- lang: eng
text: 'Blind signatures allow users to obtain signatures on messages hidden from
the signer; moreover, the signer cannot link the resulting message/signature pair
to the signing session. This paper presents blind signature schemes, in which
the number of interactions between the user and the signer is minimal and whose
blind signatures are short. Our schemes are defined over bilinear groups and are
proved secure in the common-reference-string model without random oracles and
under standard assumptions: CDH and the decision-linear assumption. (We also give
variants over asymmetric groups based on similar assumptions.) The blind signatures
are Waters signatures, which consist of 2 group elements. Moreover, we instantiate
partially blind signatures, where the message consists of a part hidden from the
signer and a commonly known public part, and schemes achieving perfect blindness.
We propose new variants of blind signatures, such as signer-friendly partially
blind signatures, where the public part can be chosen by the signer without prior
agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated
messages provided by independent sources. We also extend Waters signatures to
non-binary alphabets by proving a new result on the underlying hash function. '
author:
- first_name: Olivier
full_name: Blazy, Olivier
last_name: Blazy
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: David
full_name: Pointcheval, David
last_name: Pointcheval
- first_name: Damien
full_name: Vergnaud, Damien
last_name: Vergnaud
citation:
ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal
of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477
apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short
blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477
chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud.
“Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013.
https://doi.org/10.3233/JCS-130477.
ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,”
Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.
ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures.
Journal of Computer Security. 21(5), 627–661.
mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security,
vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477.
short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer
Security 21 (2013) 627–661.
date_created: 2018-12-11T11:46:50Z
date_published: 2013-11-22T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '22'
department:
- _id: KrPi
doi: 10.3233/JCS-130477
fulldoi: https://doi.org/10.3233/JCS-130477
intvolume: ' 21'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 627 - 661
publication: Journal of Computer Security
publication_status: published
publisher: IOS Press
publist_id: '7318'
quality_controlled: '1'
scopus_import: 1
status: public
title: Short blind signatures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2013'
...
---
_id: '505'
abstract:
- lang: eng
text: Alkyd resins are polyesters containing unsaturated fatty acids that are used
as binding agents in paints and coatings. Chemical drying of these polyesters
is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid
moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective,
yet they have been proven to be carcinogenic. Therefore, strategies to replace
the cobalt-based catalyst by environmentally friendlier and less toxic alternatives
are under development. Here, we demonstrate for the first time that a laccase-mediator
system can effectively replace the heavy-metal catalyst and cross-link alkyd resins.
Interestingly, the biocatalytic reaction does not only work in aqueous media,
but also in a solid film, where enzyme diffusion is limited. Within the catalytic
cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase,
which is uniformly distributed within the drying film as evidenced by confocal
laser scanning microscopy. During gradual build-up of molecular weight, there
is a concomitant decrease of the oxygen content in the film. A new optical sensor
to follow oxygen consumption during the cross-linking reaction was developed and
validated with state of the art techniques. A remarkable feature is the low sample
amount required, which allows faster screening of new catalysts.
acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial
Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the
Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of
Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion
Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the
\ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian
Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental
Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with
the CLSM measurements."
article_processing_charge: No
author:
- first_name: Katrin
full_name: Greimel, Katrin
last_name: Greimel
- first_name: Veronika
full_name: Perz, Veronika
last_name: Perz
- first_name: Klaus
full_name: Koren, Klaus
id: 382FBD6A-F248-11E8-B48F-1D18A9856A87
last_name: Koren
- first_name: Roland
full_name: Feola, Roland
last_name: Feola
- first_name: Armin
full_name: Temel, Armin
last_name: Temel
- first_name: Christian
full_name: Sohar, Christian
last_name: Sohar
- first_name: Enrique
full_name: Herrero Acero, Enrique
last_name: Herrero Acero
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
- first_name: Georg
full_name: Guebitz, Georg
last_name: Guebitz
citation:
ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from
paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388.
doi:10.1039/c2gc36666e'
apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz,
G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking
of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e'
chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel,
Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning
Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.”
Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.'
ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints:
Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no.
2. Royal Society of Chemistry, pp. 381–388, 2013.'
ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant
I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic
cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.'
mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints:
Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no.
2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.'
short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero,
I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.
date_created: 2018-12-11T11:46:51Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2025-09-30T07:27:28Z
day: '01'
department:
- _id: HaJa
doi: 10.1039/c2gc36666e
external_id:
isi:
- '000314185900015'
fulldoi: https://doi.org/10.1039/c2gc36666e
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 381 - 388
publication: Green Chemistry
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7313'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of
alkyd resins'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2013'
...
