---
_id: '5673'
abstract:
- lang: eng
text: Cell polarity, manifested by the localization of proteins to distinct polar
plasma membrane domains, is a key prerequisite of multicellular life. In plants,
PIN auxin transporters are prominent polarity markers crucial for a plethora of
developmental processes. Cell polarity mechanisms in plants are distinct from
other eukaryotes and still largely elusive. In particular, how the cell polarities
are propagated and maintained following cell division remains unknown. Plant cytokinesis
is orchestrated by the cell plate—a transient centrifugally growing endomembrane
compartment ultimately forming the cross wall1. Trafficking of polar membrane
proteins is typically redirected to the cell plate, and these will consequently
have opposite polarity in at least one of the daughter cells2–5. Here, we provide
mechanistic insights into post-cytokinetic re-establishment of cell polarity as
manifested by the apical, polar localization of PIN2. We show that the apical
domain is defined in a cell-intrinsic manner and that re-establishment of PIN2
localization to this domain requires de novo protein secretion and endocytosis,
but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related
kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated
specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2
polarity re-establishment.
article_processing_charge: No
author:
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment
of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088.
doi:10.1038/s41477-018-0318-3
apa: Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for
cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature
Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3
chicago: Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework
for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature
Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.
ieee: M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division,” Nature Plants,
vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.
ista: Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic
re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.
mla: Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment
of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature
Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.
short: M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-12-03T00:00:00Z
date_updated: 2023-10-17T12:19:28Z
day: '03'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0318-3
ec_funded: 1
external_id:
isi:
- '000454576600017'
pmid:
- '30518833'
intvolume: ' 4'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30518833
month: '12'
oa: 1
oa_version: Submitted Version
page: 1082-1088
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity
after cell division
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '5676'
abstract:
- lang: eng
text: 'In epithelial tissues, cells tightly connect to each other through cell–cell
junctions, but they also present the remarkable capacity of reorganizing themselves
without compromising tissue integrity. Upon injury, simple epithelia efficiently
resolve small lesions through the action of actin cytoskeleton contractile structures
at the wound edge and cellular rearrangements. However, the underlying mechanisms
and how they cooperate are still poorly understood. In this study, we combine
live imaging and theoretical modeling to reveal a novel and indispensable role
for occluding junctions (OJs) in this process. We demonstrate that OJ loss of
function leads to defects in wound-closure dynamics: instead of contracting, wounds
dramatically increase their area. OJ mutants exhibit phenotypes in cell shape,
cellular rearrangements, and mechanical properties as well as in actin cytoskeleton
dynamics at the wound edge. We propose that OJs are essential for wound closure
by impacting on epithelial mechanics at the tissue level, which in turn is crucial
for correct regulation of the cellular events occurring at the wound edge.'
article_processing_charge: No
author:
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Pedro
full_name: Patricio, Pedro
last_name: Patricio
- first_name: Susana
full_name: Ponte, Susana
last_name: Ponte
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Luis
full_name: Almeida, Luis
last_name: Almeida
- first_name: André S.
full_name: Nunes, André S.
last_name: Nunes
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Antonio
full_name: Jacinto, Antonio
last_name: Jacinto
citation:
ama: Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators
of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283.
doi:10.1083/jcb.201804048
apa: Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes,
A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue
mechanics during wound repair. Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.201804048
chicago: Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg,
Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding
Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal
of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.
ieee: L. Carvalho et al., “Occluding junctions as novel regulators of tissue
mechanics during wound repair,” Journal of Cell Biology, vol. 217, no.
12. Rockefeller University Press, pp. 4267–4283, 2018.
ista: Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo
NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics
during wound repair. Journal of Cell Biology. 217(12), 4267–4283.
mla: Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics
during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller
University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.
short: L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S.
Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-13T09:11:17Z
day: '01'
department:
- _id: CaHe
doi: 10.1083/jcb.201804048
ec_funded: 1
external_id:
isi:
- '000451960800018'
pmid:
- '30228162 '
intvolume: ' 217'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30228162
month: '12'
oa: 1
oa_version: Submitted Version
page: 4267-4283
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Cell Biology
publication_identifier:
issn:
- '00219525'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Occluding junctions as novel regulators of tissue mechanics during wound repair
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 217
year: '2018'
...
---
_id: '5677'
abstract:
- lang: eng
text: 'Recently, contract-based design has been proposed as an “orthogonal” approach
that complements system design methodologies proposed so far to cope with the
complexity of system design. Contract-based design provides a rigorous scaffolding
for verification, analysis, abstraction/refinement, and even synthesis. A number
of results have been obtained in this domain but a unified treatment of the topic
that can help put contract-based design in perspective was missing. This monograph
intends to provide such a treatment where contracts are precisely defined and
characterized so that they can be used in design methodologies with no ambiguity.
In particular, this monograph identifies the essence of complex system design
using contracts through a mathematical “meta-theory”, where all the properties
of the methodology are derived from a very abstract and generic notion of contract.
We show that the meta-theory provides deep and illuminating links with existing
contract and interface theories, as well as guidelines for designing new theories.
