---
_id: '560'
abstract:
- lang: eng
text: In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500
(doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily
slow convergence speed and every natural number d ? {4, 5, . . .}, there exist
d-dimensional stochastic differential equations with infinitely often differentiable
and globally bounded coefficients such that no approximation method based on finitely
many observations of the driving Brownian motion can converge in absolute mean
to the solution faster than the given speed of convergence. In this paper, we
strengthen the above result by proving that this slow convergence phenomenon also
arises in two (d = 2) and three (d = 3) space dimensions.
article_number: '0104'
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Arnulf
full_name: Jentzen, Arnulf
last_name: Jentzen
- first_name: Diyora
full_name: Salimova, Diyora
last_name: Salimova
citation:
ama: 'Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with
arbitrarily slow convergence rates for strong approximation in two space dimensions.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104'
apa: 'Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential
equations with arbitrarily slow convergence rates for strong approximation in
two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104'
chicago: 'Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential
Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in
Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.'
ieee: 'M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and
Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.'
ista: 'Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 473(2207), 0104.'
mla: 'Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily
Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.
473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.'
short: 'M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences 473 (2017).'
date_created: 2018-12-11T11:47:11Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:03:04Z
day: '01'
department:
- _id: JaMa
doi: 10.1098/rspa.2017.0104
ec_funded: 1
intvolume: ' 473'
issue: '2207'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.03229
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
issn:
- '13645021'
publication_status: published
publisher: Royal Society of London
publist_id: '7256'
quality_controlled: '1'
scopus_import: 1
status: public
title: On stochastic differential equations with arbitrarily slow convergence rates
for strong approximation in two space dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 473
year: '2017'
...
---
_id: '561'
abstract:
- lang: eng
text: Restriction–modification systems are widespread genetic elements that protect
bacteria from bacteriophage infections by recognizing and cleaving heterologous
DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence
shows that restriction sites are significantly underrepresented in bacteriophage
genomes, presumably because bacteriophages with fewer restriction sites are more
likely to escape cleavage by restriction–modification systems. However, how mutations
in restriction sites affect the likelihood of bacteriophage escape is unknown.
Using the bacteriophage l and the restriction–modification system EcoRI, we show
that while mutation effects at different restriction sites are unequal, they are
independent. As a result, the probability of bacteriophage escape increases with
each mutated restriction site. Our results experimentally support the role of
restriction site avoidance as a response to selection imposed by restriction–modification
systems and offer an insight into the events underlying the process of bacteriophage
escape.
acknowledgement: This work was funded by an HFSP Young Investigators' grant RGY0079/2011
(C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science
at the Institute of Science and Technology Austria.
article_number: '20170646'
article_processing_charge: No
article_type: original
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape
from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646
apa: Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction
sites during escape from restriction–modification. Biology Letters. The
Royal Society. https://doi.org/10.1098/rsbl.2017.0646
chicago: Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction
Sites during Escape from Restriction–Modification.” Biology Letters. The
Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646.
ieee: M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites
during escape from restriction–modification,” Biology Letters, vol. 13,
no. 12. The Royal Society, 2017.
ista: Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during
escape from restriction–modification. Biology Letters. 13(12), 20170646.
mla: Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction
Sites during Escape from Restriction–Modification.” Biology Letters, vol.
13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.
short: M. Pleska, C.C. Guet, Biology Letters 13 (2017).
date_created: 2018-12-11T11:47:11Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-07T11:59:32Z
day: '01'
department:
- _id: CaGu
doi: 10.1098/rsbl.2017.0646
external_id:
pmid:
- '29237814'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2017.0646
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems (HFSP Young investigators' grant)
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Biology Letters
publication_identifier:
issn:
- 1744-9561
publication_status: published
publisher: The Royal Society
publist_id: '7253'
quality_controlled: '1'
related_material:
record:
- id: '9847'
relation: research_data
status: public
- id: '202'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Effects of mutations in phage restriction sites during escape from restriction–modification
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '568'
abstract:
- lang: eng
text: 'We study robust properties of zero sets of continuous maps f: X → ℝn. Formally,
we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets
of all continuous maps g closer to f than r in the max-norm. All of these sets
are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined
by A and an element of a certain cohomotopy group which (by a recent result) is
computable whenever the dimension of X is at most 2n - 3. By considering all r
> 0 simultaneously, the pointed cohomotopy groups form a persistence module-a
structure leading to persistence diagrams as in the case of persistent homology
or well groups. Eventually, we get a descriptor of persistent robust properties
of zero sets that has better descriptive power (Theorem A) and better computability
status (Theorem B) than the established well diagrams. Moreover, if we endow every
point of each zero set with gradients of the perturbation, the robust description
of the zero sets by elements of cohomotopy groups is in some sense the best possible
(Theorem C).'
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications.
2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16
apa: Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology,
Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16
chicago: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology,
Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.
ieee: P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy
and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.
ista: Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and
Applications. 19(2), 313–342.
mla: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy
and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.
short: P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.
date_created: 2018-12-11T11:47:14Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:12Z
day: '01'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4310/HHA.2017.v19.n2.a16
ec_funded: 1
intvolume: ' 19'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.04310
month: '01'
oa: 1
oa_version: Submitted Version
page: 313 - 342
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Homology, Homotopy and Applications
publication_identifier:
issn:
- '15320073'
publication_status: published
publisher: International Press
publist_id: '7246'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistence of zero sets
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2017'
...
