---
_id: '5571'
abstract:
- lang: eng
text: "This folder contains all the data used in each of the main figures of \"The
genomic characterization of the t-haplotype, a mouse meiotic driver, highlights
its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well
as in the supplementary figures. \r\n"
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:78
apa: Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:78
chicago: Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:78.
ieee: B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:78.
mla: Vicoso, Beatriz. Data for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:78.
short: B. Vicoso, (2017).
contributor:
- contributor_type: contact_person
first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
datarep_id: '78'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:16Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:78
file:
- access_level: open_access
checksum: 4520eb2b8379417ee916995719158f16
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:00Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5618'
file_name: IST-2017-78-v1+1_Data.zip
file_size: 143697895
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Data for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5572'
abstract:
- lang: eng
text: Code described in the Supplementary Methods of "The genomic characterization
of the t-haplotype, a mouse meiotic driver, highlights its complex history and
specialized biology" (Kelemen, R., Vicoso, B.)
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:79
apa: Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:79
chicago: Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:79 .
ieee: B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:79 .
mla: Vicoso, Beatriz. Code for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:79 .
short: B. Vicoso, (2017).
datarep_id: '79'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:28Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: '10.15479/AT:ISTA:79 '
file:
- access_level: open_access
checksum: 3e70a7bcd6ff0c38b79e4c8a7d137034
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:15Z
date_updated: 2020-07-14T12:47:05Z
file_id: '5643'
file_name: IST-2017-79-v1+1_Code.zip
file_size: 49823
relation: main_file
file_date_updated: 2020-07-14T12:47:05Z
has_accepted_license: '1'
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Code for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '558'
abstract:
- lang: eng
text: Immune specificity is the degree to which a host’s immune system discriminates
among various pathogens or antigenic variants. Vertebrate immune memory is highly
specific due to antibody responses. On the other hand, some invertebrates show
immune priming, i.e. improved survival after secondary exposure to a previously
encountered pathogen. Until now, specificity of priming has only been demonstrated
via the septic infection route or when live pathogens were used for priming. Therefore,
we tested for specificity in the oral priming route in the red flour beetle, Tribolium
castaneum. For priming, we used pathogen-free supernatants derived from three
different strains of the entomopathogen, Bacillus thuringiensis, which express
different Cry toxin variants known for their toxicity against this beetle. Subsequent
exposure to the infective spores showed that oral priming was specific for two
naturally occurring strains, while a third engineered strain did not induce any
priming effect. Our data demonstrate that oral immune priming with a non-infectious
bacterial agent can be specific, but the priming effect is not universal across
all bacterial strains.
article_number: '0632'
article_processing_charge: No
article_type: original
author:
- first_name: Momir
full_name: Futo, Momir
last_name: Futo
- first_name: Marie
full_name: Sell, Marie
last_name: Sell
- 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
citation:
ama: Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the
red flour beetle Tribolium castaneum. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0632
apa: Futo, M., Sell, M., Kutzer, M., & Kurtz, J. (2017). Specificity of oral
immune priming in the red flour beetle Tribolium castaneum. Biology Letters.
The Royal Society. https://doi.org/10.1098/rsbl.2017.0632
chicago: Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity
of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” Biology
Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0632.
ieee: M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming
in the red flour beetle Tribolium castaneum,” Biology Letters, vol. 13,
no. 12. The Royal Society, 2017.
ista: Futo M, Sell M, Kutzer M, Kurtz J. 2017. Specificity of oral immune priming
in the red flour beetle Tribolium castaneum. Biology Letters. 13(12), 0632.
mla: Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle
Tribolium Castaneum.” Biology Letters, vol. 13, no. 12, 0632, The Royal
Society, 2017, doi:10.1098/rsbl.2017.0632.
short: M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).
date_created: 2018-12-11T11:47:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-10-18T06:42:25Z
day: '01'
department:
- _id: SyCr
doi: 10.1098/rsbl.2017.0632
external_id:
pmid:
- '29237813'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
publication: Biology Letters
publication_identifier:
issn:
- 1744-9561
publication_status: published
publisher: The Royal Society
publist_id: '7255'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specificity of oral immune priming in the red flour beetle Tribolium castaneum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '559'
abstract:
- lang: eng
text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative
to proofs of work, which are currently used in blockchain designs like Bitcoin.
The existing PoS are based on rather sophisticated graph pebbling lower bounds.