Our study encompasses contracts for both software and systems, with emphasis on
the latter. We illustrate the use of contracts with two examples: requirement
engineering for a parking garage management, and the development of contracts
for timing and scheduling in the context of the Autosar methodology in use in
the automotive sector.'
article_processing_charge: No
article_type: original
author:
- first_name: Albert
full_name: Benveniste, Albert
last_name: Benveniste
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
- first_name: Benoît
full_name: Caillaud, Benoît
last_name: Caillaud
- first_name: Roberto
full_name: Passerone, Roberto
last_name: Passerone
- first_name: Jean Baptiste
full_name: Raclet, Jean Baptiste
last_name: Raclet
- first_name: Philipp
full_name: Reinkemeier, Philipp
last_name: Reinkemeier
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni-Vincentelli
- first_name: Werner
full_name: Damm, Werner
last_name: Damm
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
citation:
ama: Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations
and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053
apa: Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier,
P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends
in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053
chicago: Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone,
Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner
Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations
and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.
ieee: A. Benveniste et al., “Contracts for system design,” Foundations
and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers,
pp. 124–400, 2018.
ista: Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier
P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts
for system design. Foundations and Trends in Electronic Design Automation. 12(2–3),
124–400.
mla: Benveniste, Albert, et al. “Contracts for System Design.” Foundations and
Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers,
2018, pp. 124–400, doi:10.1561/1000000053.
short: A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier,
A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations
and Trends in Electronic Design Automation 12 (2018) 124–400.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-10-17T11:53:09Z
day: '01'
department:
- _id: ToHe
doi: 10.1561/1000000053
intvolume: ' 12'
issue: 2-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-00757488/
month: '05'
oa: 1
oa_version: Submitted Version
page: 124-400
publication: Foundations and Trends in Electronic Design Automation
publication_identifier:
issn:
- 1551-3939
publication_status: published
publisher: Now Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contracts for system design
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2018'
...
---
_id: '5679'
abstract:
- lang: eng
text: We study the almost-sure termination problem for probabilistic programs. First,
we show that supermartingales with lower bounds on conditional absolute difference
provide a sound approach for the almost-sure termination problem. Moreover, using
this approach we can obtain explicit optimal bounds on tail probabilities of non-termination
within a given number of steps. Second, we present a new approach based on Central
Limit Theorem for the almost-sure termination problem, and show that this approach
can establish almost-sure termination of programs which none of the existing approaches
can handle. Finally, we discuss algorithmic approaches for the two above methods
that lead to automated analysis techniques for almost-sure termination of probabilistic
programs.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of
probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11'
apa: 'Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure
termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201).
Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS,
Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11'
chicago: Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches
for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu,
11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.
ieee: M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination
of probabilistic programs,” presented at the 16th Asian Symposium on Programming
Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.
ista: Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination
of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems,
APLAS, LNCS, vol. 11275, 181–201.
mla: Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic
Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201,
doi:10.1007/978-3-030-02768-1_11.
short: M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.
conference:
end_date: 2018-12-06
location: Wellington, New Zealand
name: 16th Asian Symposium on Programming Languages and Systems, APLAS
start_date: 2018-12-02
date_created: 2018-12-16T22:59:20Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2025-06-02T08:53:41Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-030-02768-1_11
editor:
- first_name: Sukyoung
full_name: Ryu, Sukyoung
last_name: Ryu
external_id:
arxiv:
- '1806.06683'
isi:
- '000916310900011'
intvolume: ' 11275'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1806.06683
month: '12'
oa: 1
oa_version: Preprint
page: 181-201
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_identifier:
isbn:
- '9783030027674'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: New approaches for almost-sure termination of probabilistic programs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11275
year: '2018'
...
---
_id: '5686'
article_processing_charge: No
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. An Austrian Proposal for the Classification of Open Access Tuples
(COAT) - Distinguish Different Open Access Types beyond Colors.; 2018. doi:10.5281/zenodo.1244154
apa: Danowski, P. (2018). An Austrian proposal for the Classification of Open
Access Tuples (COAT) - Distinguish different Open Access types beyond colors.
https://doi.org/10.5281/zenodo.1244154
chicago: Danowski, Patrick. An Austrian Proposal for the Classification of Open
Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors,
2018. https://doi.org/10.5281/zenodo.1244154.
ieee: P. Danowski, An Austrian proposal for the Classification of Open Access
Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018.
ista: Danowski P. 2018. An Austrian proposal for the Classification of Open Access
Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p.
mla: Danowski, Patrick. An Austrian Proposal for the Classification of Open Access
Tuples (COAT) - Distinguish Different Open Access Types beyond Colors. 2018,
doi:10.5281/zenodo.1244154.
short: P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples
(COAT) - Distinguish Different Open Access Types beyond Colors, 2018.
date_created: 2018-12-17T10:28:26Z
date_published: 2018-05-09T00:00:00Z
date_updated: 2023-10-17T11:33:57Z
day: '09'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.1244154
file:
- access_level: open_access
checksum: 6cb95f8772491d155ce77c6160655fff
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T09:06:51Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5872'
file_name: 2018_WorkingPaper_Danowski.pdf
file_size: 202798
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '5'
publication_status: published
related_material:
record:
- id: '6657'
relation: later_version
status: public
scopus_import: 1
status: public
title: An Austrian proposal for the Classification of Open Access Tuples (COAT) -
Distinguish different Open Access types beyond colors
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: working_paper
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5751'
abstract:
- lang: eng
text: 'Because of the intrinsic randomness of the evolutionary process, a mutant
with a fitness advantage has some chance to be selected but no certainty. Any
experiment that searches for advantageous mutants will lose many of them due to
random drift. It is therefore of great interest to find population structures
that improve the odds of advantageous mutants. Such structures are called amplifiers
of natural selection: they increase the probability that advantageous mutants
are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous
mutants, even for very small fitness advantage. Despite intensive research over
the past decade, arbitrarily strong amplifiers have remained rare. Here we show
how to construct a large variety of them. Our amplifiers are so simple that they
could be useful in biotechnology, when optimizing biological molecules, or as
a diagnostic tool, when searching for faster dividing cells or viruses. They could
also occur in natural population structures.'
article_number: '71'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection
Using Evolutionary Graph Theory.” Communications Biology. Springer Nature,
2018. https://doi.org/10.1038/s42003-018-0078-7.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 1(1), 71.
mla: Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers
of Natural Selection Using Evolutionary Graph Theory.” Communications Biology,
vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology
1 (2018).
date_created: 2018-12-18T13:22:58Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2024-02-21T13:48:42Z
day: '14'
ddc:
- '004'
- '519'
- '576'
department:
- _id: KrCh
doi: 10.1038/s42003-018-0078-7
ec_funded: 1
external_id:
isi:
- '000461126500071'
file:
- access_level: open_access
checksum: a9db825fa3b64a51ff3de035ec973b3e
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:37:04Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5752'
file_name: 2018_CommBiology_Pavlogiannis.pdf
file_size: 1804194
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file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 1'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
pubrep_id: '1045'
quality_controlled: '1'
related_material:
record:
- id: '7196'
relation: part_of_dissertation
status: public
- id: '5559'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Construction of arbitrarily strong amplifiers of natural selection using evolutionary
graph theory
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: 1
year: '2018'
...