---
_id: '569'
abstract:
- lang: eng
text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow
in animal cells, yet its filament organization and the mechanism of contractility
is not well understood. We quantified actin filament order in human cells using
fluorescence polarization microscopy and found that cleavage furrow ingression
initiates by contraction of an equatorial actin network with randomly oriented
filaments. The network subsequently gradually reoriented actin filaments along
the cell equator. This strictly depended on myosin II activity, suggesting local
network reorganization by mechanical forces. Cortical laser microsurgery revealed
that during cytokinesis progression, mechanical tension increased substantially
along the direction of the cell equator, while the network contracted laterally
along the pole-to-pole axis without a detectable increase in tension. Our data
suggest that an asymmetric increase in cortical tension promotes filament reorientation
along the cytokinetic cleavage furrow, which might have implications for diverse
other biological processes involving actomyosin rings.
article_number: e30867
author:
- first_name: Felix
full_name: Spira, Felix
last_name: Spira
- first_name: Sara
full_name: Cuylen Haering, Sara
last_name: Cuylen Haering
- first_name: Shalin
full_name: Mehta, Shalin
last_name: Mehta
- first_name: Matthias
full_name: Samwer, Matthias
last_name: Samwer
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Amitabh
full_name: Verma, Amitabh
last_name: Verma
- first_name: Rudolf
full_name: Oldenbourg, Rudolf
last_name: Oldenbourg
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Daniel
full_name: Gerlich, Daniel
last_name: Gerlich
citation:
ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells
initiates by contraction of an equatorial actomyosin network composed of randomly
oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867
apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma,
A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.30867
chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne
Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich.
“Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin
Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences
Publications, 2017. https://doi.org/10.7554/eLife.30867.
ieee: F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg
R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. eLife.
6, e30867.
mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction
of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.”
ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.
short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma,
R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2023-02-23T12:30:29Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.30867
file:
- access_level: open_access
checksum: ba09c1451153d39e4f4b7cee013e314c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:40Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4829'
file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf
file_size: 9666973
relation: main_file
- access_level: open_access
checksum: 01eb51f1d6ad679947415a51c988e137
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:41Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4830'
file_name: IST-2017-919-v1+2_elife-30867-v1.pdf
file_size: 5951246
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7245'
pubrep_id: '919'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin
network composed of randomly oriented filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '570'
abstract:
- lang: eng
text: 'Most phenotypes are determined by molecular systems composed of specifically
interacting molecules. However, unlike for individual components, little is known
about the distributions of mutational effects of molecular systems as a whole.
We ask how the distribution of mutational effects of a transcriptional regulatory
system differs from the distributions of its components, by first independently,
and then simultaneously, mutating a transcription factor and the associated promoter
it represses. We find that the system distribution exhibits increased phenotypic
variation compared to individual component distributions - an effect arising from
intermolecular epistasis between the transcription factor and its DNA-binding
site. In large part, this epistasis can be qualitatively attributed to the structure
of the transcriptional regulatory system and could therefore be a common feature
in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the
constraints of individual components, thereby increasing phenotypic variation
that selection could act on and facilitating adaptive evolution. '
article_number: e28921
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- 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: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure
determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017).
Regulatory network structure determines patterns of intermolecular epistasis.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin
C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”
ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.
ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory
network structure determines patterns of intermolecular epistasis,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network
structure determines patterns of intermolecular epistasis. eLife. 6, e28921.
mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of
Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications,
2017, doi:10.7554/eLife.28921.
short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-13T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
- _id: JoBo
- _id: NiBa
doi: 10.7554/eLife.28921
ec_funded: 1
file:
- access_level: open_access
checksum: 273ab17f33305e4eaafd911ff88e7c5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:42Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5096'
file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf
file_size: 8453470
relation: main_file
- access_level: open_access
checksum: b433f90576c7be597cd43367946f8e7f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:43Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5097'
file_name: IST-2017-918-v1+2_elife-28921-v3.pdf
file_size: 1953221
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7244'
pubrep_id: '918'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulatory network structure determines patterns of intermolecular epistasis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '572'
abstract:
- lang: eng
text: In this review, we summarize the different biosynthesis-related pathways that
contribute to the regulation of endogenous auxin in plants. We demonstrate that
all known genes involved in auxin biosynthesis also have a role in root formation,
from the initiation of a root meristem during embryogenesis to the generation
of a functional root system with a primary root, secondary lateral root branches
and adventitious roots. Furthermore, the versatile adaptation of root development
in response to environmental challenges is mediated by both local and distant
control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial
and temporal regulation of auxin biosynthesis plays a central role in determining
root architecture.
article_number: '2587'
article_processing_charge: No
author:
- first_name: Damilola
full_name: Olatunji, Damilola
last_name: Olatunji
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
citation:
ama: Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in
plant root development. International Journal of Molecular Sciences. 2017;18(12).
doi:10.3390/ijms18122587
apa: Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous
auxin levels in plant root development. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms18122587
chicago: Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous
Auxin Levels in Plant Root Development.” International Journal of Molecular
Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.
ieee: D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels
in plant root development,” International Journal of Molecular Sciences,
vol. 18, no. 12. MDPI, 2017.
ista: Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels
in plant root development. International Journal of Molecular Sciences. 18(12),
2587.
mla: Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root
Development.” International Journal of Molecular Sciences, vol. 18, no.
