---
_id: '1019'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: Argyridou E, Huylmans AK, Königer A, Parsch J. X-linkage is not a general inhibitor
of tissue-specific gene expression in Drosophila melanogaster. Heredity.
2017;119(1):27-34. doi:10.1038/hdy.2017.12
apa: Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2017.12
chicago: Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch. “X-Linkage
Is Not a General Inhibitor of Tissue-Specific Gene Expression in Drosophila Melanogaster.”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2017.12.
ieee: E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,”
Heredity, vol. 119, no. 1. Nature Publishing Group, pp. 27–34, 2017.
ista: Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. X-linkage is not a general
inhibitor of tissue-specific gene expression in Drosophila melanogaster. Heredity.
119(1), 27–34.
mla: Argyridou, Eliza, et al. “X-Linkage Is Not a General Inhibitor of Tissue-Specific
Gene Expression in Drosophila Melanogaster.” Heredity, vol. 119, no. 1,
Nature Publishing Group, 2017, pp. 27–34, doi:10.1038/hdy.2017.12.
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, Heredity 119 (2017) 27–34.
date_created: 2018-12-11T11:49:43Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-22T09:41:21Z
day: '01'
department:
- _id: BeVi
doi: 10.1038/hdy.2017.12
external_id:
isi:
- '000405397800004'
intvolume: ' 119'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 27 - 34
publication: Heredity
publication_identifier:
issn:
- 0018067X
publication_status: published
publisher: Nature Publishing Group
publist_id: '6374'
quality_controlled: '1'
related_material:
record:
- id: '9861'
relation: research_data
status: public
scopus_import: '1'
status: public
title: X-linkage is not a general inhibitor of tissue-specific gene expression in
Drosophila melanogaster
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 119
year: '2017'
...
---
_id: '9861'
abstract:
- lang: eng
text: As a consequence of its difference in copy number between males and females,
the X chromosome is subject to unique evolutionary forces and gene regulatory
mechanisms. Previous studies of Drosophila melanogaster have shown that the expression
of X-linked, testis-specific reporter genes is suppressed in the male germline.
However, it is not known whether this phenomenon is restricted to testis-expressed
genes or if it is a more general property of genes with tissue-specific expression,
which are also underrepresented on the X chromosome. To test this, we compared
the expression of three tissue-specific reporter genes (ovary, accessory gland
and Malpighian tubule) inserted at various autosomal and X-chromosomal locations.
In contrast to testis-specific reporter genes, we found no reduction of X-linked
expression in any of the other tissues. In accessory gland and Malpighian tubule,
we detected higher expression of the X-linked reporter genes, which suggests that
they are at least partially dosage compensated. We found no difference in the
tissue-specificity of X-linked and autosomal reporter genes. These findings indicate
that, in general, the X chromosome is not a detrimental environment for tissue-specific
gene expression and that the suppression of X-linked expression is limited to
the male germline.
article_processing_charge: No
author:
- first_name: Eliza
full_name: Argyridou, Eliza
last_name: Argyridou
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Annabella
full_name: Königer, Annabella
last_name: Königer
- first_name: John
full_name: Parsch, John
last_name: Parsch
citation:
ama: 'Argyridou E, Huylmans AK, Königer A, Parsch J. Data from: X-linkage is not
a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.
2017. doi:10.5061/dryad.02f6r'
apa: 'Argyridou, E., Huylmans, A. K., Königer, A., & Parsch, J. (2017). Data
from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster. Dryad. https://doi.org/10.5061/dryad.02f6r'
chicago: 'Argyridou, Eliza, Ann K Huylmans, Annabella Königer, and John Parsch.
“Data from: X-Linkage Is Not a General Inhibitor of Tissue-Specific Gene Expression
in Drosophila Melanogaster.” Dryad, 2017. https://doi.org/10.5061/dryad.02f6r.'
ieee: 'E. Argyridou, A. K. Huylmans, A. Königer, and J. Parsch, “Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster.”
Dryad, 2017.'
ista: 'Argyridou E, Huylmans AK, Königer A, Parsch J. 2017. Data from: X-linkage
is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster,
Dryad, 10.5061/dryad.02f6r.'
mla: 'Argyridou, Eliza, et al. Data from: X-Linkage Is Not a General Inhibitor
of Tissue-Specific Gene Expression in Drosophila Melanogaster. Dryad, 2017,
doi:10.5061/dryad.02f6r.'
short: E. Argyridou, A.K. Huylmans, A. Königer, J. Parsch, (2017).
date_created: 2021-08-10T08:12:52Z
date_published: 2017-02-14T00:00:00Z
date_updated: 2023-09-22T09:41:20Z
day: '14'
department:
- _id: BeVi
doi: 10.5061/dryad.02f6r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.02f6r
month: '02'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1019'
relation: used_in_publication
status: public
status: public
title: 'Data from: X-linkage is not a general inhibitor of tissue-specific gene expression
in Drosophila melanogaster'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1006'
abstract:
- lang: eng
text: 'Background: The phenomenon of immune priming, i.e. enhanced protection following
a secondary exposure to a pathogen, has now been demonstrated in a wide range
of invertebrate species. Despite accumulating phenotypic evidence, knowledge of
its mechanistic underpinnings is currently very limited. Here we used the system
of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus
thuringiensis (Bt) to further our molecular understanding of the oral immune priming
phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants)
of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon
later challenge exposure, using a whole-transcriptome sequencing approach. Results:
Whereas gene expression of individuals primed with the orally non-pathogenic strain
showed minor changes to controls, we found that priming with the pathogenic strain
induced regulation of a large set of distinct genes, many of which are known immune
candidates. Intriguingly, the immune repertoire activated upon priming and subsequent
challenge qualitatively differed from the one mounted upon infection with Bt without
previous priming. Moreover, a large subset of priming-specific genes showed an
inverse regulation compared to their regulation upon challenge only. Conclusions:
Our data demonstrate that gene expression upon infection is strongly affected
by previous immune priming. We hypothesise that this shift in gene expression
indicates activation of a more targeted and efficient response towards a previously
encountered pathogen, in anticipation of potential secondary encounter.'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: Greenwood J, Milutinovic B, Peuß R, et al. Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.
BMC Genomics. 2017;18(1):329. doi:10.1186/s12864-017-3705-7
apa: Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Oral immune priming with Bacillus thuringiensis induces
a shift in the gene expression of Tribolium castaneum larvae. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-017-3705-7
chicago: Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Oral Immune
Priming with Bacillus Thuringiensis Induces a Shift in the Gene Expression of
Tribolium Castaneum Larvae.” BMC Genomics. BioMed Central, 2017. https://doi.org/10.1186/s12864-017-3705-7.
ieee: J. Greenwood et al., “Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae,” BMC
Genomics, vol. 18, no. 1. BioMed Central, p. 329, 2017.
ista: Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Oral immune priming with Bacillus thuringiensis induces a shift
in the gene expression of Tribolium castaneum larvae. BMC Genomics. 18(1), 329.
mla: Greenwood, Jenny, et al. “Oral Immune Priming with Bacillus Thuringiensis Induces
a Shift in the Gene Expression of Tribolium Castaneum Larvae.” BMC Genomics,
vol. 18, no. 1, BioMed Central, 2017, p. 329, doi:10.1186/s12864-017-3705-7.
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, BMC Genomics 18 (2017) 329.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1186/s12864-017-3705-7
external_id:
isi:
- '000400625200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:46Z
date_updated: 2018-12-12T10:16:46Z
file_id: '5236'
file_name: IST-2017-814-v1+1_s12864-017-3705-7.pdf
file_size: 2379672
relation: main_file
file_date_updated: 2018-12-12T10:16:46Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '329'
publication: BMC Genomics
publication_identifier:
issn:
- '14712164'
publication_status: published
publisher: BioMed Central
publist_id: '6392'
pubrep_id: '814'
quality_controlled: '1'
related_material:
record:
- id: '9859'
relation: research_data
status: public
- id: '9860'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Oral immune priming with Bacillus thuringiensis induces a shift in the gene
expression of Tribolium castaneum larvae
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: 18
year: '2017'
...
---
_id: '1011'
abstract:
- lang: eng
text: Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly
equivalent, are standard models for interprocedural analysis. Yet RSMs are more
convenient as they (a) explicitly model function calls and returns, and (b) specify
many natural parameters for algorithmic analysis, e.g., the number of entries
and exits. We consider a general framework where RSM transitions are labeled from
a semiring and path properties are algebraic with semiring operations, which can
model, e.g., interprocedural reachability and dataflow analysis problems. Our
main contributions are new algorithms for several fundamental problems. As compared
to a direct translation of RSMs to PDSs and the best-known existing bounds of
PDSs, our analysis algorithm improves the complexity for finite-height semirings
(that subsumes reachability and standard dataflow properties). We further consider
the problem of extracting distance values from the representation structures computed
by our algorithm, and give efficient algorithms that distinguish the complexity
of a one-time preprocessing from the complexity of each individual query. Another
advantage of our algorithm is that our improvements carry over to the concurrent
setting, where we improve the bestknown complexity for the context-bounded analysis
of concurrent RSMs. Finally, we provide a prototype implementation that gives
a significant speed-up on several benchmarks from the SLAM/SDV project.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Samarth
full_name: Mishra, Samarth
last_name: Mishra
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. Faster algorithms for weighted
recursive state machines. In: Yang H, ed. Vol 10201. Springer; 2017:287-313. doi:10.1007/978-3-662-54434-1_11'
apa: 'Chatterjee, K., Kragl, B., Mishra, S., & Pavlogiannis, A. (2017). Faster
algorithms for weighted recursive state machines. In H. Yang (Ed.) (Vol. 10201,
pp. 287–313). Presented at the ESOP: European Symposium on Programming, Uppsala,
Sweden: Springer. https://doi.org/10.1007/978-3-662-54434-1_11'
chicago: Chatterjee, Krishnendu, Bernhard Kragl, Samarth Mishra, and Andreas Pavlogiannis.
“Faster Algorithms for Weighted Recursive State Machines.” edited by Hongseok
Yang, 10201:287–313. Springer, 2017. https://doi.org/10.1007/978-3-662-54434-1_11.
ieee: 'K. Chatterjee, B. Kragl, S. Mishra, and A. Pavlogiannis, “Faster algorithms
for weighted recursive state machines,” presented at the ESOP: European Symposium
on Programming, Uppsala, Sweden, 2017, vol. 10201, pp. 287–313.'
ista: 'Chatterjee K, Kragl B, Mishra S, Pavlogiannis A. 2017. Faster algorithms
for weighted recursive state machines. ESOP: European Symposium on Programming,
LNCS, vol. 10201, 287–313.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Weighted Recursive
State Machines. Edited by Hongseok Yang, vol. 10201, Springer, 2017, pp. 287–313,
doi:10.1007/978-3-662-54434-1_11.
short: K. Chatterjee, B. Kragl, S. Mishra, A. Pavlogiannis, in:, H. Yang (Ed.),
Springer, 2017, pp. 287–313.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'ESOP: European Symposium on Programming'
start_date: 2017-04-22
date_created: 2018-12-11T11:49:41Z
date_published: 2017-03-19T00:00:00Z
date_updated: 2023-09-22T09:44:50Z
day: '19'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-54434-1_11
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
external_id:
isi:
- '000681702400011'
intvolume: ' 10201'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.04914
month: '03'
oa: 1
oa_version: Submitted Version
page: 287 - 313
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster algorithms for weighted recursive state machines
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10201
year: '2017'
...