---
_id: '5757'
abstract:
- lang: eng
text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences
of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference
genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid
sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile
S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous
polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous
divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants
were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions
with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic
sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS;
⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript
in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous
diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (#
of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total
# of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent
sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in
the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous
evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence
data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression
values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized
across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK ,
ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile
S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites,
excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all
covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with
the Eyre-Walker and Keightley method on binned data and using all variants."
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection
in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757
apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster.” Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:/5757
chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the
Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology
Austria, 2018. https://doi.org/10.15479/at:ista:/5757.
ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of
selection in Drosophila melanogaster.’” Institute of Science and Technology Austria,
2018.
ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster’, Institute of Science and Technology
Austria, 10.15479/at:ista:/5757.
mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy
of Selection in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2018, doi:10.15479/at:ista:/5757.
short: C. Fraisse, (2018).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
- first_name: Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2018-12-19T14:22:35Z
date_published: 2018-12-19T00:00:00Z
date_updated: 2024-02-21T13:59:18Z
day: '19'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/at:ista:/5757
ec_funded: 1
file:
- access_level: open_access
checksum: aed7ee9ca3f4dc07d8a66945f68e13cd
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:52Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5758'
file_name: FileS1.zip
file_size: 369837892
relation: main_file
- access_level: open_access
checksum: 3592e467b4d8206650860b612d6e12f3
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5759'
file_name: FileS2.zip
file_size: 84856909
relation: main_file
- access_level: open_access
checksum: c37ac5d5437c457338afc128c1240655
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5760'
file_name: FileS3.txt
file_size: 881133
relation: main_file
- access_level: open_access
checksum: 943dfd14da61817441e33e3e3cb8cdb9
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5761'
file_name: FileS4.txt
file_size: 883742
relation: main_file
- access_level: open_access
checksum: 1c669b6c4690ec1bbca3e2da9f566d17
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5762'
file_name: FileS5.txt
file_size: 2495437
relation: main_file
- access_level: open_access
checksum: f40f661b987ca6fb6b47f650cbbb04e6
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5763'
file_name: FileS6.txt
file_size: 15913457
relation: main_file
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checksum: 25f41e5b8a075669c6c88d4c6713bf6f
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5764'
file_name: FileS7.txt
file_size: 2584120
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checksum: f6c0bd3e63e14ddf5445bd69b43a9152
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5765'
file_name: FileS8.txt
file_size: 2446059
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checksum: 0fe7a58a030b11bf3b9c8ff7a7addcae
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5766'
file_name: FileS9.txt
file_size: 100737
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
keyword:
- (mal)adaptation
- pleiotropy
- selective constraint
- evo-devo
- gene expression
- Drosophila melanogaster
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6089'
relation: research_paper
status: public
status: public
title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in
Drosophila melanogaster"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5767'
abstract:
- lang: eng
text: 'Cuprate superconductors have long been thought of as having strong electronic
correlations but negligible spin-orbit coupling. Using spin- and angle-resolved
photoemission spectroscopy, we discovered that one of the most studied cuprate
superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking
that circles the Brillouin zone center and a spin-layer locking that allows states
of opposite spin to be localized in different parts of the unit cell. Our findings
pose challenges for the vast majority of models of cuprates, such as the Hubbard
model and its variants, where spin-orbit interaction has been mostly neglected,
and open the intriguing question of how the high-temperature superconducting state
emerges in the presence of this nontrivial spin texture. '
acknowledgement: ' M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS
Initiative through grant GBMF4307'
article_processing_charge: No
article_type: original
author:
- first_name: Kenneth
full_name: Gotlieb, Kenneth
last_name: Gotlieb
- first_name: Chiu-Yun
full_name: Lin, Chiu-Yun
last_name: Lin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Wentao
full_name: Zhang, Wentao
last_name: Zhang
- first_name: Christopher L.
full_name: Smallwood, Christopher L.
last_name: Smallwood
- first_name: Christopher
full_name: Jozwiak, Christopher
last_name: Jozwiak
- first_name: Hiroshi
full_name: Eisaki, Hiroshi
last_name: Eisaki
- first_name: Zahid
full_name: Hussain, Zahid
last_name: Hussain
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
- first_name: Alessandra
full_name: Lanzara, Alessandra
last_name: Lanzara
citation:
ama: Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275.
doi:10.1126/science.aao0980
apa: Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak,
C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aao0980
chicago: Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher
L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath,
and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science. American Association for the Advancement
of Science, 2018. https://doi.org/10.1126/science.aao0980.
ieee: K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor,” Science, vol. 362, no. 6420. American Association
for the Advancement of Science, pp. 1271–1275, 2018.
ista: Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H,
Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.
mla: Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association
for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.
short: K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H.
Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.
date_created: 2018-12-19T14:53:50Z
date_published: 2018-12-14T00:00:00Z
date_updated: 2023-09-18T08:11:56Z
day: '14'
department:
- _id: MaSe
doi: 10.1126/science.aao0980
external_id:
isi:
- '000452994400048'
intvolume: ' 362'
isi: 1
issue: '6420'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.aao0980
month: '12'
oa: 1
oa_version: Published Version
page: 1271-1275
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 362
year: '2018'
...