12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.
short: D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular
Sciences 18 (2017).
date_created: 2018-12-11T11:47:15Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:03:16Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms18122587
file:
- access_level: open_access
checksum: 82d51f11e493f7eec02976d9a9a9805e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:55Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4718'
file_name: IST-2017-917-v1+1_ijms-18-02587.pdf
file_size: 920962
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_status: published
publisher: MDPI
publist_id: '7242'
pubrep_id: '917'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of endogenous auxin levels in plant root development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '601'
abstract:
- lang: eng
text: 'The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple
roles in chromatin transcription and genomic regulation. Paf1C comprises the five
subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II
(Pol II) transcription elongation complex (EC). Here we report the reconstitution
of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound
to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy
and crosslinking data reveal that Paf1C is highly mobile and extends over the
outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer
and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent
with the structural observations, the initiation factor TFIIF impairs Paf1C binding
to Pol II, whereas the elongation factor TFIIS enhances it. We further show that
Paf1C is globally required for normal mRNA transcription in yeast. These results
provide a three-dimensional framework for further analysis of Paf1C function in
transcription through chromatin. '
article_number: '15741'
article_processing_charge: No
author:
- first_name: Youwei
full_name: Xu, Youwei
last_name: Xu
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Chung
full_name: Lee, Chung
last_name: Lee
- first_name: Kerstin
full_name: Maier, Kerstin
last_name: Maier
- first_name: Björn
full_name: Schwalb, Björn
last_name: Schwalb
- first_name: Dimitri
full_name: Tegunov, Dimitri
last_name: Tegunov
- first_name: Jürgen
full_name: Plitzko, Jürgen
last_name: Plitzko
- first_name: Henning
full_name: Urlaub, Henning
last_name: Urlaub
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS
transcription elongation complex. Nature Communications. 2017;8. doi:10.1038/ncomms15741
apa: Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer,
P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation
complex. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15741
chicago: Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri
Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of
the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15741.
ieee: Y. Xu et al., “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription
elongation complex,” Nature Communications, vol. 8. Nature Publishing Group,
2017.
ista: Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub
H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription
elongation complex. Nature Communications. 8, 15741.
mla: Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription
Elongation Complex.” Nature Communications, vol. 8, 15741, Nature Publishing
Group, 2017, doi:10.1038/ncomms15741.
short: Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko,
H. Urlaub, P. Cramer, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:25Z
date_published: 2017-06-06T00:00:00Z
date_updated: 2021-01-12T08:05:40Z
day: '06'
ddc:
- '570'
doi: 10.1038/ncomms15741
extern: '1'
file:
- access_level: open_access
checksum: 940742282a9a285dc4aeae0c2b5ebe96
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T14:48:10Z
date_updated: 2020-07-14T12:47:16Z
file_id: '5865'
file_name: 2017_NatureComm_Xu.pdf
file_size: 3018075
relation: main_file
file_date_updated: 2020-07-14T12:47:16Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7203'
quality_controlled: '1'
status: public
title: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation
complex
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '6013'
abstract:
- lang: eng
text: The first hundred attoseconds of the electron dynamics during strong field
tunneling ionization are investigated. We quantify theoretically how the electron’s
classical trajectories in the continuum emerge from the tunneling process and
test the results with those achieved in parallel from attoclock measurements.
An especially high sensitivity on the tunneling barrier is accomplished here by
comparing the momentum distributions of two atomic species of slightly deviating
atomic potentials (argon and krypton) being ionized under absolutely identical
conditions with near-infrared laser pulses (1300 nm). The agreement between experiment
and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing
longitudinal momentum of the electron at the “tunnel exit.”
article_number: '023201'
arxiv: 1
author:
- first_name: Nicolas
full_name: Camus, Nicolas
last_name: Camus
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Lutz
full_name: Fechner, Lutz
last_name: Fechner
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Martin
full_name: Laux, Martin
last_name: Laux
- first_name: Yonghao
full_name: Mi, Yonghao
last_name: Mi
- first_name: Karen Z.
full_name: Hatsagortsyan, Karen Z.
last_name: Hatsagortsyan
- first_name: Thomas
full_name: Pfeifer, Thomas
last_name: Pfeifer
- first_name: Christoph H.
full_name: Keitel, Christoph H.
last_name: Keitel
- first_name: Robert
full_name: Moshammer, Robert
last_name: Moshammer
citation:
ama: Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling
time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201
apa: Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer,
R. (2017). Experimental evidence for quantum tunneling time. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201
chicago: Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin
Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel,
and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201.
ieee: N. Camus et al., “Experimental evidence for quantum tunneling time,”
Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017.
ista: Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ,
Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling
time. Physical Review Letters. 119(2), 023201.
mla: Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.”
Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society,
2017, doi:10.1103/PhysRevLett.119.023201.
short: N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan,
T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).
date_created: 2019-02-14T15:24:13Z
date_published: 2017-07-14T00:00:00Z
date_updated: 2023-02-23T11:13:36Z
day: '14'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.119.023201
external_id:
arxiv:
- '1611.03701'
intvolume: ' 119'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.03701
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '313'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Experimental evidence for quantum tunneling time
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '604'
abstract:
- lang: eng
text: In several settings of physics and chemistry one has to deal with molecules
interacting with some kind of an external environment, be it a gas, a solution,
or a crystal surface. Understanding molecular processes in the presence of such
a many-particle bath is inherently challenging, and usually requires large-scale
numerical computations. Here, we present an alternative approach to the problem,
based on the notion of the angulon quasiparticle. We show that molecules rotating
inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons,
and therefore can be described by straightforward solutions of a simple microscopic
Hamiltonian. Casting the problem in the language of angulons allows us not only
to greatly simplify it, but also to gain insights into the origins of the observed
phenomena and to make predictions for future experimental studies.
alternative_title:
- Theoretical and Computational Chemistry Series
author:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
citation:
ama: 'Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder
A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero
. Vol 11. Theoretical and Computational Chemistry Series. The Royal Society
of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444'
apa: 'Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with
a many-particle environment: From ultracold gases to helium nanodroplets. In O.
Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and
Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of
Chemistry. https://doi.org/10.1039/9781782626800-00444'
chicago: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting
with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.”
In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ,
edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational
Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.'
ieee: 'M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu
and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.'
ista: 'Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational
Chemistry Series, vol. 11, 444–495.'
mla: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting
with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.”
Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ,
edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of
Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444.'
short: 'M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of
Chemistry, 2017, pp. 444–495.'
date_created: 2018-12-11T11:47:27Z
date_published: 2017-12-14T00:00:00Z
date_updated: 2021-01-12T08:05:50Z
day: '14'
department:
- _id: MiLe
doi: 10.1039/9781782626800-00444
editor:
- first_name: Oliver
full_name: Dulieu, Oliver
last_name: Dulieu
- first_name: Andreas
full_name: Osterwalder, Andreas
last_name: Osterwalder
intvolume: ' 11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.06753
month: '12'
oa: 1
oa_version: Submitted Version
page: 444 - 495
publication: 'Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero '
publication_identifier:
issn:
- '20413181'
publication_status: published
publisher: The Royal Society of Chemistry
publist_id: '7201'
quality_controlled: '1'
scopus_import: 1
series_title: Theoretical and Computational Chemistry Series
status: public
title: 'Molecular impurities interacting with a many-particle environment: From ultracold
gases to helium nanodroplets'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2017'
...
---
_id: '605'
abstract:
- lang: eng
text: 'Position based cryptography (PBC), proposed in the seminal work of Chandran,
Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing
cryptographic schemes in which the identity of the user is his geographic position.
Chandran et al. construct PBC schemes for secure positioning and position-based
key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart
from bounded memory, their security proofs need a strong additional restriction
on the power of the adversary: he cannot compute joint functions of his inputs.
Removing this assumption is left as an open problem. We show that an answer to
this question would resolve a long standing open problem in multiparty communication
complexity: finding a function that is hard to compute with low communication
complexity in the simultaneous message model, but easy to compute in the fully
adaptive model. On a more positive side: we also show some implications in the
other direction, i.e.: we prove that lower bounds on the communication complexity
of certain multiparty problems imply existence of PBC primitives. Using this result
we then show two attractive ways to “bypass” our hardness result: the first uses
the random oracle model, the second weakens the locality requirement in the bounded-storage
model to online computability. The random oracle construction is arguably one
of the simplest proposed so far in this area. Our results indicate that constructing
improved provably secure protocols for PBC requires a better understanding of
multiparty communication complexity. This is yet another example where negative
results in one area (in our case: lower bounds in multiparty communication complexity)
can be used to construct secure cryptographic schemes.'
alternative_title:
- LNCS
author:
- first_name: Joshua
full_name: Brody, Joshua
last_name: Brody
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography
and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677.
Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3'
apa: 'Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position
based cryptography and multiparty communication complexity. In Y. Kalai &
L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography
Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3'
chicago: Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak.
“Position Based Cryptography and Multiparty Communication Complexity.” edited
by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3.
ieee: 'J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography
and multiparty communication complexity,” presented at the TCC: Theory of Cryptography
Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.'
ista: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography
and multiparty communication complexity. TCC: Theory of Cryptography Conference,
LNCS, vol. 10677, 56–81.'
mla: Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication
Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer,
2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3.
short: J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin
(Eds.), Springer, 2017, pp. 56–81.
conference:
end_date: 2017-11-15
location: Baltimore, MD, United States
name: 'TCC: Theory of Cryptography Conference'
start_date: 2017-11-12
date_created: 2018-12-11T11:47:27Z
date_published: 2017-11-05T00:00:00Z
date_updated: 2021-01-12T08:05:53Z
day: '05'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70500-2_3
ec_funded: 1
editor:
- first_name: Yael
full_name: Kalai, Yael
last_name: Kalai
- first_name: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
intvolume: ' 10677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/536
month: '11'
oa: 1
oa_version: Submitted Version
page: 56 - 81
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331970499-9
publication_status: published
publisher: Springer
publist_id: '7200'
quality_controlled: '1'
scopus_import: 1
status: public
title: Position based cryptography and multiparty communication complexity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10677
year: '2017'
...
---
_id: '609'
abstract:
- lang: eng
text: Several cryptographic schemes and applications are based on functions that
are both reasonably efficient to compute and moderately hard to invert, including
client puzzles for Denial-of-Service protection, password protection via salted
hashes, or recent proof-of-work blockchain systems. Despite their wide use, a
definition of this concept has not yet been distilled and formalized explicitly.