---
_id: '1004'
abstract:
- lang: eng
text: The fundamental tasks of the root system are, besides anchoring, mediating
interactions between plant and soil and providing the plant with water and nutrients.
The architecture of the root system is controlled by endogenous mechanisms that
constantly integrate environmental signals, such as availability of nutrients
and water. Extremely important for efficient soil exploitation and survival under
less favorable conditions is the developmental flexibility of the root system
that is largely determined by its postembryonic branching capacity. Modulation
of initiation and outgrowth of lateral roots provides roots with an exceptional
plasticity, allows optimal adjustment to underground heterogeneity, and enables
effective soil exploitation and use of resources. Here we discuss recent advances
in understanding the molecular mechanisms that shape the plant root system and
integrate external cues to adapt to the changing environment.
article_processing_charge: No
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010
apa: Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching.
Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010
chicago: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010.
ieee: K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current
Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017.
ista: Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current
Opinion in Genetics & Development. 45, 82–89.
mla: Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.”
Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017,
pp. 82–89, doi:10.1016/j.gde.2017.03.010.
short: K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017)
82–89.
date_created: 2018-12-11T11:49:38Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:48:15Z
day: '01'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1016/j.gde.2017.03.010
external_id:
isi:
- '000404880400013'
pmid:
- '28391060'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T08:00:36Z
date_updated: 2019-04-17T08:00:36Z
file_id: '6336'
file_name: Otvos_Benkova_CurOpDevBiol_2017.pdf
file_size: 364133
relation: main_file
success: 1
file_date_updated: 2019-04-17T08:00:36Z
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 82 - 89
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Current Opinion in Genetics & Development
publication_identifier:
issn:
- 0959437X
publication_status: published
publisher: Elsevier
publist_id: '6394'
pubrep_id: '1017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatiotemporal mechanisms of root branching
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: 45
year: '2017'
...
---
_id: '1010'
abstract:
- lang: eng
text: 'We prove a local law in the bulk of the spectrum for random Gram matrices
XX∗, a generalization of sample covariance matrices, where X is a large matrix
with independent, centered entries with arbitrary variances. The limiting eigenvalue
density that generalizes the Marchenko-Pastur law is determined by solving a system
of nonlinear equations. Our entrywise and averaged local laws are on the optimal
scale with the optimal error bounds. They hold both in the square case (hard edge)
and in the properly rectangular case (soft edge). In the latter case we also establish
a macroscopic gap away from zero in the spectrum of XX∗. '
article_number: '25'
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Local law for random Gram matrices. Electronic
Journal of Probability. 2017;22. doi:10.1214/17-EJP42
apa: Alt, J., Erdös, L., & Krüger, T. H. (2017). Local law for random Gram matrices.
Electronic Journal of Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/17-EJP42
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Law for Random
Gram Matrices.” Electronic Journal of Probability. Institute of Mathematical
Statistics, 2017. https://doi.org/10.1214/17-EJP42.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local law for random Gram matrices,”
Electronic Journal of Probability, vol. 22. Institute of Mathematical Statistics,
2017.
ista: Alt J, Erdös L, Krüger TH. 2017. Local law for random Gram matrices. Electronic
Journal of Probability. 22, 25.
mla: Alt, Johannes, et al. “Local Law for Random Gram Matrices.” Electronic Journal
of Probability, vol. 22, 25, Institute of Mathematical Statistics, 2017, doi:10.1214/17-EJP42.
short: J. Alt, L. Erdös, T.H. Krüger, Electronic Journal of Probability 22 (2017).
date_created: 2018-12-11T11:49:40Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:45:23Z
day: '08'
ddc:
- '510'
- '539'
department:
- _id: LaEr
doi: 10.1214/17-EJP42
ec_funded: 1
external_id:
arxiv:
- '1606.07353'
isi:
- '000396611900025'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:39Z
date_updated: 2018-12-12T10:13:39Z
file_id: '5024'
file_name: IST-2017-807-v1+1_euclid.ejp.1488942016.pdf
file_size: 639384
relation: main_file
file_date_updated: 2018-12-12T10:13:39Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6386'
pubrep_id: '807'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local law for random Gram matrices
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: 22
year: '2017'
...
---
_id: '1009'
abstract:
- lang: eng
text: A standard objective in partially-observable Markov decision processes (POMDPs)
is to find a policy that maximizes the expected discounted-sum payoff. However,
such policies may still permit unlikely but highly undesirable outcomes, which
is problematic especially in safety-critical applications. Recently, there has
been a surge of interest in POMDPs where the goal is to maximize the probability
to ensure that the payoff is at least a given threshold, but these approaches
do not consider any optimization beyond satisfying this threshold constraint.
In this work we go beyond both the “expectation” and “threshold” approaches and
consider a “guaranteed payoff optimization (GPO)” problem for POMDPs, where we
are given a threshold t and the objective is to find a policy σ such that a) each
possible outcome of σ yields a discounted-sum payoff of at least t, and b) the
expected discounted-sum payoff of σ is optimal (or near-optimal) among all policies
satisfying a). We present a practical approach to tackle the GPO problem and evaluate
it on standard POMDP benchmarks.
acknowledgement: 'he research leading to these results was supported by the Austrian
Science Fund (FWF) NFN Grant no. S11407-N23 (RiSE/SHiNE); two ERC Starting grants
(279307: Graph Games, 279499: inVEST); the Vienna Science and Tech- nology Fund
(WWTF) through project ICT15-003; and the People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734].'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Guillermo
full_name: Pérez, Guillermo
last_name: Pérez
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
- first_name: Djordje
full_name: Zikelic, Djordje
last_name: Zikelic
citation:
ama: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. Optimizing expectation
with guarantees in POMDPs. In: Proceedings of the 31st AAAI Conference on Artificial
Intelligence. Vol 5. AAAI Press; 2017:3725-3732.'
apa: 'Chatterjee, K., Novotný, P., Pérez, G., Raskin, J., & Zikelic, D. (2017).
Optimizing expectation with guarantees in POMDPs. In Proceedings of the 31st
AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3725–3732). San Francisco,
CA, United States: AAAI Press.'
chicago: Chatterjee, Krishnendu, Petr Novotný, Guillermo Pérez, Jean Raskin, and
Djordje Zikelic. “Optimizing Expectation with Guarantees in POMDPs.” In Proceedings
of the 31st AAAI Conference on Artificial Intelligence, 5:3725–32. AAAI Press,
2017.
ieee: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, and D. Zikelic, “Optimizing
expectation with guarantees in POMDPs,” in Proceedings of the 31st AAAI Conference
on Artificial Intelligence, San Francisco, CA, United States, 2017, vol. 5,
pp. 3725–3732.
ista: 'Chatterjee K, Novotný P, Pérez G, Raskin J, Zikelic D. 2017. Optimizing expectation
with guarantees in POMDPs. Proceedings of the 31st AAAI Conference on Artificial
Intelligence. AAAI: Conference on Artificial Intelligence vol. 5, 3725–3732.'
mla: Chatterjee, Krishnendu, et al. “Optimizing Expectation with Guarantees in POMDPs.”
Proceedings of the 31st AAAI Conference on Artificial Intelligence, vol.
5, AAAI Press, 2017, pp. 3725–32.
short: K. Chatterjee, P. Novotný, G. Pérez, J. Raskin, D. Zikelic, in:, Proceedings
of the 31st AAAI Conference on Artificial Intelligence, AAAI Press, 2017, pp.
3725–3732.
conference:
end_date: 2017-02-10
location: San Francisco, CA, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2017-02-04
date_created: 2018-12-11T11:49:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:46:41Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
isi:
- '000485630703107'
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/download/14354/14092
month: '01'
oa: 1
oa_version: Submitted Version
page: 3725 - 3732
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 31st AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '6387'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing expectation with guarantees in POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2017'
...
---
_id: '9859'
abstract:
- lang: eng
text: 'Lists of all differentially expressed genes in the different priming-challenge
treatments (compared to the fully naïve control; xlsx file). Relevant columns
include the following: sample_1 and sample_2 – treatment groups being compared;
Normalised FPKM sample_1 and sample_2 – FPKM of samples being compared; log2(fold_change)
– log2(FPKM sample 2/FPKM sample 1), i.e. negative means sample 1 upregulated
compared with sample 2, positive means sample 2 upregulated compared with sample
1; cuffdiff test_statistic – test statistic of differential expression test; p_value
– p-value of differential expression test; q_value (FDR correction) – adjusted
P-value of differential expression test. (XLSX 598 kb)'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 1: Table S1. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d1.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 1: Table S1. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 1: Table S1. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1.'
ieee: 'J. Greenwood et al., “Additional file 1: Table S1. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 1: Table S1. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d1.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 1: Table S1. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d1.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T07:59:02Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d1.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d1.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Table S1. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9860'
article_processing_charge: No
author:
- first_name: Jenny
full_name: Greenwood, Jenny
last_name: Greenwood
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Robert
full_name: Peuß, Robert
last_name: Peuß
- first_name: Sarah
full_name: Behrens, Sarah
last_name: Behrens
- first_name: Daniela
full_name: Essar, Daniela
last_name: Essar
- first_name: Philip
full_name: Rosenstiel, Philip
last_name: Rosenstiel
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
citation:
ama: 'Greenwood J, Milutinovic B, Peuß R, et al. Additional file 5: Table S3. of
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression
of Tribolium castaneum larvae. 2017. doi:10.6084/m9.figshare.c.3756974_d5.v1'
apa: 'Greenwood, J., Milutinovic, B., Peuß, R., Behrens, S., Essar, D., Rosenstiel,
P., … Kurtz, J. (2017). Additional file 5: Table S3. of Oral immune priming with
Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum
larvae. Springer Nature. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1'
chicago: 'Greenwood, Jenny, Barbara Milutinovic, Robert Peuß, Sarah Behrens, Daniela
Essar, Philip Rosenstiel, Hinrich Schulenburg, and Joachim Kurtz. “Additional
File 5: Table S3. of Oral Immune Priming with Bacillus Thuringiensis Induces a
Shift in the Gene Expression of Tribolium Castaneum Larvae.” Springer Nature,
2017. https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1.'
ieee: 'J. Greenwood et al., “Additional file 5: Table S3. of Oral immune
priming with Bacillus thuringiensis induces a shift in the gene expression of
Tribolium castaneum larvae.” Springer Nature, 2017.'
ista: 'Greenwood J, Milutinovic B, Peuß R, Behrens S, Essar D, Rosenstiel P, Schulenburg
H, Kurtz J. 2017. Additional file 5: Table S3. of Oral immune priming with Bacillus
thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae,
Springer Nature, 10.6084/m9.figshare.c.3756974_d5.v1.'
mla: 'Greenwood, Jenny, et al. Additional File 5: Table S3. of Oral Immune Priming
with Bacillus Thuringiensis Induces a Shift in the Gene Expression of Tribolium
Castaneum Larvae. Springer Nature, 2017, doi:10.6084/m9.figshare.c.3756974_d5.v1.'