---
_id: '5770'
abstract:
- lang: eng
text: Retroviruses assemble and bud from infected cells in an immature form and
require proteolytic maturation for infectivity. The CA (capsid) domains of the
Gag polyproteins assemble a protein lattice as a truncated sphere in the immature
virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements;
a subset of cleaved CA subsequently assembles into the mature core, whose architecture
varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus
and serves as the basis of retroviral vectors, but the structure of the MLV CA
layer is unknown. Here we have combined X-ray crystallography with cryoelectron
tomography to determine the structures of immature and mature MLV CA layers within
authentic viral particles. This reveals the structural changes associated with
maturation, and, by comparison with HIV-1, uncovers conserved and variable features.
In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which
adopts variable, multilayered morphologies and does not form a closed structure.
Unlike in HIV-1, there is similarity between protein–protein interfaces in the
immature MLV CA layer and those in the mature CA layer, and structural maturation
of MLV could be achieved through domain rotations that largely maintain hexameric
interactions. Nevertheless, the dramatic architectural change on maturation indicates
that extensive disassembly and reassembly are required for mature core growth.
The core morphology suggests that wrapping of the genome in CA sheets may be sufficient
to protect the MLV ribonucleoprotein during cell entry.
article_processing_charge: No
author:
- first_name: Kun
full_name: Qu, Kun
last_name: Qu
- first_name: Bärbel
full_name: Glass, Bärbel
last_name: Glass
- first_name: Michal
full_name: Doležal, Michal
last_name: Doležal
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Brice
full_name: Murciano, Brice
last_name: Murciano
- first_name: Alan
full_name: Rein, Alan
last_name: Rein
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
- first_name: Hans-Georg
full_name: Kräusslich, Hans-Georg
last_name: Kräusslich
- first_name: John A. G.
full_name: Briggs, John A. G.
last_name: Briggs
citation:
ama: Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and
mature murine leukemia virus capsids. Proceedings of the National Academy of
Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115
apa: Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs,
J. A. G. (2018). Structure and architecture of immature and mature murine leukemia
virus capsids. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115
chicago: Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano,
Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G.
Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus
Capsids.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.
ieee: K. Qu et al., “Structure and architecture of immature and mature murine
leukemia virus capsids,” Proceedings of the National Academy of Sciences,
vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760,
2018.
ista: Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T,
Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature
murine leukemia virus capsids. Proceedings of the National Academy of Sciences.
115(50), E11751–E11760.
mla: Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia
Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115,
no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60,
doi:10.1073/pnas.1811580115.
short: K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová,
T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy
of Sciences 115 (2018) E11751–E11760.
date_created: 2018-12-20T21:09:37Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-19T09:57:45Z
day: '11'
department:
- _id: FlSc
doi: 10.1073/pnas.1811580115
external_id:
isi:
- '000452866000022'
pmid:
- '30478053'
intvolume: ' 115'
isi: 1
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30478053
month: '12'
oa: 1
oa_version: Submitted Version
page: E11751-E11760
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and architecture of immature and mature murine leukemia virus capsids
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '5780'
abstract:
- lang: eng
text: Bioluminescence is found across the entire tree of life, conferring a spectacular
set of visually oriented functions from attracting mates to scaring off predators.
Half a dozen different luciferins, molecules that emit light when enzymatically
oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis
has been described in full, which is found only in bacteria. Here, we report identification
of the fungal luciferase and three other key enzymes that together form the biosynthetic
cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite.
Introduction of the identified genes into the genome of the yeast Pichia pastoris
along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent
in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis
cycle and found that fungal bioluminescence emerged through a series of events
that included two independent gene duplications. The retention of the duplicated
enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication
was followed by functional sequence divergence of enzymes of at least one gene
in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence
proceeded through several closely related stepping stone nonluminescent biochemical
reactions with adaptive roles. The availability of a complete eukaryotic luciferin
biosynthesis pathway provides several applications in biomedicine and bioengineering.
article_processing_charge: No
author:
- first_name: Alexey A.
full_name: Kotlobay, Alexey A.
last_name: Kotlobay
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Yuliana A.
full_name: Mokrushina, Yuliana A.
last_name: Mokrushina
- first_name: Marina
full_name: Marcet-Houben, Marina
last_name: Marcet-Houben
- first_name: Ekaterina O.
full_name: Serebrovskaya, Ekaterina O.
last_name: Serebrovskaya
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Andrey Y.
full_name: Gorokhovatsky, Andrey Y.
last_name: Gorokhovatsky
- first_name: Andrey
full_name: Vvedensky, Andrey
last_name: Vvedensky
- first_name: Konstantin V.
full_name: Purtov, Konstantin V.
last_name: Purtov
- first_name: Valentin N.
full_name: Petushkov, Valentin N.
last_name: Petushkov
- first_name: Natalja S.
full_name: Rodionova, Natalja S.
last_name: Rodionova
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Liliia
full_name: Fakhranurova, Liliia
last_name: Fakhranurova
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Rustam
full_name: Ziganshin, Rustam
last_name: Ziganshin
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Zinaida M.
full_name: Kaskova, Zinaida M.
last_name: Kaskova
- first_name: Victoria
full_name: Shender, Victoria
last_name: Shender
- first_name: Maxim
full_name: Abakumov, Maxim
last_name: Abakumov
- first_name: Tatiana O.
full_name: Abakumova, Tatiana O.
last_name: Abakumova
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Fedor M.
full_name: Eroshkin, Fedor M.
last_name: Eroshkin
- first_name: Andrey G.
full_name: Zaraisky, Andrey G.
last_name: Zaraisky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Tatiana Y.
full_name: Mitiouchkina, Tatiana Y.
last_name: Mitiouchkina
- first_name: Eugene P.
full_name: Kopantzev, Eugene P.
last_name: Kopantzev
- first_name: Hans E.
