---
_id: '69'
abstract:
- lang: eng
text: 'A qubit, a unit of quantum information, is essentially any quantum mechanical
two-level system which can be coherently controlled. Still, to be used for computation,
it has to fulfill criteria. Qubits, regardless of the system in which they are
realized, suffer from decoherence. This leads to loss of the information stored
in the qubit. The upper bound of the time scale on which decoherence happens is
set by the spin relaxation time. In this thesis I studied a two-level system consisting
of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire.
Such Ge hut wires have emerged as a promising material system for the realization
of spin qubits, due to the combination of two significant properties: long spin
coherence time as expected for group IV semiconductors due to the low hyperfine
interaction and a strong valence band spin-orbit coupling. Here, I present how
to fabricate quantum dot devices suitable for electrical transport measurements.
Coupled quantum dot devices allowed the realization of a charge sensor, which
is electrostatically and tunnel coupled to a quantum dot. By integrating the charge
sensor into a radio-frequency reflectometry setup, I performed for the first time
single-shot readout measurements of hole spins and extracted the hole spin relaxation
times in Ge hut wires.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
citation:
ama: Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires.
2018. doi:10.15479/AT:ISTA:TH_1047
apa: Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in
Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047
chicago: Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge
Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047.
ieee: L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,”
Institute of Science and Technology Austria, 2018.
ista: Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut
wires. Institute of Science and Technology Austria.
mla: Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut
Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047.
short: L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '01'
ddc:
- '530'
- '600'
degree_awarded: PhD
department:
- _id: GeKa
- _id: GradSch
doi: 10.15479/AT:ISTA:TH_1047
file:
- access_level: open_access
checksum: c570b656e30749cd65b1c7e13a9ce0a8
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:00:40Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6247'
file_name: 2018_Thesis_Vukusic.pdf
file_size: 28452385
relation: main_file
- access_level: closed
checksum: 7856771d9cd401fe0b311191076db6e1
content_type: application/zip
creator: dernst
date_created: 2019-04-09T07:00:40Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6248'
file_name: 2018_Thesis_Vukusic_source.zip
file_size: 53058704
relation: source_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '103'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7985'
pubrep_id: '1047'
related_material:
record:
- id: '23'
relation: part_of_dissertation
status: public
- id: '840'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Charge sensing and spin relaxation times of holes in Ge hut wires
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
arxiv: 1
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2021-01-12T08:09:33Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
intvolume: ' 171'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2018'
...
---
_id: '10'
abstract:
- lang: eng
text: Genomic imprinting is an epigenetic process that leads to parent of origin-specific
gene expression in a subset of genes. Imprinted genes are essential for brain
development, and deregulation of imprinting is associated with neurodevelopmental
diseases and the pathogenesis of psychiatric disorders. However, the cell-type
specificity of imprinting at single cell resolution, and how imprinting and thus
gene dosage regulates neuronal circuit assembly is still largely unknown. Here,
MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic
imprinting at single cell level. By visualizing MADM-induced uniparental disomies
(UPDs) in distinct colors at single cell level in genetic mosaic animals, this
experimental paradigm provides a unique quantitative platform to systematically
assay the UPD-mediated imbalances in imprinted gene expression at unprecedented
resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics
analysis was established and applied to systematically map cell-type-specific
‘imprintomes’ in the mouse brain. The results revealed that parental-specific
expression of imprinted genes per se is rarely cell-type-specific even at the
individual cell level. Conversely, when we extended the comparison to downstream
responses resulting from imbalanced imprinted gene expression, we discovered an
unexpectedly high degree of cell-type specificity. Furthermore, we determined
a novel function of genomic imprinting in cortical astrocyte production and in
olfactory bulb (OB) granule cell generation. These results suggest important functional
implication of genomic imprinting for generating cell-type diversity in the brain.