Instead, either the applications are proven directly based on the assumptions
underlying the function, or some property of the function is proven, but the security
of the application is argued only informally. The goal of this work is to provide
a (universal) definition that decouples the efforts of designing new moderately
hard functions and of building protocols based on them, serving as an interface
between the two. On a technical level, beyond the mentioned definitions, we instantiate
the model for four different notions of hardness. We extend the work of Alwen
and Serbinenko (STOC 2015) by providing a general tool for proving security for
the first notion of memory-hard functions that allows for provably secure applications.
The tool allows us to recover all of the graph-theoretic techniques developed
for proving security under the older, non-composable, notion of security used
by Alwen and Serbinenko. As an application of our definition of moderately hard
functions, we prove the security of two different schemes for proofs of effort
(PoE). We also formalize and instantiate the concept of a non-interactive proof
of effort (niPoE), in which the proof is not bound to a particular communication
context but rather any bit-string chosen by the prover.
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations,
and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526.
doi:10.1007/978-3-319-70500-2_17'
apa: 'Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition,
instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677,
pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United
States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17'
chicago: 'Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition,
Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526.
Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17.'
ieee: 'J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations,
and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD,
United States, 2017, vol. 10677, pp. 493–526.'
ista: 'Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations,
and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.'
mla: 'Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition,
Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin,
vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17.'
short: J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017,
pp. 493–526.
conference:
end_date: 2017-11-15
location: Baltimore, MD, United States
name: 'TCC: Theory of Cryptography'
start_date: 2017-11-12
date_created: 2018-12-11T11:47:28Z
date_published: 2017-11-05T00:00:00Z
date_updated: 2021-01-12T08:06:04Z
day: '05'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70500-2_17
editor:
- first_name: Yael
full_name: Kalai, Yael
last_name: Kalai
- first_name: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
intvolume: ' 10677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/945
month: '11'
oa: 1
oa_version: Submitted Version
page: 493 - 526
publication_identifier:
isbn:
- 978-331970499-9
publication_status: published
publisher: Springer
publist_id: '7196'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Moderately hard functions: Definition, instantiations, and applications'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10677
year: '2017'
...
---
_id: '610'
abstract:
- lang: eng
text: 'The fact that the complete graph K5 does not embed in the plane has been
generalized in two independent directions. On the one hand, the solution of the
classical Heawood problem for graphs on surfaces established that the complete
graph Kn embeds in a closed surface M (other than the Klein bottle) if and only
if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the
other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional
simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if
n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex
embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk
only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1
2k+1)bk. This is a common generalization of the case of graphs on surfaces as
well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we
prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold
with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than
the generalized Heawood inequality, but does not require the assumption that M
is (k−1)-connected. Our results generalize to maps without q-covered points, in
the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result
of Volovikov about maps that satisfy a certain homological triviality condition.'
acknowledgement: The work by Z. P. was partially supported by the Israel Science Foundation
grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project
CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced
Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria,
supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced
grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National
Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration
between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized
Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7'
apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner,
U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores
type nonembeddability result. Israel Journal of Mathematics. Springer.
https://doi.org/10.1007/s11856-017-1607-7'
chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer,
and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores
Type Nonembeddability Result.” Israel Journal of Mathematics. Springer,
2017. https://doi.org/10.1007/s11856-017-1607-7.'
ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner,
“On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp.
841–866, 2017.'
ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized
Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result. Israel Journal of Mathematics. 222(2), 841–866.'
mla: 'Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds:
A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics,
vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.'
short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel
Journal of Mathematics 222 (2017) 841–866.
date_created: 2018-12-11T11:47:29Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-02-23T10:02:13Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-017-1607-7
ec_funded: 1
intvolume: ' 222'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.09063
month: '10'
oa: 1
oa_version: Preprint
page: 841 - 866
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '7194'
quality_controlled: '1'
related_material:
record:
- id: '1511'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'On generalized Heawood inequalities for manifolds: A van Kampen–Flores type
nonembeddability result'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 222
year: '2017'
...
---
_id: '6113'
author:
- first_name: Shigekazu
full_name: Oda, Shigekazu
last_name: Oda
- first_name: Yu
full_name: Toyoshima, Yu
last_name: Toyoshima
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 2017;114(23):E4658-E4665. doi:10.1073/pnas.1614596114
apa: Oda, S., Toyoshima, Y., & de Bono, M. (2017). Modulation of sensory information
processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1614596114
chicago: Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory
Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1614596114.
ieee: S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans,” Proceedings of the National Academy
of Sciences, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665,
2017.
ista: Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 114(23), E4658–E4665.
mla: Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:10.1073/pnas.1614596114.
short: S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of
Sciences 114 (2017) E4658–E4665.
date_created: 2019-03-19T13:29:51Z
date_published: 2017-06-06T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '06'
ddc:
- '570'
doi: 10.1073/pnas.1614596114
extern: '1'
external_id:
pmid:
- '28536200'
file:
- access_level: open_access
checksum: 9e42ce47090ecdad7d76f2dbdebb924e
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:42:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6114'
file_name: 2017_PNAS_Oda.pdf
file_size: 1469622
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: E4658-E4665
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Modulation of sensory information processing by a neuroglobin in Caenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '6115'
abstract:
- lang: eng
text: Animals adjust their behavioral priorities according to momentary needs and
prior experience. We show that Caenorhabditis elegans changes how it processes
sensory information according to the oxygen environment it experienced recently.