---
_id: '507'
abstract:
- lang: eng
text: Fertilization in flowering plants requires the temporal and spatial coordination
of many developmental processes, including pollen production, anther dehiscence,
ovule production, and pollen tube elongation. However, it remains elusive as to
how this coordination occurs during reproduction. Here, we present evidence that
endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays
a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays
multiple defects in pollen production and viability, as well as elongation of
staminal filaments and pollen tubes, all of which are pivotal processes needed
for fertilization. Of these abnormalities, the defects in elongation of staminal
filaments and pollen tubes were partially rescued by exogenous auxin. Moreover,
DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments
and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed
defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl)
pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar
localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments.
Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an
inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent
endocytosis plays a crucial role in coordinating the multiple developmental aspects
of male reproductive organs by modulating cellular auxin level through the regulation
of the amount and polarity of PINs.
article_processing_charge: No
author:
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Dae
full_name: Kim, Dae
last_name: Kim
- first_name: Hyangju
full_name: Kang, Hyangju
last_name: Kang
- first_name: Ilka
full_name: Reichardt, Ilka
last_name: Reichardt
- first_name: Eun
full_name: Sohn, Eun
last_name: Sohn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Gerd
full_name: Juergens, Gerd
last_name: Juergens
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
citation:
ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis
is crucial for male reproductive organ development in arabidopsis. Plant Cell.
2013;25(8):2970-2985. doi:10.1105/tpc.113.114264
apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013).
Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis. Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.113.114264
chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt,
Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex
2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.”
Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264.
ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial
for male reproductive organ development in arabidopsis,” Plant Cell, vol.
25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.
ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens
G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for
male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.
mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial
for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol.
25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264.
short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml,
G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-09-30T07:17:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114264
external_id:
isi:
- '000324920500019'
pmid:
- '23975898'
fulldoi: https://doi.org/10.1105/tpc.113.114264
intvolume: ' 25'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2970 - 2985
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7312'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2013'
...
---
_id: '508'
abstract:
- lang: eng
text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen
species with microbicidal activity. It is composed of two membrane-spanning subunits,
gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic
subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively).
Mutations in any of these genes can result in chronic granulomatous disease, a
primary immunodeficiency characterized by recurrent infections. Using evolutionary
mapping, we determined that episodes of adaptive natural selection have shaped
the extracellular portion of gp91-phox during the evolution of mammals, which
suggests that this region may have a function in host-pathogen interactions. On
the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2,
and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of
European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the
pattern of CYBA diversity is compatible with balancing natural selection, perhaps
mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern
of diversity characterized by a differentiated haplotype structure. Our study
provides insight into the role of pathogen-driven natural selection in an innate
immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic
NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other
complex diseases.
article_processing_charge: No
author:
- first_name: Eduardo
full_name: Tarazona Santos, Eduardo
last_name: Tarazona Santos
- first_name: Moara
full_name: Machado, Moara
last_name: Machado
- first_name: Wagner
full_name: Magalhães, Wagner
last_name: Magalhães
- first_name: Renee
full_name: Chen, Renee
last_name: Chen
- first_name: Fernanda
full_name: Lyon, Fernanda
last_name: Lyon
- first_name: Laurie
full_name: Burdett, Laurie
last_name: Burdett
- first_name: Andrew
full_name: Crenshaw, Andrew
last_name: Crenshaw
- first_name: Cristina
full_name: Fabbri, Cristina
last_name: Fabbri
- first_name: Latife
full_name: Pereira, Latife
last_name: Pereira
- first_name: Laelia
full_name: Pinto, Laelia
last_name: Pinto
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Ben
full_name: Sestanovich, Ben
last_name: Sestanovich
- first_name: Meredith
full_name: Yeager, Meredith
last_name: Yeager
- first_name: Stephen
full_name: Chanock, Stephen
last_name: Chanock
citation:
ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of
the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications.
Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119'
apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett,
L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes
CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119'
chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen,
Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics
of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.”
Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.'
ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH
oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular
Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167,
2013.'
ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw
A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M,
Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB,
CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution.
30(9), 2157–2167.'
mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH
Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular
Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp.
2157–67, doi:10.1093/molbev/mst119.'
short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett,
A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich,
M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2025-09-30T07:13:08Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst119
external_id:
isi:
- '000323616600014'
pmid:
- '23821607'
fulldoi: https://doi.org/10.1093/molbev/mst119
intvolume: ' 30'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/
month: '09'
oa: 1
oa_version: Submitted Version
page: 2157 - 2167
pmid: 1
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7310'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and
NCF4: Functional implications'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 30
year: '2013'
...