In addition, MADM provides a powerful tool to study candidate genes by concomitant
genetic manipulation and fluorescent labelling of single cells. MADM-based candidate
gene approach was utilized to identify potential imprinted genes involved in the
generation of cortical astrocytes and OB granule cells. We investigated p57Kip2,
a maternally expressed gene and known cell cycle regulator. Although we found
that p57Kip2 does not play a role in these processes, we detected an unexpected
function of the paternal allele previously thought to be silent. Finally, we took
advantage of a key property of MADM which is to allow unambiguous investigation
of environmental impact on single cells. The experimental pipeline based on FACS
and RNA-seq analysis of MADM-labeled cells was established to probe the functional
differences of single cell loss of gene function compared to global loss of function
on a transcriptional level. With this method, both common and distinct responses
were isolated due to cell-autonomous and non-autonomous effects acting on genotypically
identical cells. As a result, transcriptional changes were identified which result
solely from the surrounding environment. Using the MADM technology to study genomic
imprinting at single cell resolution, we have identified cell-type-specific gene
expression, novel gene function and the impact of environment on single cell transcriptomes.
Together, these provide important insights to the understanding of mechanisms
regulating cell-type specificity and thus diversity in the brain.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
citation:
ama: Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139.
doi:10.15479/AT:ISTA:th1057
apa: Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057
chicago: Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.
ieee: S. Laukoter, “Role of genomic imprinting in cerebral cortex development,”
Institute of Science and Technology Austria, 2018.
ista: Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria.
mla: Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development.
Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.
short: S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:08Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-07T12:40:44Z
day: '21'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: SiHi
doi: 10.15479/AT:ISTA:th1057
file:
- access_level: closed
checksum: 41fdbf5fdce312802935d88a8ad9932c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2019-11-23T23:30:03Z
embargo_to: open_access
file_id: '6396'
file_name: Thesis_LaukoterSusanne_FINAL.docx
file_size: 17949175
relation: source_file
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checksum: 53001a9a0c9e570e598d861bb0af28aa
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-11-21
file_id: '6397'
file_name: Thesis_LaukoterSusanne_FINAL.pdf
file_size: 21187245
relation: main_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1 - 139
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8046'
pubrep_id: '1057'
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Role of genomic imprinting in cerebral cortex development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '1012'
abstract:
- lang: eng
text: We prove a new central limit theorem (CLT) for the difference of linear eigenvalue
statistics of a Wigner random matrix H and its minor H and find that the fluctuation
is much smaller than the fluctuations of the individual linear statistics, as
a consequence of the strong correlation between the eigenvalues of H and H. In
particular, our theorem identifies the fluctuation of Kerov's rectangular Young
diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic
shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel
measure follow the same limiting shape. For this, algebraically motivated, ensemble
a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar
to our result but the variance is different, indicating that the analogy between
the two models has its limitations. Moreover, our theorem shows that Borodin's
result [7] on the convergence of the spectral distribution of Wigner matrices
to a Gaussian free field also holds in derivative sense.
article_processing_charge: No
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing
wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298.
doi:10.1093/imrn/rnw330
apa: Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young
diagrams of interlacing wigner eigenvalues. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330
chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330.
ieee: L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues,” International Mathematics Research Notices,
vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.
ista: Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10),
3255–3298.
mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.
short: L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018
(2018) 3255–3298.
date_created: 2018-12-11T11:49:41Z
date_published: 2018-05-18T00:00:00Z
date_updated: 2023-09-22T09:44:21Z
day: '18'
department:
- _id: LaEr
doi: 10.1093/imrn/rnw330
ec_funded: 1
external_id:
arxiv:
- '1608.05163'
isi:
- '000441668300009'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05163
month: '05'
oa: 1
oa_version: Preprint
page: 3255-3298
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: International Mathematics Research Notices
publication_identifier:
issn:
- '10737928'
publication_status: published
publisher: Oxford University Press
publist_id: '6383'
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '10286'
abstract:
- lang: eng
text: 'In this paper, we evaluate clock signals generated in ring oscillators and
self-timed rings and the way their jitter can be transformed into random numbers.