C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that
attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged
activity differences in a circuit that continuously signals O2 levels. A sustained
change in the activity of O2-sensing neurons reprograms the properties of their
postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled
to the ASK and ADL pheromone sensors that respectively drive pheromone attraction
and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness
of these neurons. These circuit changes provide a physiological correlate of altered
pheromone valence. Our results suggest C. elegans stores a memory of recent O2
experience in the RMG circuit and illustrate how a circuit is flexibly sculpted
to guide behavioral decisions in a context-dependent manner.
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence
inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
2017;114(16):4195-4200. doi:10.1073/pnas.1618934114
apa: Fenk, L. A., & de Bono, M. (2017). Memory of recent oxygen experience switches
pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1618934114
chicago: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience
Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1618934114.
ieee: L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans,” Proceedings of the National Academy of Sciences,
vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.
ista: Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
114(16), 4195–4200.
mla: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches
Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy
of Sciences, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200,
doi:10.1073/pnas.1618934114.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114
(2017) 4195–4200.
date_created: 2019-03-19T13:46:36Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '18'
ddc:
- '570'
doi: 10.1073/pnas.1618934114
extern: '1'
external_id:
pmid:
- '28373553'
file:
- access_level: open_access
checksum: 1801bc8319b752fa17598004ec375279
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:00:42Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6116'
file_name: 2017_PNAS_Fenk.pdf
file_size: 1217696
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 4195-4200
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Memory of recent oxygen experience switches pheromone valence inCaenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '6117'
abstract:
- lang: eng
text: 'Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates
responses to pathogens or tissue damage, and drives autoimmune diseases. Little
is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like
properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter
their response properties and contribution to behaviour. Using unbiased genetic
screens, we delineate an IL-17 signalling pathway and show that it acts in the
RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to
input from oxygen sensors, and renders sustained escape from 21% oxygen transient
and contingent on additional stimuli. Over-activating IL-17 receptors abnormally
heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency
can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in
adults can rescue mutant defects within 6 h. These findings reveal a non-immunological
role of IL-17 modulating circuit function and behaviour.'
author:
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Eisuke
full_name: Itakura, Eisuke
last_name: Itakura
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Ming
full_name: Sheng, Ming
last_name: Sheng
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Rebecca A.
full_name: Butcher, Rebecca A.
last_name: Butcher
- first_name: Ramanujan S.
full_name: Hegde, Ramanujan S.
last_name: Hegde
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Chen C, Itakura E, Nelson GM, et al. IL-17 is a neuromodulator of Caenorhabditis
elegans sensory responses. Nature. 2017;542(7639):43-48. doi:10.1038/nature20818
apa: Chen, C., Itakura, E., Nelson, G. M., Sheng, M., Laurent, P., Fenk, L. A.,
… de Bono, M. (2017). IL-17 is a neuromodulator of Caenorhabditis elegans sensory
responses. Nature. Springer Nature. https://doi.org/10.1038/nature20818
chicago: Chen, Changchun, Eisuke Itakura, Geoffrey M. Nelson, Ming Sheng, Patrick
Laurent, Lorenz A. Fenk, Rebecca A. Butcher, Ramanujan S. Hegde, and Mario de
Bono. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.”
Nature. Springer Nature, 2017. https://doi.org/10.1038/nature20818.
ieee: C. Chen et al., “IL-17 is a neuromodulator of Caenorhabditis elegans
sensory responses,” Nature, vol. 542, no. 7639. Springer Nature, pp. 43–48,
2017.
ista: Chen C, Itakura E, Nelson GM, Sheng M, Laurent P, Fenk LA, Butcher RA, Hegde
RS, de Bono M. 2017. IL-17 is a neuromodulator of Caenorhabditis elegans sensory
responses. Nature. 542(7639), 43–48.
mla: Chen, Changchun, et al. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans
Sensory Responses.” Nature, vol. 542, no. 7639, Springer Nature, 2017,
pp. 43–48, doi:10.1038/nature20818.
short: C. Chen, E. Itakura, G.M. Nelson, M. Sheng, P. Laurent, L.A. Fenk, R.A. Butcher,
R.S. Hegde, M. de Bono, Nature 542 (2017) 43–48.
date_created: 2019-03-19T14:06:41Z
date_published: 2017-02-02T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '02'
doi: 10.1038/nature20818
extern: '1'
external_id:
pmid:
- ' 28099418'
intvolume: ' 542'
issue: '7639'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/28099418
month: '02'
oa: 1
oa_version: Submitted Version
page: 43-48
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
- 1476-4687
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 542
year: '2017'
...