short: J. Greenwood, B. Milutinovic, R. Peuß, S. Behrens, D. Essar, P. Rosenstiel,
H. Schulenburg, J. Kurtz, (2017).
date_created: 2021-08-10T08:07:12Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-22T09:47:44Z
day: '26'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.c.3756974_d5.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.c.3756974_d5.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '1006'
relation: used_in_publication
status: public
status: public
title: 'Additional file 5: Table S3. of Oral immune priming with Bacillus thuringiensis
induces a shift in the gene expression of Tribolium castaneum larvae'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1002'
abstract:
- lang: eng
text: " We present an interactive design system to create functional mechanical
\ objects. Our computational approach allows novice users to retarget an existing
mechanical template to a user-specified input shape. Our proposed representation
for a mechanical template encodes a parameterized mechanism, mechanical constraints
that ensure a physically valid configuration, spatial relationships of mechanical
parts to the user-provided shape, and functional constraints that specify an intended
functionality. We provide an intuitive interface and optimization-in-the-loop
approach for finding a valid configuration of the mechanism and the shape to
ensure that higher-level functional goals are met. Our algorithm interactively
optimizes the mechanism while the user manipulates the placement of mechanical
components and the shape. Our system allows users to efficiently explore various
design choices and to synthesize customized mechanical objects that can be fabricated
with rapid prototyping technologies. We demonstrate the efficacy of our approach
by retargeting various mechanical templates to different shapes and fabricating
the resulting functional mechanical objects.\r\n"
alternative_title:
- ACM Transactions on Graphics
article_number: '81'
article_processing_charge: No
author:
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Duygu
full_name: Ceylan, Duygu
last_name: Ceylan
- first_name: Wilmot
full_name: Li, Wilmot
last_name: Li
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. Functionality-aware retargeting
of mechanisms to 3D shapes. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073710'
apa: 'Zhang, R., Auzinger, T., Ceylan, D., Li, W., & Bickel, B. (2017). Functionality-aware
retargeting of mechanisms to 3D shapes (Vol. 36). Presented at the SIGGRAPH: Computer
Graphics and Interactive Techniques, Los Angeles, CA, United States : ACM. https://doi.org/10.1145/3072959.3073710'
chicago: Zhang, Ran, Thomas Auzinger, Duygu Ceylan, Wilmot Li, and Bernd Bickel.
“Functionality-Aware Retargeting of Mechanisms to 3D Shapes,” Vol. 36. ACM, 2017.
https://doi.org/10.1145/3072959.3073710.
ieee: 'R. Zhang, T. Auzinger, D. Ceylan, W. Li, and B. Bickel, “Functionality-aware
retargeting of mechanisms to 3D shapes,” presented at the SIGGRAPH: Computer Graphics
and Interactive Techniques, Los Angeles, CA, United States , 2017, vol. 36, no.
4.'
ista: 'Zhang R, Auzinger T, Ceylan D, Li W, Bickel B. 2017. Functionality-aware
retargeting of mechanisms to 3D shapes. SIGGRAPH: Computer Graphics and Interactive
Techniques, ACM Transactions on Graphics, vol. 36, 81.'
mla: Zhang, Ran, et al. Functionality-Aware Retargeting of Mechanisms to 3D Shapes.
Vol. 36, no. 4, 81, ACM, 2017, doi:10.1145/3072959.3073710.
short: R. Zhang, T. Auzinger, D. Ceylan, W. Li, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-03
location: 'Los Angeles, CA, United States '
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques'
start_date: 2017-07-30
date_created: 2018-12-11T11:49:38Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:49:31Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073710
ec_funded: 1
external_id:
isi:
- '000406432100049'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:05Z
date_updated: 2018-12-12T10:09:05Z
file_id: '4728'
file_name: IST-2018-1050-v1+1_MechRet.pdf
file_size: 25463895
relation: main_file
file_date_updated: 2018-12-12T10:09:05Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '6396'
pubrep_id: '1050'
quality_controlled: '1'
related_material:
record:
- id: '8386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functionality-aware retargeting of mechanisms to 3D shapes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1001'
abstract:
- lang: eng
text: We present a computational approach for designing CurveUps, curvy shells that
form from an initially flat state. They consist of small rigid tiles that are
tightly held together by two pre-stretched elastic sheets attached to them. Our
method allows the realization of smooth, doubly curved surfaces that can be fabricated
as a flat piece. Once released, the restoring forces of the pre-stretched sheets
support the object to take shape in 3D. CurveUps are structurally stable in their
target configuration. The design process starts with a target surface. Our method
generates a tile layout in 2D and optimizes the distribution, shape, and attachment
areas of the tiles to obtain a configuration that is fabricable and in which the
curved up state closely matches the target. Our approach is based on an efficient
approximate model and a local optimization strategy for an otherwise intractable
nonlinear optimization problem. We demonstrate the effectiveness of our approach
for a wide range of shapes, all realized as physical prototypes.
alternative_title:
- ACM Transactions on Graphics
article_number: '64'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Eder
full_name: Miguel, Eder
last_name: Miguel
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates
with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:10.1145/3072959.3073709'
apa: 'Guseinov, R., Miguel, E., & Bickel, B. (2017). CurveUps: Shaping objects
from flat plates with tension-actuated curvature (Vol. 36). Presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles,
CA, United States: ACM. https://doi.org/10.1145/3072959.3073709'
chicago: 'Guseinov, Ruslan, Eder Miguel, and Bernd Bickel. “CurveUps: Shaping Objects
from Flat Plates with Tension-Actuated Curvature,” Vol. 36. ACM, 2017. https://doi.org/10.1145/3072959.3073709.'
ieee: 'R. Guseinov, E. Miguel, and B. Bickel, “CurveUps: Shaping objects from flat
plates with tension-actuated curvature,” presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United
States, 2017, vol. 36, no. 4.'
ista: 'Guseinov R, Miguel E, Bickel B. 2017. CurveUps: Shaping objects from flat
plates with tension-actuated curvature. SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 36, 64.'
mla: 'Guseinov, Ruslan, et al. CurveUps: Shaping Objects from Flat Plates with
Tension-Actuated Curvature. Vol. 36, no. 4, 64, ACM, 2017, doi:10.1145/3072959.3073709.'
short: R. Guseinov, E. Miguel, B. Bickel, in:, ACM, 2017.
conference:
end_date: 2017-08-25
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:49:58Z
day: '01'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3072959.3073709
ec_funded: 1
external_id:
isi:
- '000406432100032'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:24Z
date_updated: 2018-12-12T10:10:24Z
file_id: '4811'
file_name: IST-2018-1053-v1+1_CurveUp.pdf
file_size: 36159696
relation: main_file
file_date_updated: 2018-12-12T10:10:24Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_status: published
publisher: ACM
publist_id: '6397'
pubrep_id: '1053'
quality_controlled: '1'
related_material:
record:
- id: '8366'
relation: dissertation_contains
status: public
status: public
title: 'CurveUps: Shaping objects from flat plates with tension-actuated curvature'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1003'
abstract:
- lang: eng
text: Network games (NGs) are played on directed graphs and are extensively used
in network design and analysis. Search problems for NGs include finding special
strategy profiles such as a Nash equilibrium and a globally optimal solution.
The networks modeled by NGs may be huge. In formal verification, abstraction has
proven to be an extremely effective technique for reasoning about systems with
big and even infinite state spaces. We describe an abstraction-refinement methodology
for reasoning about NGs. Our methodology is based on an abstraction function that
maps the state space of an NG to a much smaller state space. We search for a global
optimum and a Nash equilibrium by reasoning on an under- and an overapproximation
defined on top of this smaller state space. When the approximations are too coarse
to find such profiles, we refine the abstraction function. Our experimental results
demonstrate the efficiency of the methodology.
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning
about network games. In: AAAI Press; 2017:70-76. doi:10.24963/ijcai.2017/11'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). An abstraction-refinement
methodology for reasoning about network games (pp. 70–76). Presented at the IJCAI:
International Joint Conference on Artificial Intelligence , Melbourne, Australia:
AAAI Press. https://doi.org/10.24963/ijcai.2017/11'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement
Methodology for Reasoning about Network Games,” 70–76. AAAI Press, 2017. https://doi.org/10.24963/ijcai.2017/11.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology
for reasoning about network games,” presented at the IJCAI: International Joint
Conference on Artificial Intelligence , Melbourne, Australia, 2017, pp. 70–76.'
ista: 'Avni G, Guha S, Kupferman O. 2017. An abstraction-refinement methodology
for reasoning about network games. IJCAI: International Joint Conference on Artificial
Intelligence , 70–76.'
mla: Avni, Guy, et al. An Abstraction-Refinement Methodology for Reasoning about
Network Games. AAAI Press, 2017, pp. 70–76, doi:10.24963/ijcai.2017/11.
short: G. Avni, S. Guha, O. Kupferman, in:, AAAI Press, 2017, pp. 70–76.
conference:
end_date: 2017-08-25
location: Melbourne, Australia
name: 'IJCAI: International Joint Conference on Artificial Intelligence '
start_date: 2017-08-19
date_created: 2018-12-11T11:49:38Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T09:49:00Z
day: '30'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.24963/ijcai.2017/11
external_id:
isi:
- '000764137500011'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:58Z
date_updated: 2018-12-12T10:16:58Z
file_id: '5249'
file_name: IST-2017-818-v1+1_allIJCAI_CR.pdf
file_size: 365172
relation: main_file
file_date_updated: 2018-12-12T10:16:58Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 70 - 76
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '10450823'
publication_status: published
publisher: AAAI Press
publist_id: '6395'
pubrep_id: '818'
quality_controlled: '1'
related_material:
record:
- id: '6006'
relation: later_version
status: public
scopus_import: '1'
status: public
title: An abstraction-refinement methodology for reasoning about network games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1000'
abstract:
- lang: eng
text: 'We study probabilistic models of natural images and extend the autoregressive
family of PixelCNN models by incorporating latent variables. Subsequently, we
describe two new generative image models that exploit different image transformations
as latent variables: a quantized grayscale view of the image or a multi-resolution
image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN
models: 1) their tendency to focus on low-level image details, while largely ignoring
high-level image information, such as object shapes, and 2) their computationally
costly procedure for image sampling. We experimentally demonstrate benefits of
our LatentPixelCNN models, in particular showing that they produce much more realistically
looking image samples than previous state-of-the-art probabilistic models. '
acknowledgement: We thank Tim Salimans for spotting a mistake in our preliminary arXiv
manuscript. This work was funded by the European Research Council under the European
Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural
image modeling. In: 34th International Conference on Machine Learning.
Vol 70. JMLR; 2017:1905-1914.'
apa: 'Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables
for natural image modeling. In 34th International Conference on Machine Learning
(Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.'
chicago: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” In 34th International Conference on
Machine Learning, 70:1905–14. JMLR, 2017.
ieee: A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for
natural image modeling,” in 34th International Conference on Machine Learning,
Sydney, Australia, 2017, vol. 70, pp. 1905–1914.
ista: 'Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for
natural image modeling. 34th International Conference on Machine Learning. ICML:
International Conference on Machine Learning vol. 70, 1905–1914.'
mla: Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary
Variables for Natural Image Modeling.” 34th International Conference on Machine
Learning, vol. 70, JMLR, 2017, pp. 1905–14.
short: A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine
Learning, JMLR, 2017, pp. 1905–1914.
conference:
end_date: 2017-08-11
location: Sydney, Australia
name: 'ICML: International Conference on Machine Learning'
start_date: 2017-08-06
date_created: 2018-12-11T11:49:37Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-22T09:50:41Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1612.08185'
isi:
- '000683309501102'
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.08185
month: '08'
oa: 1
oa_version: Submitted Version
page: 1905 - 1914
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: 34th International Conference on Machine Learning
publication_identifier:
isbn:
- 978-151085514-4
publication_status: published
publisher: JMLR
publist_id: '6398'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PixelCNN models with auxiliary variables for natural image modeling
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 70
year: '2017'
...