full_name: Waldenmaier, Hans E.
last_name: Waldenmaier
- first_name: Anderson G.
full_name: Oliveira, Anderson G.
last_name: Oliveira
- first_name: Yuichi
full_name: Oba, Yuichi
last_name: Oba
- first_name: Ekaterina
full_name: Barsova, Ekaterina
last_name: Barsova
- first_name: Ekaterina A.
full_name: Bogdanova, Ekaterina A.
last_name: Bogdanova
- first_name: Toni
full_name: Gabaldón, Toni
last_name: Gabaldón
- first_name: Cassius V.
full_name: Stevani, Cassius V.
last_name: Stevani
- first_name: Sergey
full_name: Lukyanov, Sergey
last_name: Lukyanov
- first_name: Ivan V.
full_name: Smirnov, Ivan V.
last_name: Smirnov
- first_name: Josef I.
full_name: Gitelson, Josef I.
last_name: Gitelson
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
citation:
ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115
apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya,
E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115
chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben,
Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et
al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.
ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system
from fungi,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732,
2018.
ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO,
Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov
VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova
AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin
FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier
HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov
S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable
bioluminescent system from fungi. Proceedings of the National Academy of Sciences
of the United States of America. 115(50), 12728–12732.
mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from
Fungi.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32,
doi:10.1073/pnas.1803615115.
short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya,
N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov,
V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya,
R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova,
I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y.
Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova,
E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson,
F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences
of the United States of America 115 (2018) 12728–12732.
date_created: 2018-12-23T22:59:18Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-11T14:04:05Z
day: '11'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1073/pnas.1803615115
external_id:
isi:
- '000452866000068'
file:
- access_level: open_access
checksum: 46b2c12185eb2ddb598f4c7b4bd267bf
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T15:21:40Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5926'
file_name: 2018_PNAS_Kotlobay.pdf
file_size: 1271988
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 12728-12732
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encodable bioluminescent system from fungi
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '5787'
abstract:
- lang: eng
text: "Branching morphogenesis remains a subject of abiding interest. Although
\ much is \r\nknown about the gene regulatory programs and signaling pathways
that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic
features of branched \r\norgans, including their size, network topology and
\ spatial patterning, are encoded. \r\nLately, it has been proposed that,
these features can be explained quantitatively in \r\nseveral organs within a
single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions
\ and cell lineage tracing, it has been argued that morphogenesis follows
\ \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing
progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive
a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation.
By correlating differentiation or cell cycle exit \r\nwith proximity to maturing
ducts, this dynamic results in the specification of a com-\r\nplex network of
\ defined density and statistical organization. These results suggest \r\nthat,
for several mammalian tissues, branched epithelial structures develop as a self-
\r\norganized process, reliant upon a strikingly simple, but generic,
\ set of local rules, \r\nwithout recourse to a rigid and deterministic
\ sequence of genetically programmed \r\nevents. Here, we review the basis
of these findings and discuss their implications."
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
citation:
ama: Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development
Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570
apa: Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching
morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570
chicago: Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching
Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.
ieee: E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,”
Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521,
2018.
ista: Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis.
Development Growth and Differentiation. 60(9), 512–521.
mla: Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching
Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9,
Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.
short: E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018)
512–521.
date_created: 2018-12-30T22:59:14Z
date_published: 2018-12-09T00:00:00Z
date_updated: 2023-09-19T09:32:49Z
day: '09'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1111/dgd.12570
external_id:
isi:
- '000453555100002'
file:
- access_level: open_access
checksum: a6d30b0785db902c734a84fecb2eadd9
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T10:40:46Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5933'
file_name: 2018_DevGrowh_Hannezo.pdf
file_size: 1313606
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '9'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 512-521
publication: Development Growth and Differentiation
publication_identifier:
issn:
- '00121592'
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical theory of branching morphogenesis
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: 60
year: '2018'
...
---
_id: '5788'
abstract:
- lang: eng
text: In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner or payoff of the game. Such
games are central in formal verification since they model the interaction between
a non-terminating system and its environment. We study bidding games in which
the players bid for the right to move the token. Two bidding rules have been defined.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the “bank” rather than the
other player. While poorman reachability games have been studied before, we present,
for the first time, results on infinite-duration poorman games. A central quantity
in these games is the ratio between the two players’ initial budgets. The questions
we study concern a necessary and sufficient ratio with which a player can achieve
a goal. For reachability objectives, such threshold ratios are known to exist
for both bidding rules. We show that the properties of poorman reachability games
extend to complex qualitative objectives such as parity, similarly to the Richman
case. Our most interesting results concern quantitative poorman games, namely
poorman mean-payoff games, where we construct optimal strategies depending on
the initial ratio, by showing a connection with random-turn based games. The connection
in itself is interesting, because it does not hold for reachability poorman games.
We also solve the complexity problems that arise in poorman bidding games.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games.
In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2'
apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration
poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International
Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2'
chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration
Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.
ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding
games,” presented at the 14th International Conference on Web and Internet Economics,
WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.
ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding
games. 14th International Conference on Web and Internet Economics, WINE, LNCS,
vol. 11316, 21–36.
mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316,
Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.
conference:
end_date: 2018-12-17
location: Oxford, UK
name: 14th International Conference on Web and Internet Economics, WINE
start_date: 2018-12-15
date_created: 2018-12-30T22:59:14Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-12T07:44:01Z
day: '21'
department:
- _id: ToHe
doi: 10.1007/978-3-030-04612-5_2
external_id:
arxiv:
- '1804.04372'
isi:
- '000865933000002'
intvolume: ' 11316'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04372
month: '11'
oa: 1
oa_version: Preprint
page: 21-36
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
isbn:
- '9783030046118'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infinite-duration poorman-bidding games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11316
year: '2018'
...