---
_id: '613'
abstract:
- lang: eng
text: 'Bacteria in groups vary individually, and interact with other bacteria and
the environment to produce population-level patterns of gene expression. Investigating
such behavior in detail requires measuring and controlling populations at the
single-cell level alongside precisely specified interactions and environmental
characteristics. Here we present an automated, programmable platform that combines
image-based gene expression and growth measurements with on-line optogenetic expression
control for hundreds of individual Escherichia coli cells over days, in a dynamically
adjustable environment. This integrated platform broadly enables experiments that
bridge individual and population behaviors. We demonstrate: (i) population structuring
by independent closed-loop control of gene expression in many individual cells,
(ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid
bio-digital circuits in single cells, and freely specifiable digital communication
between individual bacteria. These examples showcase the potential for real-time
integration of theoretical models with measurement and control of many individual
cells to investigate and engineer microbial population behavior.'
acknowledgement: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis,
M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and
Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich,
T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild,
B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin
for technical assistance. The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to
R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST
Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence
Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025
(COGEX) and ANR-10-BINF-06-01 (ICEBERG).
article_number: '1535'
article_processing_charge: Yes (in subscription journal)
author:
- 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: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population
behavior through computer interfaced control of individual cells. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01683-1
apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017).
Shaping bacterial population behavior through computer interfaced control of individual
cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1
chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin
C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control
of Individual Cells.” Nature Communications. Nature Publishing Group, 2017.
https://doi.org/10.1038/s41467-017-01683-1.
ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping
bacterial population behavior through computer interfaced control of individual
cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group,
2017.
ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial
population behavior through computer interfaced control of individual cells. Nature
Communications. 8(1), 1535.
mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer
Interfaced Control of Individual Cells.” Nature Communications, vol. 8,
no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications
8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:06:15Z
day: '01'
ddc:
- '576'
- '579'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41467-017-01683-1
ec_funded: 1
file:
- access_level: open_access
checksum: 44bb5d0229926c23a9955d9fe0f9723f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:05Z
date_updated: 2020-07-14T12:47:20Z
file_id: '5190'
file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf
file_size: 1951699
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file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7191'
pubrep_id: '911'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shaping bacterial population behavior through computer interfaced control of
individual cells
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '614'
abstract:
- lang: eng
text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated
WZ sex chromosomes. However, in most lineages outside of the division Ditrysia,
as well as in the sister order Trichoptera, females lack a W chromosome. The W
is therefore thought to have been acquired secondarily. Here we compare the genomes
of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three
models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex
chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment
of a B chromosome). We show that the gene content of the Z is highly conserved
across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes
moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome
fusion). Our comparative genomics analysis therefore supports the secondary acquisition
of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme
stability of well-differentiated sex chromosomes.'
article_number: '1486'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z
chromosome suggests a non canonical origin of the W. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01663-5
apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation
of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5
chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation
of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.
ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the
Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W. Nature Communications.
8(1), 1486.
mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome
Suggests a Non Canonical Origin of the W.” Nature Communications, vol.
8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.
short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1038/s41467-017-01663-5
external_id:
pmid:
- '29133797'
file:
- access_level: open_access
checksum: 4da2651303c8afc2f7fc419be42a2433
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T15:55:50Z
date_updated: 2020-07-14T12:47:20Z
file_id: '7562'
file_name: 2017_NatureComm_Fraisse.pdf
file_size: 1201520
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7190'
pubrep_id: '910'
quality_controlled: '1'
related_material:
record:
- id: '7163'
relation: popular_science
status: public
scopus_import: 1
status: public
title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical
origin of the W
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '615'
abstract:
- lang: eng
text: We show that the Dyson Brownian Motion exhibits local universality after a
very short time assuming that local rigidity and level repulsion of the eigenvalues
hold. These conditions are verified, hence bulk spectral universality is proven,
for a large class of Wigner-like matrices, including deformed Wigner ensembles
and ensembles with non-stochastic variance matrices whose limiting densities differ
from Wigner's semicircle law.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Erdös L, Schnelli K. Universality for random matrix flows with time dependent
density. Annales de l’institut Henri Poincare (B) Probability and Statistics.
2017;53(4):1606-1656. doi:10.1214/16-AIHP765
apa: Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows
with time dependent density. Annales de l’institut Henri Poincare (B) Probability
and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765
chicago: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows
with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability
and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765.
ieee: L. Erdös and K. Schnelli, “Universality for random matrix flows with time
dependent density,” Annales de l’institut Henri Poincare (B) Probability and
Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656,
2017.
ista: Erdös L, Schnelli K. 2017. Universality for random matrix flows with time
dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics.
53(4), 1606–1656.
mla: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with
Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability
and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017,
pp. 1606–56, doi:10.1214/16-AIHP765.
short: L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability
and Statistics 53 (2017) 1606–1656.
date_created: 2018-12-11T11:47:30Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:06:22Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/16-AIHP765
ec_funded: 1
intvolume: ' 53'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.00650
month: '11'
oa: 1
oa_version: Submitted Version
page: 1606 - 1656
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- '02460203'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7189'
quality_controlled: '1'
scopus_import: 1
status: public
title: Universality for random matrix flows with time dependent density
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2017'
...
---
_id: '618'
abstract:
- lang: eng
text: 'Background: Increasing temperatures are predicted to strongly impact host-parasite
interactions, but empirical tests are rare. Host species that are naturally exposed
to a broad temperature spectrum offer the possibility to investigate the effects
of elevated temperatures on hosts and parasites. Using three-spined sticklebacks,
Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776),
originating from a cold and a warm water site of a volcanic lake, we subjected
sympatric and allopatric host-parasite combinations to cold and warm conditions
in a fully crossed design. We predicted that warm temperatures would promote the
development of the parasites, while the hosts might benefit from cooler temperatures.