We show that counting the periods of the jittery clock signal produces random
numbers of significantly better quality than the methods in which the jittery
signal is simply sampled (the case in almost all current methods). Moreover, we
use the counter values to characterize and continuously monitor the source of
randomness. However, instead of using the widely used statistical variance, we
propose to use Allan variance to do so. There are two main advantages: Allan variance
is insensitive to low frequency noises such as flicker noise that are known to
be autocorrelated and significantly less circuitry is required for its computation
than that used to compute commonly used variance. We also show that it is essential
to use a differential principle of randomness extraction from the jitter based
on the use of two identical oscillators to avoid autocorrelations originating
from external and internal global jitter sources and that this fact is valid for
both kinds of rings. Last but not least, we propose a method of statistical testing
based on high order Markov model to show the reduced dependencies when the proposed
randomness extraction is applied.'
article_processing_charge: No
article_type: original
author:
- first_name: Elie Noumon
full_name: Allini, Elie Noumon
last_name: Allini
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
- first_name: Oto
full_name: Petura, Oto
last_name: Petura
- first_name: Florent
full_name: Bernard, Florent
last_name: Bernard
- first_name: Marek
full_name: Laban, Marek
last_name: Laban
- first_name: Viktor
full_name: Fischer, Viktor
last_name: Fischer
citation:
ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and
monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242.
doi:10.13154/tches.v2018.i3.214-242
apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer,
V. (2018). Evaluation and monitoring of free running oscillators serving as source
of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems.
International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242
chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek
Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems. International Association for Cryptologic Research,
2018. https://doi.org/10.13154/tches.v2018.i3.214-242.
ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer,
“Evaluation and monitoring of free running oscillators serving as source of randomness,”
IACR Transactions on Cryptographic Hardware and Embedded Systems, vol.
2018, no. 3. International Association for Cryptologic Research, pp. 214–242,
2018.
ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation
and monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.
mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic
Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.
short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR
Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-11-15T10:48:49Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/tches.v2018.i3.214-242
file:
- access_level: open_access
checksum: b816b848f046c48a8357700d9305dce5
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T10:27:29Z
date_updated: 2021-11-15T10:27:29Z
file_id: '10289'
file_name: 2018_IACR_Allini.pdf
file_size: 955755
relation: main_file
success: 1
file_date_updated: 2021-11-15T10:27:29Z
has_accepted_license: '1'
intvolume: ' 2018'
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 214-242
publication: IACR Transactions on Cryptographic Hardware and Embedded Systems
publication_identifier:
eissn:
- 2569-2925
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluation and monitoring of free running oscillators serving as source of
randomness
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2018
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '1064'
abstract:
- lang: eng
text: 'In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by
P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it
is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot
be separated into two subfamilies by a straight line disjoint from the disks.
In this note we show that essentially the same idea may work for different analogues
and generalizations of their result. In particular, we prove the following: Given
a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety
coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate
of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane
disjoint from the homothets.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Mikhail
full_name: Grigorev, Mikhail
last_name: Grigorev
citation:
ama: Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W.
Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009.
doi:10.1007/s00454-017-9883-x
apa: Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering
theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-017-9883-x
chicago: Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle
Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational
Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.
ieee: A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem
by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry,
vol. 59, no. 4. Springer, pp. 1001–1009, 2018.
ista: Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by
A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.
mla: Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and
R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer,
2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.
short: A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry
59 (2018) 1001–1009.
date_created: 2018-12-11T11:49:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:51Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-017-9883-x
ec_funded: 1
external_id:
isi:
- '000432205500011'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:27:36Z
date_updated: 2019-01-18T09:27:36Z
file_id: '5844'
file_name: 2018_DiscreteComp_Akopyan.pdf
file_size: 482518
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:27:36Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1001-1009
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the circle covering theorem by A.W. Goodman and R.E. Goodman
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 59
year: '2018'
...