---
_id: '5791'
abstract:
- lang: eng
text: Due to data compression or low resolution, nearby vertices and edges of a
graph drawing may be bundled to a common node or arc. We model such a “compromised”
drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily
small ε>0 into a proper drawing (in which the vertices are distinct points, any
two edges intersect in finitely many points, and no three edges have a common
interior point) that minimizes the number of crossings. An ε-perturbation, for
every ε>0, is given by a piecewise linear map (Formula Presented), where with
||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution
for this optimization problem when G is a cycle and the map φ has no spurs (i.e.,
no two adjacent edges are mapped to overlapping arcs). We also show that the problem
becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii)
when φ may have spurs and G is a cycle or a union of disjoint paths.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba D.
full_name: Tóth, Csaba D.
last_name: Tóth
citation:
ama: 'Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282.
Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16'
apa: 'Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings
(Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization,
Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16'
chicago: Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed
Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.
ieee: R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented
at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282,
pp. 229–241.
ista: Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph
Drawing and Network Visualization, LNCS, vol. 11282, 229–241.
mla: Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings.
Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16.
short: R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.
conference:
end_date: 2018-09-28
location: Barcelona, Spain
name: Graph Drawing and Network Visualization
start_date: 2018-09-26
date_created: 2018-12-30T22:59:15Z
date_published: 2018-12-18T00:00:00Z
date_updated: 2023-09-11T12:49:55Z
day: '18'
department:
- _id: UlWa
doi: 10.1007/978-3-030-04414-5_16
external_id:
arxiv:
- '1808.07608'
isi:
- '000672802500016'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.07608
month: '12'
oa: 1
oa_version: Preprint
page: 229-241
publication_identifier:
isbn:
- '9783030044138'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crossing minimization in perturbed drawings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: '11282 '
year: '2018'
...
---
_id: '5794'
abstract:
- lang: eng
text: We present an approach to interacting quantum many-body systems based on the
notion of quantum groups, also known as q-deformed Lie algebras. In particular,
we show that, if the symmetry of a free quantum particle corresponds to a Lie
group G, in the presence of a many-body environment this particle can be described
by a deformed group, Gq. Crucially, the single deformation parameter, q, contains
all the information about the many-particle interactions in the system. We exemplify
our approach by considering a quantum rotor interacting with a bath of bosons,
and demonstrate that extracting the value of q from closed-form solutions in the
perturbative regime allows one to predict the behavior of the system for arbitrary
values of the impurity-bath coupling strength, in good agreement with nonperturbative
calculations. Furthermore, the value of the deformation parameter allows one to
predict at which coupling strengths rotor-bath interactions result in a formation
of a stable quasiparticle. The approach based on quantum groups does not only
allow for a drastic simplification of impurity problems, but also provides valuable
insights into hidden symmetries of interacting many-particle systems.
article_number: '255302'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302
apa: Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as
hidden symmetries of quantum impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302
chicago: Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum
Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.
ieee: E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries
of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American
Physical Society, 2018.
ista: Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 121(25), 255302.
mla: Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum
Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.
short: E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-01-06T22:59:12Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2023-09-15T12:09:06Z
day: '17'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.255302
ec_funded: 1
external_id:
arxiv:
- '1809.00222'
isi:
- '000454178600009'
intvolume: ' 121'
isi: 1
issue: '25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.00222
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum groups as hidden symmetries of quantum impurities
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 121
year: '2018'
...
---
_id: '58'
abstract:
- lang: eng
text: 'Inside a two-dimensional region (``cake""), there are m nonoverlapping
tiles of a certain kind (``toppings""). We want to expand the toppings
while keeping them nonoverlapping, and possibly add some blank pieces of the same
``certain kind,"" such that the entire cake is covered. How many blanks
must we add? We study this question in several cases: (1) The cake and toppings
are general polygons. (2) The cake and toppings are convex figures. (3) The cake
and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear
polygon and the toppings are axis-parallel rectangles. In all four cases, we provide
tight bounds on the number of blanks.'
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: Erel
full_name: Segal Halevi, Erel
last_name: Segal Halevi
citation:
ama: Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM
Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X
apa: Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements.
SIAM Journal on Discrete Mathematics. Society for Industrial and Applied
Mathematics . https://doi.org/10.1137/16M110407X
chicago: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal
Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial
and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.
ieee: A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,”
SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial
and Applied Mathematics , pp. 2242–2257, 2018.
ista: Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements.
SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.
mla: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.”
SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial
and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.
short: A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018)
2242–2257.
date_created: 2018-12-11T11:44:24Z
date_published: 2018-09-06T00:00:00Z
date_updated: 2023-09-11T12:48:39Z
day: '06'
department:
- _id: HeEd
doi: 10.1137/16M110407X
ec_funded: 1
external_id:
arxiv:
- '1604.00960'
isi:
- '000450810500036'
intvolume: ' 32'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.00960
month: '09'
oa: 1
oa_version: Preprint
page: 2242 - 2257
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: SIAM Journal on Discrete Mathematics
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7996'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting blanks in polygonal arrangements
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '5816'
abstract:
- lang: eng
text: Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance,
but quantum error correction requires millions of physical qubits and therefore
a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out
problems, microwave sources required for qubit manipulation might be embedded
close to the qubit chip, typically operating at temperatures below 4 K. Here,
we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe
voltage controlled oscillator at cryogenic temperature. We determined the frequency
and output power dependence on temperature and magnetic field up to 5 T and measured
the temperature influence on its noise performance. The device maintains its full
functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3%
with respect to the carrier frequency at 300 K, and the output power at 4 K increases
by 10 dB relative to the output power at 300 K. The frequency tuning range of
approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic
field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency
at zero magnetic field.
article_number: '114701'
article_processing_charge: No
arxiv: 1
author:
- first_name: Arne
full_name: Hollmann, Arne
last_name: Hollmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Maciej
full_name: Kucharski, Maciej
last_name: Kucharski
- first_name: Dietmar
full_name: Kissinger, Dietmar
last_name: Kissinger
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Lars R.
full_name: Schreiber, Lars R.
last_name: Schreiber
citation:
ama: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30
GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments.