---
_id: '998'
abstract:
- lang: eng
text: 'A major open problem on the road to artificial intelligence is the development
of incrementally learning systems that learn about more and more concepts over
time from a stream of data. In this work, we introduce a new training strategy,
iCaRL, that allows learning in such a class-incremental way: only the training
data for a small number of classes has to be present at the same time and new
classes can be added progressively. iCaRL learns strong classifiers and a data
representation simultaneously. This distinguishes it from earlier works that were
fundamentally limited to fixed data representations and therefore incompatible
with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet
ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period
of time where other strategies quickly fail. '
article_processing_charge: No
author:
- first_name: Sylvestre Alvise
full_name: Rebuffi, Sylvestre Alvise
last_name: Rebuffi
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier
and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587'
apa: 'Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL:
Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.587'
chicago: 'Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph
Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42.
IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.'
ieee: 'S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental
classifier and representation learning,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542.'
ista: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier
and representation learning. CVPR: Computer Vision and Pattern Recognition vol.
2017, 5533–5542.'
mla: 'Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation
Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.'
short: S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
date_created: 2018-12-11T11:49:37Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-22T09:51:58Z
day: '14'
department:
- _id: ChLa
- _id: ChWo
doi: 10.1109/CVPR.2017.587
ec_funded: 1
external_id:
isi:
- '000418371405066'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.07725
month: '04'
oa: 1
oa_version: Submitted Version
page: 5533 - 5542
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6400'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'iCaRL: Incremental classifier and representation learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:55:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
file:
- access_level: open_access
checksum: 6d4c38cb1347fd43620d1736c6df5c79
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6329'
file_name: 2017_Evolution_Sachdeva_supplement.pdf
file_size: 625260
relation: main_file
- access_level: open_access
checksum: f1d90dd8831b44baf49b4dd176f263af
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6330'
file_name: 2017_Evolution_Sachdeva_article.pdf
file_size: 520110
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: '1478 - 1493 '
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '988'
abstract:
- lang: eng
text: The current-phase relation (CPR) of a Josephson junction (JJ) determines how
the supercurrent evolves with the superconducting phase difference across the
junction. Knowledge of the CPR is essential in order to understand the response
of a JJ to various external parameters. Despite the rising interest in ultraclean
encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we
use a fully gate-tunable graphene superconducting quantum intereference device
(SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in
the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently
controlling the critical current of the JJs, we can operate the SQUID either in
a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us
to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found
to be skewed, deviating significantly from a sinusoidal form. The skewness can
be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance
oscillations of the ballistic graphene cavity. We compare our experiments with
tight-binding calculations that include realistic graphene-superconductor interfaces
and find a good qualitative agreement.
article_processing_charge: No
author:
- first_name: Gaurav
full_name: Nanda, Gaurav
last_name: Nanda
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Péter
full_name: Rakyta, Péter
last_name: Rakyta
- first_name: Andor
full_name: Kormányos, Andor
last_name: Kormányos
- first_name: Reinhold
full_name: Kleiner, Reinhold
last_name: Kleiner
- first_name: Dieter
full_name: Koelle, Dieter
last_name: Koelle
- first_name: Kazuo
full_name: Watanabe, Kazuo
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Lieven
full_name: Vandersypen, Lieven
last_name: Vandersypen
- first_name: Srijit
full_name: Goswami, Srijit
last_name: Goswami
citation:
ama: Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097
apa: Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R.,
Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene
Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097
chicago: Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold
Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen,
and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097.
ieee: G. Nanda et al., “Current-phase relation of ballistic graphene Josephson
junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp.
3396–3401, 2017.
ista: Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe
K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic
graphene Josephson junctions. Nano Letters. 17(6), 3396–3401.
mla: Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson
Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017,
pp. 3396–401, doi:10.1021/acs.nanolett.7b00097.
short: G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle,
K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017)
3396–3401.
date_created: 2018-12-11T11:49:33Z
date_published: 2017-05-05T00:00:00Z
date_updated: 2023-09-22T09:56:21Z
day: '05'
ddc:
- '621'
department:
- _id: NanoFab
doi: 10.1021/acs.nanolett.7b00097
external_id:
isi:
- '000403631600011'
file:
- access_level: open_access
checksum: 22021daa90cf13b01becd776838acb7b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:50Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5037'
file_name: IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf
file_size: 508638
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 3396 - 3401
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6412'
pubrep_id: '826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Current-phase relation of ballistic graphene Josephson junctions
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: 17
year: '2017'
...
---
_id: '993'
abstract:
- lang: eng
text: In real-world applications, observations are often constrained to a small
fraction of a system. Such spatial subsampling can be caused by the inaccessibility
or the sheer size of the system, and cannot be overcome by longer sampling. Spatial
subsampling can strongly bias inferences about a system’s aggregated properties.
To overcome the bias, we derive analytically a subsampling scaling framework that
is applicable to different observables, including distributions of neuronal avalanches,
of number of people infected during an epidemic outbreak, and of node degrees.
We demonstrate how to infer the correct distributions of the underlying full system,
how to apply it to distinguish critical from subcritical systems, and how to disentangle
subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal
avalanche models and to recordings from developing neural networks. We show that
only mature, but not young networks follow power-law scaling, indicating self-organization
to criticality during development.
article_number: '15140'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Anna
full_name: Levina (Martius), Anna
id: 35AF8020-F248-11E8-B48F-1D18A9856A87
last_name: Levina (Martius)
- first_name: Viola
full_name: Priesemann, Viola
last_name: Priesemann
citation:
ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications.
2017;8. doi:10.1038/ncomms15140
apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140
chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140.
ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications.
8, 15140.
mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature
Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140.
short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-04T00:00:00Z
date_updated: 2023-09-22T09:54:07Z
day: '04'
ddc:
- '005'
- '571'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1038/ncomms15140
ec_funded: 1
external_id:
isi:
- '000400560700001'
file:
- access_level: open_access
checksum: 9880212f8c4c53404c7c6fbf9023c53a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:05Z
date_updated: 2020-07-14T12:48:19Z
file_id: '5122'
file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf
file_size: 746224
relation: main_file
file_date_updated: 2020-07-14T12:48:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '05'
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
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6406'
pubrep_id: '819'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subsampling scaling
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: 8
year: '2017'
...
---
_id: '995'
abstract:
- lang: eng
text: Recently it was shown that an impurity exchanging orbital angular momentum
with a surrounding bath can be described in terms of the angulon quasiparticle
[Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor
dressed by a many-particle field of boson excitations, and can be formed out of,
for example, a molecule or a nonspherical atom in superfluid helium, or out of
an electron coupled to lattice phonons or a Bose condensate. Here we develop an
approach to the angulon based on the path-integral formalism, which sets the ground
for a systematic, perturbative treatment of the angulon problem. The resulting
perturbation series can be interpreted in terms of Feynman diagrams, from which,
in turn, one can derive a set of diagrammatic rules. These rules extend the machinery
of the graphical theory of angular momentum - well known from theoretical atomic
spectroscopy - to the case where an environment with an infinite number of degrees
of freedom is present. In particular, we show that each diagram can be interpreted
as a 'skeleton', which enforces angular momentum conservation, dressed by an additional
many-body contribution. This connection between the angulon theory and the graphical
theory of angular momentum is particularly important as it allows to systematically
and substantially simplify the analytical representation of each diagram. In order
to exemplify the technique, we calculate the 1- and 2-loop contributions to the
angulon self-energy, the spectral function, and the quasiparticle weight. The
diagrammatic theory we develop paves the way to investigate next-to-leading order
quantities in a more compact way compared to the variational approaches.
article_number: '085410'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting
with a many-particle environment. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410
apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum
impurities interacting with a many-particle environment. Physical Review B
- Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410
chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital
Quantum Impurities Interacting with a Many-Particle Environment.” Physical
Review B - Condensed Matter and Materials Physics. American Physical Society,
2017. https://doi.org/10.1103/PhysRevB.96.085410.
ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017.
ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment. Physical Review B - Condensed Matter
and Materials Physics. 96(8), 085410.
mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum
Impurities Interacting with a Many-Particle Environment.” Physical Review B
- Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American
Physical Society, 2017, doi:10.1103/PhysRevB.96.085410.
short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 96 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-08-07T00:00:00Z
date_updated: 2023-09-22T09:53:17Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.96.085410
external_id:
isi:
- '000407017100009'
intvolume: ' 96'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _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 B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle
environment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '989'
abstract:
- lang: eng
text: We present a generalized optimal transport model in which the mass-preserving
constraint for the L2-Wasserstein distance is relaxed by introducing a source
term in the continuity equation. The source term is also incorporated in the path
energy by means of its squared L2-norm in time of a functional with linear growth
in space. This extension of the original transport model enables local density
modulations, which is a desirable feature in applications such as image warping
and blending. A key advantage of the use of a functional with linear growth in
space is that it allows for singular sources and sinks, which can be supported
on points or lines. On a technical level, the L2-norm in time ensures a disintegration
of the source in time, which we use to obtain the well-posedness of the model
and the existence of geodesic paths. The numerical discretization is based on
the proximal splitting approach [18] and selected numerical test cases show the
potential of the proposed approach. Furthermore, the approach is applied to the
warping and blending of textures.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Martin
full_name: Rumpf, Martin
last_name: Rumpf
- first_name: Stefan
full_name: Simon, Stefan
last_name: Simon
citation:
ama: 'Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation.
In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577.
doi:10.1007/978-3-319-58771-4_45'
apa: 'Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing
with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.)
(Vol. 10302, pp. 563–577). Presented at the SSVM: Scale Space and Variational
Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45'
chicago: Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing
with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm
Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45.
ieee: J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity
modulation,” presented at the SSVM: Scale Space and Variational Methods in Computer
Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577.
ista: Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity
modulation. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS,
vol. 10302, 563–577.
mla: Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation.
Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45.
short: J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.),
Springer, 2017, pp. 563–577.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T09:55:50Z
day: '18'
department:
- _id: JaMa
doi: 10.1007/978-3-319-58771-4_45
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
external_id:
isi:
- '000432210900045'
intvolume: ' 10302'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 563 - 577
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6410'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transport based image morphing with intensity modulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10302
year: '2017'
...
---
_id: '994'
abstract:
- lang: eng
text: The formation of vortices is usually considered to be the main mechanism of
angular momentum disposal in superfluids. Recently, it was predicted that a superfluid
can acquire angular momentum via an alternative, microscopic route -- namely,
through interaction with rotating impurities, forming so-called `angulon quasiparticles'
[Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to
transfer of a small number of angular momentum quanta from the impurity to the
superfluid, as opposed to vortex instabilities, where angular momentum is quantized
in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules)
represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically
3D as well, as opposed to a merely planar rotation which is inherent to vortices.