Much simpler and in several aspects more efficient schemes based on inverting
random functions have been suggested, but they don’t give meaningful security
guarantees due to existing time-memory trade-offs. In particular, Hellman showed
that any permutation over a domain of size N can be inverted in time T by an algorithm
that is given S bits of auxiliary information whenever (Formula presented). For
functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To
prove lower bounds, one considers an adversary who has access to an oracle f:
[ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈
Ω(N) and holds for random functions and permutations. We construct functions that
provably require more time and/or space to invert. Specifically, for any constant
k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk)
(in particular, S= T≈ (Formula presented). Our construction does not contradict
Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in
forward direction. However, its entire function table can be computed in time
quasilinear in N, which is sufficient for the PoS application. Our simplest construction
is built from a random function oracle g: [N] × [N] → [ N] and a random permutation
oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with
π being any involution without a fixed point, e.g. flipping all the bits. For
this function we prove that any adversary who gets S bits of auxiliary information,
makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must
satisfy S2· T∈ Ω(ϵ2N2).'
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Bram
full_name: Cohen, Bram
last_name: Cohen
- first_name: Danylo
full_name: Khilko, Danylo
last_name: Khilko
- 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: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
citation:
ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s
time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer;
2017:357-379. doi:10.1007/978-3-319-70697-9_13'
apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., &
Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to
proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory
and Applications of Cryptology and Information Security, Hong Kong, China: Springer.
https://doi.org/10.1007/978-3-319-70697-9_13'
chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z
Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications
to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13.
ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L.
Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of
space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and
Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.'
ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond
Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT:
Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625,
357–379.'
mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with
Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13.
short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin,
in:, Springer, 2017, pp. 357–379.
conference:
end_date: 2017-12-07
location: Hong Kong, China
name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security'
start_date: 2017-12-03
date_created: 2018-12-11T11:47:10Z
date_published: 2017-11-18T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '18'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70697-9_13
ec_funded: 1
intvolume: ' 10625'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/893.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 357 - 379
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331970696-2
publication_status: published
publisher: Springer
publist_id: '7257'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10625
year: '2017'
...
---
_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: '567'
abstract:
- lang: eng
text: "This book is a concise and self-contained introduction of recent techniques
to prove local spectral universality for large random matrices. Random matrix
theory is a fast expanding research area, and this book mainly focuses on the
methods that the authors participated in developing over the past few years. Many
other interesting topics are not included, and neither are several new developments
within the framework of these methods. The authors have chosen instead to present
key concepts that they believe are the core of these methods and should be relevant
for future applications. They keep technicalities to a minimum to make the book
accessible to graduate students. With this in mind, they include in this book
the basic notions and tools for high-dimensional analysis, such as large deviation,
entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n"
alternative_title:
- Courant Lecture Notes
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28.
American Mathematical Society; 2017. doi:10.1090/cln/028
apa: Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory
(Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028
chicago: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix
Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017.
https://doi.org/10.1090/cln/028.
ieee: L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory,
vol. 28. American Mathematical Society, 2017.
ista: Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 226p.
mla: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory.
Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.
short: L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 2017.
date_created: 2018-12-11T11:47:13Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-05-24T06:57:28Z
day: '01'
department:
- _id: LaEr
doi: 10.1090/cln/028
ec_funded: 1
intvolume: ' 28'
language:
- iso: eng
month: '01'
oa_version: None
page: '226'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
eisbn:
- 978-1-4704-4194-4
isbn:
- 9-781-4704-3648-3
publication_status: published
publisher: American Mathematical Society
publist_id: '7247'
quality_controlled: '1'
series_title: Courant Lecture Notes
status: public
title: A Dynamical Approach to Random Matrix Theory
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
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: '571'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis and play diverse
roles during immune responses. Despite these versatile tasks in mammalian biology,
their skills on a cellular level are deemed limited, mainly consisting in rolling,
adhesion, and aggregate formation. Here, we identify an unappreciated asset of
platelets and show that adherent platelets use adhesion receptors to mechanically
probe the adhesive substrate in their local microenvironment. When actomyosin-dependent
traction forces overcome substrate resistance, platelets migrate and pile up the
adhesive substrate together with any bound particulate material. They use this
ability to act as cellular scavengers, scanning the vascular surface for potential
invaders and collecting deposited bacteria. Microbe collection by migrating platelets
boosts the activity of professional phagocytes, exacerbating inflammatory tissue
injury in sepsis. This assigns platelets a central role in innate immune responses
and identifies them as potential targets to dampen inflammatory tissue damage
in clinical scenarios of severe systemic infection. In addition to their role
in thrombosis and hemostasis, platelets can also migrate to sites of infection
to help trap bacteria and clear the vascular surface.