---
_id: '107'
abstract:
- lang: eng
text: 'We introduce the notion of “non-malleable codes” which relaxes the notion
of error correction and error detection. Informally, a code is non-malleable if
the message contained in a modified codeword is either the original message, or
a completely unrelated value. In contrast to error correction and error detection,
non-malleability can be achieved for very rich classes of modifications. We construct
an efficient code that is non-malleable with respect to modifications that affect
each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set
it to either 0 or 1), but independently of the value of the other bits of the
codeword. Using the probabilistic method, we also show a very strong and general
statement: there exists a non-malleable code for every “small enough” family F
of functions via which codewords can be modified. Although this probabilistic
method argument does not directly yield efficient constructions, it gives us efficient
non-malleable codes in the random-oracle model for very general classes of tampering
functions—e.g., functions where every bit in the tampered codeword can depend
arbitrarily on any 99% of the bits in the original codeword. As an application
of non-malleable codes, we show that they provide an elegant algorithmic solution
to the task of protecting functionalities implemented in hardware (e.g., signature
cards) against “tampering attacks.” In such attacks, the secret state of a physical
system is tampered, in the hopes that future interaction with the modified system
will reveal some secret information. This problem was previously studied in the
work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security”
(ATP). We show that non-malleable codes can be used to achieve important improvements
over the prior work. In particular, we show that any functionality can be made
secure against a large class of tampering attacks, simply by encoding the secret
state with a non-malleable code while it is stored in memory.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- 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: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the
ACM. 2018;65(4). doi:10.1145/3178432
apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes.
Journal of the ACM. ACM. https://doi.org/10.1145/3178432
chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable
Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.
ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal
of the ACM, vol. 65, no. 4. ACM, 2018.
ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of
the ACM. 65(4), 20.
mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM,
vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.
short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:05:17Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3178432
ec_funded: 1
external_id:
isi:
- '000442938200004'
intvolume: ' 65'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2009/608
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7947'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-malleable codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
date_created: 2021-06-07T06:11:28Z
date_published: 2018-05-15T00:00:00Z
date_updated: 2021-12-14T07:53:40Z
day: '15'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1713333115
extern: '1'
external_id:
pmid:
- '29712855'
file:
- access_level: open_access
checksum: 810260dc0e3cc3033e15c19ad0dc123e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T06:16:38Z
date_updated: 2021-06-07T06:16:38Z
file_id: '9472'
file_name: 2018_PNAS_Frost.pdf
file_size: 3045260
relation: main_file
success: 1
file_date_updated: 2021-06-07T06:16:38Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '20'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: E4720-E4729
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: 'https://doi.org/10.1101/187674 '
scopus_import: '1'
status: public
title: FACT complex is required for DNA demethylation at heterochromatin during reproduction
in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '9807'
abstract:
- lang: eng
text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295339.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:26:53Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295339.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295339.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9808'
abstract:
- lang: eng
text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295369.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:31:57Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295369.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295369.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9810'
article_processing_charge: No
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018.
doi:10.1371/journal.pbio.2005971.s008
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used
in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.
ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library
of Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.
mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library
of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, (2018).
date_created: 2021-08-06T12:43:44Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971.s008
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '82'
relation: used_in_publication
status: public
status: public
title: Numerical data used in figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9811'
abstract:
- lang: eng
text: This document contains additional supporting evidence presented as supplemental
tables. (XLSX 50Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 1: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 1: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401390.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.'
mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:53:49Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401390.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401390.v1
month: '05'
oa: 1
oa_version: Preprint
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9812'
abstract:
- lang: eng
text: This document contains the full list of genes with their respective significance
and dN/dS values. (TXT 4499Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 2: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 2: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401414.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.'
mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:58:25Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401414.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401414.v1
month: '05'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 2: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2025-05-28T11:57:01Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:18Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2023-09-18T09:29:07Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '423'
relation: used_in_publication
status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...