Herein we show that the angulon theory can explain the anomalous broadening of
the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid
helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities
in experiment.
article_processing_charge: No
author:
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra
of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602
apa: Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities
in the spectra of matrix-isolated molecules. Physical Review Materials.
American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602
chicago: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602.
ieee: I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules,” Physical Review Materials, vol.
1, no. 3. American Physical Society, 2017.
ista: Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the
spectra of matrix-isolated molecules. Physical Review Materials. 1(3).
mla: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities
in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials,
vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602.
short: I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017).
date_created: 2018-12-11T11:49:35Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2023-09-22T09:53:42Z
day: '08'
department:
- _id: MiLe
doi: 10.1103/PhysRevMaterials.1.035602
ec_funded: 1
external_id:
isi:
- '000416564000004'
intvolume: ' 1'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.09220
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Materials
publication_status: published
publisher: American Physical Society
publist_id: '6405'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1
year: '2017'
...
---
_id: '991'
abstract:
- lang: eng
text: Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for
lysosome fusion, but its function at fast synapses is controversial. The paper
by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held
in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains,
resulting in reliable and temporally precise high-frequency transmission. Thus,
a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse.
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696.
doi:10.1016/j.neuron.2017.05.011'
apa: 'Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011'
chicago: 'Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.”
Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.'
ieee: 'C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron,
vol. 94, no. 4. Elsevier, pp. 694–696, 2017.'
ista: 'Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4),
694–696.'
mla: 'Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron,
vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.'
short: C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2023-09-22T09:54:37Z
day: '17'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2017.05.011
external_id:
isi:
- '000401415100002'
intvolume: ' 94'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 694 - 696
publication: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '6408'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Synaptotagmins: That’s why so many'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 94
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
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creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
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file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
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: 6
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
- access_level: open_access
checksum: 29a1b5db458048d3bd5c67e0e2a56818
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5064'
file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf
file_size: 998157
relation: main_file
- access_level: open_access
checksum: 7b78401e52a576cf3e6bbf8d0abadc17
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:15Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5065'
file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf
file_size: 9715993
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
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: 8
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:58:02Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10427
year: '2017'
...
---
_id: '953'
abstract:
- lang: eng
text: 'The role of natural selection in the evolution of adaptive phenotypes has
undergone constant probing by evolutionary biologists, employing both theoretical
and empirical approaches. As Darwin noted, natural selection can act together
with other processes, including random changes in the frequencies of phenotypic
differences that are not under strong selection, and changes in the environment,
which may reflect evolutionary changes in the organisms themselves. As understanding
of genetics developed after 1900, the new genetic discoveries were incorporated
into evolutionary biology. The resulting general principles were summarized by
Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine
how recent advances in genetics, developmental biology and molecular biology,
including epigenetics, relate to today''s understanding of the evolution of adaptations.
We illustrate how careful genetic studies have repeatedly shown that apparently
puzzling results in a wide diversity of organisms involve processes that are consistent
with neo-Darwinism. They do not support important roles in adaptation for processes
such as directed mutation or the inheritance of acquired characters, and therefore
no radical revision of our understanding of the mechanism of adaptive evolution
is needed.'
article_number: '20162864'
article_processing_charge: No
author:
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences.
2017;284(1855). doi:10.1098/rspb.2016.2864
apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources
of adaptive evolution. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864
chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The
Sources of Adaptive Evolution.” Proceedings of the Royal Society of London
Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.
ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive
evolution,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 284, no. 1855. Royal Society, The, 2017.
ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855),
20162864.
mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 284, no.
1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.
short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society
of London Series B Biological Sciences 284 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-22T10:01:48Z
day: '31'
department:
- _id: NiBa
doi: 10.1098/rspb.2016.2864
external_id:
isi:
- '000405148800021'
pmid:
- '28566483'
intvolume: ' 284'
isi: 1
issue: '1855'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6462'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sources of adaptive evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 284
year: '2017'
...
---
_id: '959'
abstract:
- lang: eng
text: In this work it is shown that scale-free tails in metabolic flux distributions
inferred in stationary models are an artifact due to reactions involved in thermodynamically
unfeasible cycles, unbounded by physical constraints and in principle able to
perform work without expenditure of free energy. After implementing thermodynamic
constraints by removing such loops, metabolic flux distributions scale meaningfully
with the physical limiting factors, acquiring in turn a richer multimodal structure
potentially leading to symmetry breaking while optimizing for objective functions.
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419
apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419
chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.
ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics,” Physical Review E Statistical Nonlinear
and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p.
062419, 2017.
ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 95(6), 062419.
mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of
Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.
short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95
(2017) 062419.
date_created: 2018-12-11T11:49:25Z
date_published: 2017-06-28T00:00:00Z
date_updated: 2023-09-22T09:59:01Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.95.062419
ec_funded: 1
external_id:
isi:
- '000404546400004'
intvolume: ' 95'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1703.00853.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: '062419'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6446'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scales and multimodal flux distributions in stationary metabolic network models
via thermodynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '956'
abstract:
- lang: eng
text: We study a class of ergodic quantum Markov semigroups on finite-dimensional
unital C⁎-algebras. These semigroups have a unique stationary state σ, and we
are concerned with those that satisfy a quantum detailed balance condition with
respect to σ. We show that the evolution on the set of states that is given by
such a quantum Markov semigroup is gradient flow for the relative entropy with
respect to σ in a particular Riemannian metric on the set of states. This metric
is a non-commutative analog of the 2-Wasserstein metric, and in several interesting
cases we are able to show, in analogy with work of Otto on gradient flows with
respect to the classical 2-Wasserstein metric, that the relative entropy is strictly
and uniformly convex with respect to the Riemannian metric introduced here. As
a consequence, we obtain a number of new inequalities for the decay of relative
entropy for ergodic quantum Markov semigroups with detailed balance.
article_processing_charge: No
author:
- first_name: Eric
full_name: Carlen, Eric
last_name: Carlen
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov
semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869.
doi:10.1016/j.jfa.2017.05.003
apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for
quantum Markov semigroups with detailed balance. Journal of Functional Analysis.
Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003
chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for
Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis.
Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.
ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance,” Journal of Functional Analysis,
vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.
ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5),
1810–1869.
mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum
Markov Semigroups with Detailed Balance.” Journal of Functional Analysis,
vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.
short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-22T10:00:18Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2017.05.003
external_id:
isi:
- '000406082300005'
intvolume: ' 273'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01254
month: '09'
oa: 1
oa_version: Submitted Version
page: 1810 - 1869
publication: Journal of Functional Analysis
publication_identifier:
issn:
- '00221236'
publication_status: published
publisher: Academic Press
publist_id: '6452'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed
balance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 273
year: '2017'
...
---
_id: '952'
abstract:
- lang: eng
text: A novel strategy for controlling the spread of arboviral diseases such as
dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing
Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness
costs through lower viability or fecundity. These maternally inherited bacteria
also produce a frequency-dependent advantage for infected females by inducing
cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected
females mated to infected males. These competing effects, a frequency-dependent
advantage and frequency-independent costs, produce bistable Wolbachia frequency
dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing
Wolbachia transinfections through local populations; but below pˆ, infection frequencies
tend to decline to zero. If pˆ is not too high, CI also drives spatial spread
once infections become established over sufficiently large areas. We illustrate
how simple models provide testable predictions concerning the spatial and temporal
dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape
of spreading waves, and the conditions for initiating spread from local introductions.
First, we consider the robustness of diffusion-based predictions to incorporating
two important features of wMel-Aedes aegypti biology that may be inconsistent
with the diffusion approximations, namely fast local dynamics induced by complete
CI (i.e., all embryos produced from incompatible crosses die) and long-tailed,
non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed
dispersal changes wave-width predictions only slightly; but it can significantly
reduce wave speed relative to the diffusion prediction; it also allows smaller
local introductions to initiate spatial spread. Second, we use approximations
for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected
Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti
populations near Cairns, Australia that demonstrate long-distance dispersal and
provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally,
we apply our analyses to produce operational guidelines for efficient transformation
of vector populations over large areas. We demonstrate that even very slow spatial
spread, on the order of 10-20 m/month (as predicted), can produce area-wide population
transformation within a few years following initial releases covering about 20-30%
of the target area.
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models
predict slow but effective spatial spread in Aedes aegypti. Theoretical Population
Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003'
apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia:
Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing
Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.”
Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.'
ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti,” Theoretical
Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.'
ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. 115, 45–60.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia:
Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical
Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.'
short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.
date_created: 2018-12-11T11:49:22Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T10:02:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.03.003
external_id:
pmid:
- '28411063'
file:
- access_level: open_access
checksum: 9aeff86fa7de69f7a15cf4fc60d57d01
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T06:39:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6327'
file_name: 2017_TheoreticalPopulationBio_Turelli.pdf
file_size: 2073856
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 115'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 45 - 60
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- '00405809'
publication_status: published
publisher: Elsevier
publist_id: '6463'
pubrep_id: '972'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective
spatial spread in Aedes aegypti'
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: '2017'
...
---
_id: '951'
abstract:
- lang: eng
text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control,
particularly as they have the potential to self-spread following local introductions.
To test this, we followed the frequency of the transinfected Wolbachia strain
wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated
locations within the city in early 2013. Spatial spread was analysed graphically
using interpolation and by fitting a statistical model describing the position
and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and
0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per
year, roughly consistent with theoretical predictions. In contrast, the smallest
release (0.11 km2) produced erratic temporal and spatial dynamics, with little
evidence of spread after 2 years. This is consistent with the prediction concerning
fitness-decreasing Wolbachia transinfections that a minimum release area is needed
to achieve stable local establishment and spread in continuous habitats. Our graphical
and likelihood analyses produced broadly consistent estimates of wave speed and
wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental
heterogeneity will affect large-scale Wolbachia transformations of urban mosquito
populations. The persistence and spread of Wolbachia in release areas meeting
minimum area requirements indicates the promise of successful large-scale population
transfo
article_number: e2001894
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous
spatial spread of dengue-suppressing Wolbachia through an urban population of
Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous
Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of
Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.
ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,”
PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction
and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban
population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.
mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of
Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS
Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology
15 (2017).
date_created: 2018-12-11T11:49:22Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:52Z
day: '30'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894
external_id:
isi:
- '000402520000012'
file:
- access_level: open_access
checksum: 107d290bd1159ec77b734eb2824b01c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:30Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4691'
file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf
file_size: 5541206
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '6464'
pubrep_id: '843'
quality_controlled: '1'
related_material:
record:
- id: '9856'
relation: research_data
status: public
- id: '9857'
relation: research_data
status: public
- id: '9858'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia
through an urban population of Aedes Aegypti
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: '2017'
...
---
_id: '947'
abstract:
- lang: eng
text: Viewing the ways a living cell can organize its metabolism as the phase space
of a physical system, regulation can be seen as the ability to reduce the entropy
of that space by selecting specific cellular configurations that are, in some
sense, optimal. Here we quantify the amount of regulation required to control
a cell's growth rate by a maximum-entropy approach to the space of underlying
metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern
as described by genome-scale models. We link the mean growth rate achieved by
a population of cells to the minimal amount of metabolic regulation needed to
achieve it through a phase diagram that highlights how growth suppression can
be as costly (in regulatory terms) as growth enhancement. Moreover, we provide
an interpretation of the inverse temperature β controlling maximum-entropy distributions
based on the underlying growth dynamics. Specifically, we show that the asymptotic
value of β for a cell population can be expected to depend on (i) the carrying
capacity of the environment, (ii) the initial size of the colony, and (iii) the
probability distribution from which the inoculum was sampled. Results obtained
for E. coli and human cells are found to be remarkably consistent with empirical
evidence.
article_number: '010401'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular
growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics
. 2017;96(1). doi:10.1103/PhysRevE.96.010401
apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic
cost of cellular growth control. Physical Review E Statistical Nonlinear and
Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401
chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying
the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401.
ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost
of cellular growth control,” Physical Review E Statistical Nonlinear and Soft
Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.
ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost
of cellular growth control. Physical Review E Statistical Nonlinear and Soft
Matter Physics . 96(1), 010401.
mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth
Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics
, vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.
short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical
Nonlinear and Soft Matter Physics 96 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2023-09-22T10:03:50Z
day: '10'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.010401
ec_funded: 1
external_id:
isi:
- '000405194200002'
intvolume: ' 96'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.00219
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6470'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the entropic cost of cellular growth control
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '9858'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities,
Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities,
Wolbachia Infection Status and Housing Characteristics.” Public Library of Science,
2017. https://doi.org/10.1371/journal.pbio.2001894.s016.
ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file
with data on mosquito densities, Wolbachia infection status and housing characteristics,
Public Library of Science, 10.1371/journal.pbio.2001894.s016.
mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia
Infection Status and Housing Characteristics. Public Library of Science, 2017,
doi:10.1371/journal.pbio.2001894.s016.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:47:07Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s016
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Excel file with data on mosquito densities, Wolbachia infection status and
housing characteristics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9857'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed
wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies
and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed
WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science
, 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.
ieee: T. Schmidt et al., “Supporting information concerning observed wMel
frequencies and analyses of habitat variables.” Public Library of Science , 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting
information concerning observed wMel frequencies and analyses of habitat variables,
Public Library of Science , 10.1371/journal.pbio.2001894.s015.
mla: Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies
and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:41:52Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s015
month: '05'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Supporting information concerning observed wMel frequencies and analyses of
habitat variables
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9856'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional
likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Supporting Information concerning additional likelihood
analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional
Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.
ieee: T. Schmidt et al., “Supporting Information concerning additional likelihood
analyses and results.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting
Information concerning additional likelihood analyses and results, Public Library
of Science, 10.1371/journal.pbio.2001894.s014.
mla: Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood
Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:36:04Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s014
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Supporting Information concerning additional likelihood analyses and results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '945'
abstract:
- lang: eng
text: While chromosome-wide dosage compensation of the X chromosome has been found
in many species, studies in ZW clades have indicated that compensation of the
Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show
complete compensation of the Z chromosome, while others lack full equalization,
but what drives these inconsistencies is unclear. Here, we compare patterns of
male and female gene expression on the Z chromosome of two closely related butterfly
species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths
species, Plodia interpunctella and Bombyx mori, which were previously found to
differ in the extent to which they equalize Z-linked gene expression between the
sexes. We find that, while some species and tissues seem to have incomplete dosage
compensation, this is in fact due to the accumulation of male-biased genes and
the depletion of female-biased genes on the Z chromosome. Once this is accounted
for, the Z chromosome is fully compensated in all four species, through the up-regulation
of Z expression in females and in some cases additional down-regulation in males.
We further find that both sex-biased genes and Z-linked genes have increased rates
of expression divergence in this clade, and that this can lead to fast shifts
in patterns of gene expression even between closely related species. Taken together,
these results show that the uneven distribution of sex-biased genes on sex chromosomes
can confound conclusions about dosage compensation and that Z chromosome-wide
dosage compensation is not only possible but ubiquitous among Lepidoptera.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in
Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190
apa: Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation
is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z
chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190
chicago: Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation
Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z
Chromosome.” Molecular Biology and Evolution. Oxford University Press,
2017. https://doi.org/10.1093/molbev/msx190.
ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome,”
Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press,
pp. 2637–2649, 2017.
ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 34(10), 2637–2649.
mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera,
but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology
and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49,
doi:10.1093/molbev/msx190.
short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017)
2637–2649.
date_created: 2018-12-11T11:49:20Z
date_published: 2017-07-06T00:00:00Z
date_updated: 2023-09-26T15:36:34Z
day: '06'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1093/molbev/msx190
external_id:
isi:
- '000411814800016'
file:
- access_level: open_access
checksum: 009fd68043211d645ceb9d1de28274f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:23Z
date_updated: 2020-07-14T12:48:15Z
file_id: '4810'
file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf
file_size: 462863
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '10'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2637 - 2649
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- '07374038'
publication_status: published
publisher: Oxford University Press
publist_id: '6472'
pubrep_id: '848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by
the masculinization of the Z chromosome
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: 34
year: '2017'
...
---
_id: '751'
abstract:
- lang: eng
text: The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath
nearly all epithelial cell types that is critical for cellular and tissue function.
It is composed of numerous components conserved among all bilaterians [1]; however,
it is unknown how all of these components are generated and subsequently constructed
to form a fully mature BM in the living animal. Although BM formation is thought
to simply involve a process of self-assembly [2], this concept suffers from a
number of logistical issues when considering its construction in vivo. First,
incorporation of BM components appears to be hierarchical [3-5], yet it is unclear
whether their production during embryogenesis must also be regulated in a temporal
fashion. Second, many BM proteins are produced not only by the cells residing
on the BM but also by surrounding cell types [6-9], and it is unclear how large,
possibly insoluble protein complexes [10] are delivered into the matrix. Here
we exploit our ability to live image and genetically dissect de novo BM formation
during Drosophila development. This reveals that there is a temporal hierarchy
of BM protein production that is essential for proper component incorporation.
Furthermore, we show that BM components require secretion by migrating macrophages
(hemocytes) during their developmental dispersal, which is critical for embryogenesis.
Indeed, hemocyte migration is essential to deliver a subset of ECM components
evenly throughout the embryo. This reveals that de novo BM construction requires
a combination of both production and distribution logistics allowing for the timely
delivery of core components.
article_processing_charge: No
author:
- first_name: Yutaka
full_name: Matsubayashi, Yutaka
last_name: Matsubayashi
- first_name: Adam
full_name: Louani, Adam
last_name: Louani
- first_name: Anca
full_name: Dragu, Anca
last_name: Dragu
- first_name: Besaiz
full_name: Sanchez Sanchez, Besaiz
last_name: Sanchez Sanchez
- first_name: Eduardo
full_name: Serna Morales, Eduardo
last_name: Serna Morales
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Gema
full_name: Vizcay, Gema
last_name: Vizcay
- first_name: Roland
full_name: Fleck, Roland
last_name: Fleck
- first_name: John
full_name: Heddleston, John
last_name: Heddleston
- first_name: Teng
full_name: Chew, Teng
last_name: Chew
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Brian
full_name: Stramer, Brian
last_name: Stramer
citation:
ama: Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components
is essential for De Novo basement membrane formation. Current Biology.
2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001
apa: Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales,
E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is
essential for De Novo basement membrane formation. Current Biology. Cell
Press. https://doi.org/10.1016/j.cub.2017.10.001
chicago: Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez,
Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source
of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current
Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001.
ieee: Y. Matsubayashi et al., “A moving source of matrix components is essential
for De Novo basement membrane formation,” Current Biology, vol. 27, no.
22. Cell Press, p. 3526–3534e.4, 2017.
ista: Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland
L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B.
2017. A moving source of matrix components is essential for De Novo basement membrane
formation. Current Biology. 27(22), 3526–3534e.4.
mla: Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential
for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no.
22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001.
short: Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales,
L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus,
B. Stramer, Current Biology 27 (2017) 3526–3534e.4.
date_created: 2018-12-11T11:48:18Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2023-09-27T12:25:31Z
day: '09'
ddc:
- '570'
- '576'
department:
- _id: DaSi
doi: 10.1016/j.cub.2017.10.001
external_id:
isi:
- '000415815800031'
file:
- access_level: open_access
checksum: 264cf6c6c3551486ba5ea786850e000a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:45Z
date_updated: 2020-07-14T12:47:59Z
file_id: '4770'
file_name: IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf
file_size: 4770657
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3526 - 3534e.4
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
publist_id: '6905'
pubrep_id: '875'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A moving source of matrix components is essential for De Novo basement membrane
formation
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: 27
year: '2017'
...
---
_id: '798'
abstract:
- lang: eng
text: Nonreciprocal circuit elements form an integral part of modern measurement
and communication systems. Mathematically they require breaking of time-reversal
symmetry, typically achieved using magnetic materials and more recently using
the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities.
Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered
electromechanic interactions. Directional circulation is achieved with controlled
phase-sensitive interference of six distinct electro-mechanical signal conversion
paths. The presented circulator is compact, its silicon-on-insulator platform
is compatible with both superconducting qubits and silicon photonics, and its
noise performance is close to the quantum limit. With a high dynamic range, a
tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter
or wavelength converter, it could pave the way for superconducting qubit processors
with multiplexed on-chip signal processing and readout.
article_number: '1304'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Mahmoud
full_name: Kalaee, Mahmoud
last_name: Kalaee
- first_name: Paul
full_name: Dieterle, Paul
last_name: Dieterle
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator.
Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01304-x
apa: Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O.,
& Fink, J. M. (2017). Mechanical on chip microwave circulator. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/s41467-017-01304-x
chicago: Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul
Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01304-x.
ieee: S. Barzanjeh et al., “Mechanical on chip microwave circulator,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM.
2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.
mla: Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” Nature
Communications, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01304-x.
short: S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M.
Fink, Nature Communications 8 (2017).
date_created: 2018-12-11T11:48:33Z
date_published: 2017-10-16T00:00:00Z
date_updated: 2023-09-27T12:11:28Z
day: '16'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/s41467-017-01304-x
ec_funded: 1
external_id:
isi:
- '000412999700021'
file:
- access_level: open_access
checksum: b68dafa71d1834c23b742cd9987a3d5f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:25Z
date_updated: 2020-07-14T12:48:06Z
file_id: '5145'
file_name: IST-2017-867-v1+1_s41467-017-01304-x.pdf
file_size: 1467696
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics'
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6855'
pubrep_id: '867'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical on chip microwave circulator
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: 8
year: '2017'
...
---
_id: '791'
abstract:
- lang: eng
text: 'Consider the following random process: we are given n queues, into which
elements of increasing labels are inserted uniformly at random. To remove an element,
we pick two queues at random, and remove the element of lower label (higher priority)
among the two. The cost of a removal is the rank of the label removed, among labels
still present in any of the queues, that is, the distance from the optimal choice
at each step. Variants of this strategy are prevalent in state-of-the-art concurrent
priority queue implementations. Nonetheless, it is not known whether such implementations
provide any rank guarantees, even in a sequential model. We answer this question,
showing that this strategy provides surprisingly strong guarantees: Although the
single-choice process, where we always insert and remove from a single randomly
chosen queue, has degrading cost, going to infinity as we increase the number
of steps, in the two choice process, the expected rank of a removed element is
O(n) while the expected worst-case cost is O(n log n). These bounds are tight,
and hold irrespective of the number of steps for which we run the process. The
argument is based on a new technical connection between "heavily loaded"
balls-into-bins processes and priority scheduling. Our analytic results inspire
a new concurrent priority queue implementation, which improves upon the state
of the art in terms of practical performance.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority
scheduling. In: Proceedings of the ACM Symposium on Principles of Distributed
Computing. Vol Part F129314. ACM; 2017:283-292. doi:10.1145/3087801.3087810'
apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Nadiradze, G. (2017). The power
of choice in priority scheduling. In Proceedings of the ACM Symposium on Principles
of Distributed Computing (Vol. Part F129314, pp. 283–292). Washington, WA,
USA: ACM. https://doi.org/10.1145/3087801.3087810'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze.