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Zerkah
full_name: Ahmad, Zerkah
last_name: Ahmad
- first_name: Gerhild
full_name: Rosenberger, Gerhild
last_name: Rosenberger
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Benjamin
full_name: Busch, Benjamin
last_name: Busch
- first_name: Gökce
full_name: Yavuz, Gökce
last_name: Yavuz
- first_name: Manja
full_name: Luckner, Manja
last_name: Luckner
- first_name: Hellen
full_name: Ishikawa Ankerhold, Hellen
last_name: Ishikawa Ankerhold
- first_name: Roman
full_name: Hennel, Roman
last_name: Hennel
- first_name: Alexandre
full_name: Benechet, Alexandre
last_name: Benechet
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Sue
full_name: Chandraratne, Sue
last_name: Chandraratne
- first_name: Irene
full_name: Schubert, Irene
last_name: Schubert
- first_name: Sebastian
full_name: Helmer, Sebastian
last_name: Helmer
- first_name: Bianca
full_name: Striednig, Bianca
last_name: Striednig
- first_name: Konstantin
full_name: Stark, Konstantin
last_name: Stark
- first_name: Marek
full_name: Janko, Marek
last_name: Janko
- first_name: Ralph
full_name: Böttcher, Ralph
last_name: Böttcher
- first_name: Admar
full_name: Verschoor, Admar
last_name: Verschoor
- first_name: Catherine
full_name: Leon, Catherine
last_name: Leon
- first_name: Christian
full_name: Gachet, Christian
last_name: Gachet
- first_name: Thomas
full_name: Gudermann, Thomas
last_name: Gudermann
- first_name: Michael
full_name: Mederos Y Schnitzler, Michael
last_name: Mederos Y Schnitzler
- first_name: Zachary
full_name: Pincus, Zachary
last_name: Pincus
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Rainer
full_name: Haas, Rainer
last_name: Haas
- first_name: Gerhard
full_name: Wanner, Gerhard
last_name: Wanner
- first_name: Kirsten
full_name: Lauber, Kirsten
last_name: Lauber
- 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: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano
scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382.
doi:10.1016/j.cell.2017.11.001
apa: Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B.,
… Massberg, S. (2017). Migrating platelets are mechano scavengers that collect
and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001
chicago: Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo
Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano
Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.11.001.
ieee: F. R. Gärtner et al., “Migrating platelets are mechano scavengers that
collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press,
pp. 1368–1382, 2017.
ista: Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner
M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert
I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet
C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner
G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers
that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.
mla: Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That
Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press,
2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.
short: F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G.
Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S.
Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher,
A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus,
M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press
171 (2017) 1368–1382.
date_created: 2018-12-11T11:47:15Z
date_published: 2017-11-30T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '30'
department:
- _id: MiSi
doi: 10.1016/j.cell.2017.11.001
ec_funded: 1
intvolume: ' 171'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1368 - 1382
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Cell Press
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7243'
quality_controlled: '1'
scopus_import: 1
status: public
title: Migrating platelets are mechano scavengers that collect and bundle bacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
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: '5799'
abstract:
- lang: eng
text: We construct a polyhedral surface called a graceful surface, which provides
best possible approximation to a given sphere regarding certain criteria. In digital
geometry terms, the graceful surface is uniquely characterized by its minimality
while guaranteeing the connectivity of certain discrete (polyhedral) curves defined
on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva
(1999) and shown to be useful for triangular mesh discretization through graceful
planes and graceful lines. In this paper we extend the considerations to a nonlinear
object such as a sphere. In particular, we investigate the properties of a discrete
geodesic path between two voxels and show that discrete 3D circles, circular arcs,
and Mobius triangles are all constructible on a graceful sphere, with guaranteed
minimum thickness and the desired connectivity in the discrete topological space.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
- first_name: Valentin E.
full_name: Brimkov, Valentin E.
last_name: Brimkov
citation:
ama: Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and
circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017
apa: Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of
graceful spheres and circular geodesics. Discrete Applied Mathematics.
Elsevier. https://doi.org/10.1016/j.dam.2015.11.017
chicago: Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra
of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics.
Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017.
ieee: R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres
and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier,
pp. 362–375, 2017.
ista: Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres
and circular geodesics. Discrete Applied Mathematics. 216, 362–375.
mla: Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.”
Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017.
short: R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017)
362–375.
date_created: 2019-01-08T20:41:12Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:03:33Z
day: '10'
doi: 10.1016/j.dam.2015.11.017
extern: '1'
intvolume: ' 216'
language:
- iso: eng
month: '01'
oa_version: None
page: 362-375
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On the polyhedra of graceful spheres and circular geodesics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 216
year: '2017'
...
---
_id: '5800'
abstract:
- lang: eng
text: This paper presents a novel study on the functional gradation of coordinate
planes in connection with the thinnest and tunnel-free (i.e., naive) discretization
of sphere in the integer space. For each of the 48-symmetric quadraginta octants
of naive sphere with integer radius and integer center, we show that the corresponding
voxel set forms a bijection with its projected pixel set on a unique coordinate
plane, which thereby serves as its functional plane. We use this fundamental property
to prove several other theoretical results for naive sphere. First, the quadraginta
octants form symmetry groups and subgroups with certain equivalent topological
properties. Second, a naive sphere is always unique and consists of fewest voxels.
Third, it is efficiently constructible from its functional-plane projection. And
finally, a special class of 4-symmetric discrete 3D circles can be constructed
on a naive sphere based on back projection from the functional plane.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants
of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83.
doi:10.1007/s10851-017-0718-4
apa: Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness
of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and
Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4
chicago: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness
of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and
Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4.
ieee: R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta
octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol.
59, no. 1. Springer Nature, pp. 69–83, 2017.
ista: Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta
octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.
mla: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of
Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision,
vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4.
short: R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017)
69–83.
date_created: 2019-01-08T20:42:08Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '01'
doi: 10.1007/s10851-017-0718-4
extern: '1'
intvolume: ' 59'
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 69-83
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On the functionality and usefulness of Quadraginta octants of naive sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2017'
...
---
_id: '5801'
abstract:
- lang: eng
text: Space filling circles and spheres have various applications in mathematical
imaging and physical modeling. In this paper, we first show how the thinnest (i.e.,
2-minimal) model of digital sphere can be augmented to a space filling model by
fixing certain “simple voxels” and “filler voxels” associated with it. Based on
elementary number-theoretic properties of such voxels, we design an efficient
incremental algorithm for generation of these space filling spheres with successively
increasing radius. The novelty of the proposed technique is established further
through circular space filling on 3D digital plane. As evident from a preliminary
set of experimental result, this can particularly be useful for parallel computing
of 3D Voronoi diagrams in the digital space.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shivam
full_name: Dwivedi, Shivam
last_name: Dwivedi
- first_name: Aniket
full_name: Gupta, Aniket
last_name: Gupta
- first_name: Siddhant
full_name: Roy, Siddhant
last_name: Roy
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental
Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th
IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359.
doi:10.1007/978-3-319-66272-5_28'
apa: 'Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast
and Efficient Incremental Algorithms for Circular and Spherical Propagation in
Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359).
Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28'
chicago: 'Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha
Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical
Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.'
ieee: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space,”
in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502,
pp. 347–359.
ista: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space.
20th IAPR International Conference. DGCI: International Conference on Discrete
Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.'
mla: Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular
and Spherical Propagation in Integer Space.” 20th IAPR International Conference,
vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28.
short: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International
Conference, Springer Nature, Cham, 2017, pp. 347–359.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:22Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:34:25Z
day: '22'
doi: 10.1007/978-3-319-66272-5_28
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 347-359
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation
in Integer Space
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '5802'
abstract:
- lang: eng
text: This papers introduces a definition of digital primitives based on focal points
and weighted distances (with positive weights). The proposed definition is applicable
to general dimensions and covers in its gamut various regular curves and surfaces
like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids,
Cartesian k-ovals, etc. Several interesting properties are presented for this
class of digital primitives such as space partitioning, topological separation,
and connectivity properties. To demonstrate further the potential of this new
way of defining digital primitives, we propose, as extension, another class of
digital conics defined by focus-directrix combination.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal
set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer
Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31'
apa: 'Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined
by weighted focal set. In 20th IAPR International Conference (Vol. 10502,
pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31'
chicago: 'Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives
Defined by Weighted Focal Set.” In 20th IAPR International Conference,
10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.'
ieee: E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted
focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017,
vol. 10502, pp. 388–398.
ista: 'Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted
focal set. 20th IAPR International Conference. DGCI: International Conference
on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.'
mla: Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th
IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98,
doi:10.1007/978-3-319-66272-5_31.
short: E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference,
Springer Nature, Cham, 2017, pp. 388–398.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:39Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:38:35Z
day: '22'
doi: 10.1007/978-3-319-66272-5_31
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 388-398
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Digital primitives defined by weighted focal set
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '5803'
abstract:
- lang: eng
text: Different distance metrics produce Voronoi diagrams with different properties.