2018;89(11). doi:10.1063/1.5038258
apa: Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., &
Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K.
Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258
chicago: Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter
Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating
at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258.
ieee: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R.
Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review
of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.
ista: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR.
2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific
Instruments. 89(11), 114701.
mla: Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4
K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing,
2018, doi:10.1063/1.5038258.
short: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber,
Review of Scientific Instruments 89 (2018).
date_created: 2019-01-10T14:22:23Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '01'
department:
- _id: GeKa
doi: 10.1063/1.5038258
external_id:
arxiv:
- '1804.09522'
isi:
- '000451735700054'
intvolume: ' 89'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.09522
month: '11'
oa: 1
oa_version: Preprint
publication: Review of Scientific Instruments
publication_identifier:
issn:
- '00346748'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 30 GHz-voltage controlled oscillator operating at 4 K
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 89
year: '2018'
...
---
_id: '5830'
abstract:
- lang: eng
text: CLE peptides have been implicated in various developmental processes of plants
and mediate their responses to environmental stimuli. However, the biological
relevance of most CLE genes remains to be functionally characterized. Here, we
report that CLE9, which is expressed in stomata, acts as an essential regulator
in the induction of stomatal closure. Exogenous application of CLE9 peptides or
overexpression of CLE9 effectively led to stomatal closure and enhanced drought
tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress.
CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants,
indicating that ABA is required for CLE9-medaited guard cell signalling. We further
deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were
responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by
the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants.
In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2)
and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished
in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively.
Collectively, our results reveal a novel ABA-dependent function of CLE9 in the
regulation of stomatal apertures, thereby suggesting a potential role of CLE9
in the stress acclimatization of plants.
article_processing_charge: No
author:
- first_name: Luosha
full_name: Zhang, Luosha
last_name: Zhang
- first_name: Xiong
full_name: Shi, Xiong
last_name: Shi
- first_name: Yutao
full_name: Zhang, Yutao
last_name: Zhang
- first_name: Jiajing
full_name: Wang, Jiajing
last_name: Wang
- first_name: Jingwei
full_name: Yang, Jingwei
last_name: Yang
- first_name: Takashi
full_name: Ishida, Takashi
last_name: Ishida
- first_name: Wenqian
full_name: Jiang, Wenqian
last_name: Jiang
- first_name: Xiangyu
full_name: Han, Xiangyu
last_name: Han
- first_name: Jingke
full_name: Kang, Jingke
last_name: Kang
- first_name: Xuening
full_name: Wang, Xuening
last_name: Wang
- first_name: Lixia
full_name: Pan, Lixia
last_name: Pan
- first_name: Shuo
full_name: Lv, Shuo
last_name: Lv
- first_name: Bing
full_name: Cao, Bing
last_name: Cao
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Jinbin
full_name: Wu, Jinbin
last_name: Wu
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Zhubing
full_name: Hu, Zhubing
last_name: Hu
- first_name: Langjun
full_name: Cui, Langjun
last_name: Cui
- first_name: Shinichiro
full_name: Sawa, Shinichiro
last_name: Sawa
- first_name: Junmin
full_name: He, Junmin
last_name: He
- first_name: Guodong
full_name: Wang, Guodong
last_name: Wang
citation:
ama: Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated
by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana.
Plant Cell and Environment. 2018. doi:10.1111/pce.13475
apa: Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018).
CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide,
and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley.
https://doi.org/10.1111/pce.13475
chicago: Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi
Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated
by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.”
Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.
ieee: L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated
by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,”
Plant Cell and Environment. Wiley, 2018.
ista: Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J,
Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang
G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen
peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.
mla: Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by
Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant
Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.
short: L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han,
J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui,
S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).
date_created: 2019-01-13T22:59:11Z
date_published: 2018-10-31T00:00:00Z
date_updated: 2023-09-11T12:43:31Z
day: '31'
department:
- _id: JiFr
doi: 10.1111/pce.13475
external_id:
isi:
- '000459014800021'
pmid:
- '30378140'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30378140
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Cell and Environment
publication_identifier:
issn:
- '01407791'
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen
peroxide, and nitric oxide in arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5858'
abstract:
- lang: eng
text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level,
and can be studied using imaging techniques such as light and fluorescence microscopy.
Imaging data provide quantitative information about biological systems; however,
mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal
mathematical modelling has helped to overcome this problem. Yet, outliers and
structured noise limit modelling of whole imaging data, and models often consider
spatial summary statistics. Here, we introduce an integrated data-driven modelling
approach that can cope with measurement artefacts and whole imaging data. Our
approach combines mechanistic models of the biological processes with robust statistical
models of the measurement process. The parameters of the integrated model are
calibrated using a maximum-likelihood approach. We used this integrated modelling
approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21).
CCL21 gradients guide dendritic cells and are important in the adaptive immune
response. Using artificial data, we verified that the integrated modelling approach
provides reliable parameter estimates in the presence of measurement noise and
that bias and variance of these estimates are reduced compared to conventional
approaches. The application to experimental data allowed the parametrization and
subsequent refinement of the model using additional mechanisms. Among other results,
model-based hypothesis testing predicted lymphatic vessel-dependent concentration
of heparan sulfate, the binding partner of CCL21. The selected model provided
an accurate description of the experimental data and was partially validated using
published data. Our findings demonstrate that integrated statistical modelling
of whole imaging data is computationally feasible and can provide novel biological
insights.
article_number: '20180600'
article_processing_charge: No
author:
- first_name: Sabrina
full_name: Hross, Sabrina
last_name: Hross
- first_name: Fabian J.
full_name: Theis, Fabian J.
last_name: Theis
- 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: Jan
full_name: Hasenauer, Jan
last_name: Hasenauer
citation:
ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial
processes using integrative modelling of noise-corrupted imaging data. Journal
of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600
apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic
description of spatial processes using integrative modelling of noise-corrupted
imaging data. Journal of the Royal Society Interface. Royal Society Publishing.
https://doi.org/10.1098/rsif.2018.0600
chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic
Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted
Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing,
2018. https://doi.org/10.1098/rsif.2018.0600.
ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description
of spatial processes using integrative modelling of noise-corrupted imaging data,”
Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society
Publishing, 2018.
ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of
spatial processes using integrative modelling of noise-corrupted imaging data.
Journal of the Royal Society Interface. 15(149), 20180600.
mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using
Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal
Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018,
doi:10.1098/rsif.2018.0600.
short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society
Interface 15 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-05T00:00:00Z
date_updated: 2023-09-13T08:55:05Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1098/rsif.2018.0600
external_id:
isi:
- '000456783800011'
file:
- access_level: open_access
checksum: 56eb4308a15b7190bff938fab1f780e8
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:46:44Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5925'
file_name: 2018_Interface_Hross.pdf
file_size: 1464288
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic description of spatial processes using integrative modelling of
noise-corrupted imaging data
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: 15
year: '2018'
...
---
_id: '5859'
abstract:
- lang: eng
text: The emergence of syntax during childhood is a remarkable example of how complex
correlations unfold in nonlinear ways through development. In particular, rapid
transitions seem to occur as children reach the age of two, which seems to separate
a two-word, tree-like network of syntactic relations among words from the scale-free
graphs associated with the adult, complex grammar. Here, we explore the evolution
of syntax networks through language acquisition using the chromatic number, which
captures the transition and provides a natural link to standard theories on syntactic
structures. The data analysis is compared to a null model of network growth dynamics
which is shown to display non-trivial and sensible differences. At a more general
level, we observe that the chromatic classes define independent regions of the
graph, and thus, can be interpreted as the footprints of incompatibility relations,
somewhat as opposed to modularity considerations.
acknowledgement: This work was supported by the James McDonnell Foundation (B.C-M.,
S.V. and R.S.)
article_number: '181286'
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Martí Sànchez
full_name: Fibla, Martí Sànchez
last_name: Fibla
- first_name: Sergi
full_name: Valverde, Sergi
last_name: Valverde
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in
the emergence of syntax networks. Royal Society Open Science. 2018;5(12).
doi:10.1098/rsos.181286
apa: Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic
transitions in the emergence of syntax networks. Royal Society Open Science.
The Royal Society. https://doi.org/10.1098/rsos.181286
chicago: Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard
Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society
Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.
ieee: B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions
in the emergence of syntax networks,” Royal Society Open Science, vol.
5, no. 12. The Royal Society, 2018.
ista: Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions
in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.
mla: Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of
Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The
Royal Society, 2018, doi:10.1098/rsos.181286.
short: B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open
Science 5 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-10-18T06:41:12Z
day: '12'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1098/rsos.181286
external_id:
isi:
- '000456566500027'
pmid:
- '30662738'
file:
- access_level: open_access
checksum: 9664d4417f6b792242e31eea77ce9501
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:38:09Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5924'
file_name: 2018_RoyalSocOS_Corominas.pdf
file_size: 646732
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Royal Society Open Science
publication_identifier:
issn:
- 2054-5703
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatic transitions in the emergence of syntax networks
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: 5
year: '2018'
...
---
_id: '5860'
abstract:
- lang: eng
text: 'A major problem for evolutionary theory is understanding the so-called open-ended
nature of evolutionary change, from its definition to its origins. Open-ended
evolution (OEE) refers to the unbounded increase in complexity that seems to characterize
evolution on multiple scales. This property seems to be a characteristic feature
of biological and technological evolution and is strongly tied to the generative
potential associated with combinatorics, which allows the system to grow and expand
their available state spaces. Interestingly, many complex systems presumably displaying
OEE, from language to proteins, share a common statistical property: the presence
of Zipf''s Law. Given an inventory of basic items (such as words or protein domains)
required to build more complex structures (sentences or proteins) Zipf''s Law
tells us that most of these elements are rare whereas a few of them are extremely
common. Using algorithmic information theory, in this paper we provide a fundamental
definition for open-endedness, which can be understood as postulates. Its statistical
counterpart, based on standard Shannon information theory, has the structure of
a variational problem which is shown to lead to Zipf''s Law as the expected consequence
of an evolutionary process displaying OEE. We further explore the problem of information
conservation through an OEE process and we conclude that statistical information
(standard Shannon information) is not conserved, resulting in the paradoxical
situation in which the increase of information content has the effect of erasing
itself. We prove that this paradox is solved if we consider non-statistical forms
of information. This last result implies that standard information theory may
not be a suitable theoretical framework to explore the persistence and increase
of the information content in OEE systems.'
article_number: '20180395'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Luís F.
full_name: Seoane, Luís F.
last_name: Seoane
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and
open-ended evolution. Journal of the Royal Society Interface. 2018;15(149).
doi:10.1098/rsif.2018.0395
apa: Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded
complexity and open-ended evolution. Journal of the Royal Society Interface.
Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395
chicago: Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law,
Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society
Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.
ieee: B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity
and open-ended evolution,” Journal of the Royal Society Interface, vol.
15, no. 149. Royal Society Publishing, 2018.
ista: Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity
and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.
mla: Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended
Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395,
Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.
short: B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface
15 (2018).
date_created: 2019-01-20T22:59:19Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-19T10:40:38Z
day: '12'
department:
- _id: EdHa
doi: 10.1098/rsif.2018.0395
external_id:
arxiv:
- '1612.01605'
isi:
- '000456783800002'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.01605
month: '12'
oa: 1
oa_version: Preprint
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zipf's Law, unbounded complexity and open-ended evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...