“The Power of Choice in Priority Scheduling.” In Proceedings of the ACM Symposium
on Principles of Distributed Computing, Part F129314:283–92. ACM, 2017. https://doi.org/10.1145/3087801.3087810.
ieee: D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice
in priority scheduling,” in Proceedings of the ACM Symposium on Principles
of Distributed Computing, Washington, WA, USA, 2017, vol. Part F129314, pp.
283–292.
ista: 'Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in
priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed
Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.'
mla: Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.”
Proceedings of the ACM Symposium on Principles of Distributed Computing,
vol. Part F129314, ACM, 2017, pp. 283–92, doi:10.1145/3087801.3087810.
short: D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the
ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.
conference:
end_date: 2017-07-27
location: Washington, WA, USA
name: 'PODC: Principles of Distributed Computing'
start_date: 2017-07-25
date_created: 2018-12-11T11:48:31Z
date_published: 2017-07-26T00:00:00Z
date_updated: 2023-09-27T12:17:59Z
day: '26'
department:
- _id: DaAl
doi: 10.1145/3087801.3087810
external_id:
isi:
- '000462995000035'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.04178
month: '07'
oa: 1
oa_version: Submitted Version
page: 283 - 292
publication: Proceedings of the ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- 978-145034992-5
publication_status: published
publisher: ACM
publist_id: '6864'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The power of choice in priority scheduling
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: Part F129314
year: '2017'
...
---
_id: '792'
abstract:
- lang: eng
text: The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler
flows, is guided by the infinity of periodic orbits embedded in their strange
attractors. Whether this is also the case for the infinite-dimensional dynamics
of Navier–Stokes equations has long been speculated, and is a topic of ongoing
study. Periodic and relative periodic solutions have been shown to be involved
in transitions to turbulence. Their relevance to turbulent dynamics – specifically,
whether periodic orbits play the same role in high-dimensional nonlinear systems
like the Navier–Stokes equations as they do in lower-dimensional systems – is
the focus of the present investigation. We perform here a detailed study of pipe
flow relative periodic orbits with energies and mean dissipations close to turbulent
values. We outline several approaches to reduction of the translational symmetry
of the system. We study pipe flow in a minimal computational cell at Re=2500,
and report a library of invariant solutions found with the aid of the method of
slices. Detailed study of the unstable manifolds of a sample of these solutions
is consistent with the picture that relative periodic orbits are embedded in the
chaotic saddle and that they guide the turbulent dynamics.
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Kimberly
full_name: Short, Kimberly
last_name: Short
- first_name: Mohammad
full_name: Farazmand, Mohammad
last_name: Farazmand
- first_name: Ashley
full_name: Willis, Ashley
last_name: Willis
- first_name: Predrag
full_name: Cvitanović, Predrag
last_name: Cvitanović
citation:
ama: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic
orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics.
2017;833:274-301. doi:10.1017/jfm.2017.699
apa: Budanur, N. B., Short, K., Farazmand, M., Willis, A., & Cvitanović, P.
(2017). Relative periodic orbits form the backbone of turbulent pipe flow. Journal
of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.699
chicago: Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and
Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe
Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.699.
ieee: N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative
periodic orbits form the backbone of turbulent pipe flow,” Journal of Fluid
Mechanics, vol. 833. Cambridge University Press, pp. 274–301, 2017.
ista: Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic
orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833,
274–301.
mla: Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent
Pipe Flow.” Journal of Fluid Mechanics, vol. 833, Cambridge University
Press, 2017, pp. 274–301, doi:10.1017/jfm.2017.699.
short: N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of
Fluid Mechanics 833 (2017) 274–301.
date_created: 2018-12-11T11:48:32Z
date_published: 2017-12-25T00:00:00Z
date_updated: 2023-09-27T12:17:35Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.699
external_id:
isi:
- '000414641700001'
intvolume: ' 833'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.03720
month: '12'
oa: 1
oa_version: Submitted Version
page: 274 - 301
project:
- _id: 25636330-B435-11E9-9278-68D0E5697425
grant_number: 11-NSF-1070
name: ROOTS Genome-wide Analysis of Root Traits
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6862'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relative periodic orbits form the backbone of turbulent pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 833
year: '2017'
...
---
_id: '796'
abstract:
- lang: eng
text: We present the fabrication and characterization of an aluminum transmon qubit
on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of
an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon
oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured
dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This
process in principle permits the co-fabrication of silicon photonic and mechanical
elements, providing a route towards chip-scale integration of electro-opto-mechanical
transducers for quantum networking of superconducting microwave quantum circuits.
The additional processing steps are compatible with established fabrication techniques
for aluminum transmon qubits on silicon.
acknowledgement: This work was supported by the AFOSR MURI Quantum Photonic Matter
(Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers
(Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter,
an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the
Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech.
A.J.K. acknowledges the IQIM Postdoctoral Fellowship.
article_number: '042603'
article_processing_charge: No
author:
- first_name: Andrew J
full_name: Keller, Andrew J
last_name: Keller
- first_name: Paul
full_name: Dieterle, Paul
last_name: Dieterle
- first_name: Michael
full_name: Fang, Michael
last_name: Fang
- first_name: Brett
full_name: Berger, Brett
last_name: Berger
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Oskar
full_name: Painter, Oskar
last_name: Painter
citation:
ama: Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits
on silicon on insulator for quantum device integration. Applied Physics Letters.
2017;111(4). doi:10.1063/1.4994661
apa: Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., & Painter,
O. (2017). Al transmon qubits on silicon on insulator for quantum device integration.
Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4994661
chicago: Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M
Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum
Device Integration.” Applied Physics Letters. American Institute of Physics,
2017. https://doi.org/10.1063/1.4994661.
ieee: A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter,
“Al transmon qubits on silicon on insulator for quantum device integration,” Applied
Physics Letters, vol. 111, no. 4. American Institute of Physics, 2017.
ista: Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon
qubits on silicon on insulator for quantum device integration. Applied Physics
Letters. 111(4), 042603.
mla: Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum
Device Integration.” Applied Physics Letters, vol. 111, no. 4, 042603,
American Institute of Physics, 2017, doi:10.1063/1.4994661.
short: A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied
Physics Letters 111 (2017).
date_created: 2018-12-11T11:48:33Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-27T12:13:36Z
day: '01'
department:
- _id: JoFi
doi: 10.1063/1.4994661
external_id:
isi:
- '000406779700031'
intvolume: ' 111'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.10195
month: '07'
oa: 1
oa_version: Submitted Version
publication: Applied Physics Letters
publication_identifier:
issn:
- '00036951'
publication_status: published
publisher: American Institute of Physics
publist_id: '6857'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Al transmon qubits on silicon on insulator for quantum device integration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 111
year: '2017'
...
---
_id: '793'
abstract:
- lang: eng
text: 'Let P be a finite point set in the plane. A cordinary triangle in P is a
subset of P consisting of three non-collinear points such that each of the three
lines determined by the three points contains at most c points of P . Motivated
by a question of Erdös, and answering a question of de Zeeuw, we prove that there
exists a constant c > 0such that P contains a c-ordinary triangle, provided
that P is not contained in the union of two lines. Furthermore, the number of
c-ordinary triangles in P is Ω(| P |). '
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Hossein
full_name: Mojarrad, Hossein
last_name: Mojarrad
- first_name: Márton
full_name: Naszódi, Márton
last_name: Naszódi
- first_name: József
full_name: Solymosi, József
last_name: Solymosi
- first_name: Sebastian
full_name: Stich, Sebastian
last_name: Stich
- first_name: May
full_name: Szedlák, May
last_name: Szedlák
citation:
ama: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence
of ordinary triangles. Computational Geometry: Theory and Applications.
2017;66:28-31. doi:10.1016/j.comgeo.2017.07.002'
apa: 'Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., & Szedlák,
M. (2017). On the existence of ordinary triangles. Computational Geometry:
Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.07.002'
chicago: 'Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian
Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” Computational
Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.07.002.'
ieee: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák,
“On the existence of ordinary triangles,” Computational Geometry: Theory and
Applications, vol. 66. Elsevier, pp. 28–31, 2017.'
ista: 'Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On
the existence of ordinary triangles. Computational Geometry: Theory and Applications.
66, 28–31.'
mla: 'Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” Computational
Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 28–31, doi:10.1016/j.comgeo.2017.07.002.'
short: 'R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational
Geometry: Theory and Applications 66 (2017) 28–31.'
date_created: 2018-12-11T11:48:32Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-27T12:15:16Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.comgeo.2017.07.002
ec_funded: 1
external_id:
isi:
- '000412039700003'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.08183
month: '01'
oa: 1
oa_version: Submitted Version
page: 28 - 31
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
issn:
- '09257721'
publication_status: published
publisher: Elsevier
publist_id: '6861'
quality_controlled: '1'
status: public
title: On the existence of ordinary triangles
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2017'
...
---
_id: '794'
abstract:
- lang: eng
text: We show that c-planarity is solvable in quadratic time for flat clustered
graphs with three clusters if the combinatorial embedding of the underlying graph
is fixed. In simpler graph-theoretical terms our result can be viewed as follows.
Given a graph G with the vertex set partitioned into three parts embedded on a
2-sphere, our algorithm decides if we can augment G by adding edges without creating
an edge-crossing so that in the resulting spherical graph the vertices of each
part induce a connected sub-graph. We proceed by a reduction to the problem of
testing the existence of a perfect matching in planar bipartite graphs. We formulate
our result in a slightly more general setting of cyclic clustered graphs, i.e.,
the simple graph obtained by contracting each cluster, where we disregard loops
and multi-edges, is a cycle.
acknowledgement: I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous
referees for many comments and suggestions that helped to improve the presentation
of the result.
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. Computational Geometry:
Theory and Applications. 2017;66:1-13. doi:10.1016/j.comgeo.2017.06.016'
apa: 'Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. Computational
Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.016'
chicago: 'Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational
Geometry: Theory and Applications. Elsevier, 2017. https://doi.org/10.1016/j.comgeo.2017.06.016.'
ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” Computational Geometry:
Theory and Applications, vol. 66. Elsevier, pp. 1–13, 2017.'
ista: 'Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry:
Theory and Applications. 66, 1–13.'
mla: 'Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” Computational
Geometry: Theory and Applications, vol. 66, Elsevier, 2017, pp. 1–13, doi:10.1016/j.comgeo.2017.06.016.'
short: 'R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.'
date_created: 2018-12-11T11:48:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-27T12:14:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.comgeo.2017.06.016
external_id:
isi:
- '000412039700001'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.01346
month: '12'
oa: 1
oa_version: Preprint
page: 1 - 13
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '6860'
quality_controlled: '1'
related_material:
record:
- id: '1165'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: C-planarity of embedded cyclic c-graphs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2017'
...