It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi
diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions.
In this paper, we first show that this metric produces a persistent VD on the
2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly
approximates the corresponding VD on the 2D real plane. Next, we show that on
a 3D digital plane D, the Euclidean metric spanning over its voxel set does not
guarantee a digital VD which is persistent with the real-space VD. As a solution,
we introduce a novel concept of functional-plane-convexity, which is ensured by
the Euclidean metric spanning over the pedal set of D. Necessary proofs and some
visual result have been provided to adjudge the merit and usefulness of the proposed
concept.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital
plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature;
2017:93-104. doi:10.1007/978-3-319-59108-7_8'
apa: 'Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi
diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256,
pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi
Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.'
ieee: 'R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on
3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer
Nature, 2017, pp. 93–104.'
ista: 'Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on
3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.'
mla: Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram
on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer
Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8.
short: R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature,
Cham, 2017, pp. 93–104.
conference:
end_date: 2017-06-21
location: Plovdiv, Bulgaria
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2017-06-19
date_created: 2019-01-08T20:42:56Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2022-01-28T07:48:24Z
day: '17'
department:
- _id: HeEd
doi: 10.1007/978-3-319-59108-7_8
extern: '1'
intvolume: ' 10256'
language:
- iso: eng
month: '05'
oa_version: None
page: 93-104
place: Cham
publication: Combinatorial image analysis
publication_identifier:
isbn:
- 978-3-319-59107-0
- 978-3-319-59108-7
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Construction of persistent Voronoi diagram on 3D digital plane
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10256
year: '2017'
...
---
_id: '593'
abstract:
- lang: eng
text: Bell correlations, indicating nonlocality in composite quantum systems, were
until recently only seen in small systems. Here, we demonstrate Bell correlations
in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective
measurements as witnesses and are statistically significant to 124 standard deviations.
The states are both generated and characterized using optical-cavity aided measurements.
author:
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed
states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401
apa: Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell
correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401
chicago: Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell
Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401.
ieee: N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations
in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol.
118, no. 14. American Physical Society, 2017.
ista: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations
in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).
mla: Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000
Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society,
2017, doi:10.1103/PhysRevLett.118.140401.
short: N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters
118 (2017).
date_created: 2018-12-11T11:47:23Z
date_published: 2017-04-03T00:00:00Z
date_updated: 2021-01-12T08:05:16Z
day: '03'
doi: 10.1103/PhysRevLett.118.140401
extern: '1'
intvolume: ' 118'
issue: '14'
language:
- iso: eng
month: '04'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7212'
status: public
title: Bell correlations in spin-squeezed states of 500 000 atoms
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '600'
abstract:
- lang: eng
text: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase
(Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine
X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular
model for basal Pol I initiation. The three-subunit CF binds upstream promoter
DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center
cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp
domains enables cleft contraction, resulting in an active Pol I conformation and
RNA synthesis. Comparison with the Pol II system suggests that promoter specificity
relies on a distinct “bendability” and “meltability” of the promoter sequence
that enables contacts between initiation factors, DNA, and polymerase.
article_processing_charge: No
author:
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Tobias
full_name: Gubbey, Tobias
last_name: Gubbey
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- first_name: Christiane
full_name: Oberthuer, Christiane
last_name: Oberthuer
- first_name: Carlo
full_name: Baejen, Carlo
last_name: Baejen
- 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: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription
initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003
apa: Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C.,
… Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation.
Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003
chicago: Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane
Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.03.003.
ieee: C. Engel et al., “Structural basis of RNA polymerase I transcription
initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.
ista: Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C,
Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation.
Cell. 169(1), 120–131.e22.
mla: Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription
Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003.
short: C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C.
Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.
date_created: 2018-12-11T11:47:25Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2021-01-12T08:05:36Z
day: '23'
doi: 10.1016/j.cell.2017.03.003
extern: '1'
intvolume: ' 169'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 120 - 131.e22
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7204'
quality_controlled: '1'
status: public
title: Structural basis of RNA polymerase I transcription initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
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'
...