We further expected adaptations to the local temperature and mutual adaptations
of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster
at warm temperatures and stickleback hosts at cold temperatures. On a finer scale,
we observed that parasites were able to exploit their hosts more efficiently at
the parasite’s temperature of origin. In contrast, host tolerance towards parasite
infection was higher when sticklebacks were infected with parasites at the parasite’s
‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite
infection induced a stronger immune response. Conclusions: Our results suggest
that increasing environmental temperatures promote the parasite rather than the
host and that host tolerance is dependent on the interaction between parasite
infection and temperature. Sticklebacks might use tolerance mechanisms towards
parasite infection in combination with their high plasticity towards temperature
changes to cope with increasing parasite infection pressures and rising temperatures.'
article_number: '52'
author:
- first_name: Frederik
full_name: Franke, Frederik
last_name: Franke
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
citation:
ama: Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. Environmental temperature
variation influences fitness trade-offs in a fish-tapeworm association . Parasites
& Vectors. 2017;10(252). doi:10.1186/s13071-017-2192-7
apa: Franke, F., Armitage, S., Kutzer, M., Kurtz, J., & Scharsack, J. (2017).
Environmental temperature variation influences fitness trade-offs in a fish-tapeworm
association . Parasites & Vectors. BioMed Central. https://doi.org/10.1186/s13071-017-2192-7
chicago: Franke, Frederik, Sophie Armitage, Megan Kutzer, Joachim Kurtz, and Jörn
Scharsack. “Environmental Temperature Variation Influences Fitness Trade-Offs
in a Fish-Tapeworm Association .” Parasites & Vectors. BioMed Central,
2017. https://doi.org/10.1186/s13071-017-2192-7.
ieee: F. Franke, S. Armitage, M. Kutzer, J. Kurtz, and J. Scharsack, “Environmental
temperature variation influences fitness trade-offs in a fish-tapeworm association
,” Parasites & Vectors, vol. 10, no. 252. BioMed Central, 2017.
ista: Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. 2017. Environmental
temperature variation influences fitness trade-offs in a fish-tapeworm association
. Parasites & Vectors. 10(252), 52.
mla: Franke, Frederik, et al. “Environmental Temperature Variation Influences Fitness
Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors, vol.
10, no. 252, 52, BioMed Central, 2017, doi:10.1186/s13071-017-2192-7.
short: F. Franke, S. Armitage, M. Kutzer, J. Kurtz, J. Scharsack, Parasites &
Vectors 10 (2017).
date_created: 2018-12-11T11:47:31Z
date_published: 2017-06-02T00:00:00Z
date_updated: 2021-01-12T08:06:35Z
day: '02'
ddc:
- '570'
doi: 10.1186/s13071-017-2192-7
extern: '1'
file:
- access_level: open_access
checksum: 742943377a38ee208108705b8e2f4dbf
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T13:45:36Z
date_updated: 2020-07-14T12:47:22Z
file_id: '5864'
file_name: 2017_Parasites_Franke.pdf
file_size: 671807
relation: main_file
file_date_updated: 2020-07-14T12:47:22Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '252'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Parasites & Vectors
publication_identifier:
issn:
- '17563305'
publication_status: published
publisher: BioMed Central
publist_id: '7186'
quality_controlled: '1'
status: public
title: 'Environmental temperature variation influences fitness trade-offs in a fish-tapeworm
association '
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2017'
...
---
_id: '6196'
abstract:
- lang: eng
text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced
by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random
permutation over n-bit strings, PMAC constitutes a provably secure variable input-length
(pseudo)random function. For adversaries making q queries, each of length at most
l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an
upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently
best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving
an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs
a mask to every message block, where the mask for the ith block is computed as
τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of
the Gray code. Our attack applies more generally to any sequence of γi’s which
contains a large coset of a subgroup of GF(2n). We then investigate if the security
of PMAC can be further improved by using τi’s that are k-wise independent, for
k > 1 (the original distribution is only 1-wise independent). We observe that
the security of PMAC will not increase in general, even if the masks are chosen
from a 2-wise independent distribution, and then prove that the security increases
to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks,
this is the best bound one can hope for, using any distribution on the masks.
Whether 3-wise independence is already sufficient to get this level of security
is left as an open problem.
author:
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- 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: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161
apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC.
IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security
of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum,
2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161.
ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR
Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum,
pp. 145–161, 2017.
ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2016(2), 145–161.
mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric
Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.
short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology
2016 (2017) 145–161.
date_created: 2019-04-04T13:48:23Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2023-09-07T12:02:27Z
day: '03'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/TOSC.V2016.I2.145-161
ec_funded: 1
file:
- access_level: open_access
checksum: f23161d685dd957ae8d7274132999684
content_type: application/pdf
creator: dernst
date_created: 2019-04-04T13:53:58Z
date_updated: 2020-07-14T12:47:24Z
file_id: '6197'
file_name: 2017_IACR_Gazi.pdf
file_size: 597335
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 2016'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 145-161
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: IACR Transactions on Symmetric Cryptology
publication_identifier:
eissn:
- 2519-173X
publication_status: published
publisher: Ruhr University Bochum
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
status: public
title: The exact security of PMAC
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image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2017'
...