---
_id: '736'
abstract:
- lang: eng
text: The neurotransmitter receptor subtype, number, density, and distribution relative
to the location of transmitter release sites are key determinants of signal transmission.
AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits
are prominently expressed in subsets of neurons capable of firing action potentials
at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms
glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform
cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics;
thus, we investigated whether the number, density, and localization of GluA3 and
GluA4 subunits in these synapses are differentially organized using quantitative
freeze-fracture replica immunogold labeling. We identify a positive correlation
between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types
of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher
density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller.
A higher number and density of GluA3 subunits are observed at AN-BC synapses,
whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses.
The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits,
particularly GluA3, are concentrated at the center of the AN-BC synapses. The
central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles
are evenly distributed along the postsynaptic density. GluA4 gold labeling was
homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits
are distributed at AN synapses in a target-cell-dependent manner.
article_processing_charge: No
author:
- first_name: María
full_name: Rubio, María
last_name: Rubio
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Elek
full_name: Molnár, Elek
last_name: Molnár
- first_name: Manabu
full_name: Abe, Manabu
last_name: Abe
- first_name: Kenji
full_name: Sakimura, Kenji
last_name: Sakimura
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Rubio M, Matsui K, Fukazawa Y, et al. The number and distribution of AMPA receptor
channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses
depend on the target cells. Brain Structure and Function. 2017;222(8):3375-3393.
doi:10.1007/s00429-017-1408-0
apa: Rubio, M., Matsui, K., Fukazawa, Y., Kamasawa, N., Harada, H., Itakura, M.,
… Shigemoto, R. (2017). The number and distribution of AMPA receptor channels
containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend
on the target cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1408-0
chicago: Rubio, María, Ko Matsui, Yugo Fukazawa, Naomi Kamasawa, Harumi Harada,
Makoto Itakura, Elek Molnár, Manabu Abe, Kenji Sakimura, and Ryuichi Shigemoto.
“The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic
GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.”
Brain Structure and Function. Springer, 2017. https://doi.org/10.1007/s00429-017-1408-0.
ieee: M. Rubio et al., “The number and distribution of AMPA receptor channels
containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend
on the target cells,” Brain Structure and Function, vol. 222, no. 8. Springer,
pp. 3375–3393, 2017.
ista: Rubio M, Matsui K, Fukazawa Y, Kamasawa N, Harada H, Itakura M, Molnár E,
Abe M, Sakimura K, Shigemoto R. 2017. The number and distribution of AMPA receptor
channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses
depend on the target cells. Brain Structure and Function. 222(8), 3375–3393.
mla: Rubio, María, et al. “The Number and Distribution of AMPA Receptor Channels
Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend
on the Target Cells.” Brain Structure and Function, vol. 222, no. 8, Springer,
2017, pp. 3375–93, doi:10.1007/s00429-017-1408-0.
short: M. Rubio, K. Matsui, Y. Fukazawa, N. Kamasawa, H. Harada, M. Itakura, E.
Molnár, M. Abe, K. Sakimura, R. Shigemoto, Brain Structure and Function 222 (2017)
3375–3393.
date_created: 2018-12-11T11:48:14Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-09-27T14:14:51Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1007/s00429-017-1408-0
external_id:
isi:
- '000414761700002'
file:
- access_level: open_access
checksum: 73787a22507de8fb585bb598e1418ca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:20Z
date_updated: 2020-07-14T12:47:56Z
file_id: '4806'
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language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3375 - 3393
publication: Brain Structure and Function
publication_identifier:
issn:
- '18632653'
publication_status: published
publisher: Springer
publist_id: '6932'
pubrep_id: '881'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The number and distribution of AMPA receptor channels containing fast kinetic
GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells
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: 222
year: '2017'
...
---
_id: '740'
abstract:
- lang: eng
text: 'Developments in bioengineering and molecular biology have introduced a palette
of genetically encoded probes for identification of specific cell populations
in electron microscopy. These probes can be targeted to distinct cellular compartments,
rendering them electron dense through a subsequent chemical reaction. These electron
densities strongly increase the local contrast in samples prepared for electron
microscopy, allowing three major advances in ultrastructural mapping of circuits:
genetic identification of circuit components, targeted imaging of regions of interest
and automated analysis of the tagged circuits. Together, the gains from these
advances can decrease the time required for the analysis of targeted circuit motifs
by over two orders of magnitude. These genetic encoded tags for electron microscopy
promise to simplify the analysis of circuit motifs and become a central tool for
structure‐function studies of synaptic connections in the brain. We review the
current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis
of neuronal structures and motifs.'
article_number: e288
article_processing_charge: No
article_type: original
author:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Shigemoto R, Jösch MA. The genetic encoded toolbox for electron microscopy
and connectomics. WIREs Developmental Biology. 2017;6(6). doi:10.1002/wdev.288
apa: Shigemoto, R., & Jösch, M. A. (2017). The genetic encoded toolbox for electron
microscopy and connectomics. WIREs Developmental Biology. Wiley-Blackwell.
https://doi.org/10.1002/wdev.288
chicago: Shigemoto, Ryuichi, and Maximilian A Jösch. “The Genetic Encoded Toolbox
for Electron Microscopy and Connectomics.” WIREs Developmental Biology.
Wiley-Blackwell, 2017. https://doi.org/10.1002/wdev.288.
ieee: R. Shigemoto and M. A. Jösch, “The genetic encoded toolbox for electron microscopy
and connectomics,” WIREs Developmental Biology, vol. 6, no. 6. Wiley-Blackwell,
2017.
ista: Shigemoto R, Jösch MA. 2017. The genetic encoded toolbox for electron microscopy
and connectomics. WIREs Developmental Biology. 6(6), e288.
mla: Shigemoto, Ryuichi, and Maximilian A. Jösch. “The Genetic Encoded Toolbox for
Electron Microscopy and Connectomics.” WIREs Developmental Biology, vol.
6, no. 6, e288, Wiley-Blackwell, 2017, doi:10.1002/wdev.288.
short: R. Shigemoto, M.A. Jösch, WIREs Developmental Biology 6 (2017).
date_created: 2018-12-11T11:48:15Z
date_published: 2017-08-11T00:00:00Z
date_updated: 2023-09-27T12:51:41Z
day: '11'
ddc:
- '570'
department:
- _id: RySh
- _id: MaJö
doi: 10.1002/wdev.288
external_id:
isi:
- '000412827400005'
pmid:
- '28800674'
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checksum: a9370f27b1591773b7a0de299bc81c8c
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creator: dernst
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date_updated: 2020-07-14T12:47:57Z
file_id: '7045'
file_name: 2017_WIREs_Shigemoto.pdf
file_size: 1647787
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has_accepted_license: '1'
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issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: WIREs Developmental Biology
publication_identifier:
issn:
- '17597684'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6927'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The genetic encoded toolbox for electron microscopy and connectomics
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '741'
abstract:
- lang: eng
text: We prove that a system of N fermions interacting with an additional particle
via point interactions is stable if the ratio of the mass of the additional particle
to the one of the fermions is larger than some critical m*. The value of m* is
independent of N and turns out to be less than 1. This fact has important implications
for the stability of the unitary Fermi gas. We also characterize the domain of
the Hamiltonian of this model, and establish the validity of the Tan relations
for all wave functions in the domain.
article_processing_charge: No
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Stability of a fermionic N+1 particle system with point
interactions. Communications in Mathematical Physics. 2017;356(1):329-355.
doi:10.1007/s00220-017-2980-0
apa: Moser, T., & Seiringer, R. (2017). Stability of a fermionic N+1 particle
system with point interactions. Communications in Mathematical Physics.
Springer. https://doi.org/10.1007/s00220-017-2980-0
chicago: Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle
System with Point Interactions.” Communications in Mathematical Physics.
Springer, 2017. https://doi.org/10.1007/s00220-017-2980-0.
ieee: T. Moser and R. Seiringer, “Stability of a fermionic N+1 particle system with
point interactions,” Communications in Mathematical Physics, vol. 356,
no. 1. Springer, pp. 329–355, 2017.
ista: Moser T, Seiringer R. 2017. Stability of a fermionic N+1 particle system with
point interactions. Communications in Mathematical Physics. 356(1), 329–355.
mla: Moser, Thomas, and Robert Seiringer. “Stability of a Fermionic N+1 Particle
System with Point Interactions.” Communications in Mathematical Physics,
vol. 356, no. 1, Springer, 2017, pp. 329–55, doi:10.1007/s00220-017-2980-0.
short: T. Moser, R. Seiringer, Communications in Mathematical Physics 356 (2017)
329–355.
date_created: 2018-12-11T11:48:15Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-09-27T12:34:15Z
day: '01'
ddc:
- '539'
department:
- _id: RoSe
doi: 10.1007/s00220-017-2980-0
ec_funded: 1
external_id:
isi:
- '000409821300010'
file:
- access_level: open_access
checksum: 0fd9435400f91e9b3c5346319a2d24e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:50Z
date_updated: 2020-07-14T12:47:57Z
file_id: '4841'
file_name: IST-2017-880-v1+1_s00220-017-2980-0.pdf
file_size: 952639
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 356'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 329 - 355
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '6926'
pubrep_id: '880'
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stability of a fermionic N+1 particle system with point interactions
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: 356
year: '2017'
...
---
_id: '739'
abstract:
- lang: eng
text: We study the norm approximation to the Schrödinger dynamics of N bosons in
with an interaction potential of the form . Assuming that in the initial state
the particles outside of the condensate form a quasi-free state with finite kinetic
energy, we show that in the large N limit, the fluctuations around the condensate
can be effectively described using Bogoliubov approximation for all . The range
of β is expected to be optimal for this large class of initial states.
article_processing_charge: No
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
citation:
ama: Nam P, Napiórkowski MM. A note on the validity of Bogoliubov correction to
mean field dynamics. Journal de Mathématiques Pures et Appliquées. 2017;108(5):662-688.
doi:10.1016/j.matpur.2017.05.013
apa: Nam, P., & Napiórkowski, M. M. (2017). A note on the validity of Bogoliubov
correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées.
Elsevier. https://doi.org/10.1016/j.matpur.2017.05.013
chicago: Nam, Phan, and Marcin M Napiórkowski. “A Note on the Validity of Bogoliubov
Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées.
Elsevier, 2017. https://doi.org/10.1016/j.matpur.2017.05.013.
ieee: P. Nam and M. M. Napiórkowski, “A note on the validity of Bogoliubov correction
to mean field dynamics,” Journal de Mathématiques Pures et Appliquées,
vol. 108, no. 5. Elsevier, pp. 662–688, 2017.
ista: Nam P, Napiórkowski MM. 2017. A note on the validity of Bogoliubov correction
to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 108(5),
662–688.
mla: Nam, Phan, and Marcin M. Napiórkowski. “A Note on the Validity of Bogoliubov
Correction to Mean Field Dynamics.” Journal de Mathématiques Pures et Appliquées,
vol. 108, no. 5, Elsevier, 2017, pp. 662–88, doi:10.1016/j.matpur.2017.05.013.
short: P. Nam, M.M. Napiórkowski, Journal de Mathématiques Pures et Appliquées 108
(2017) 662–688.
date_created: 2018-12-11T11:48:15Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-09-27T12:52:07Z
day: '01'
department:
- _id: RoSe
doi: 10.1016/j.matpur.2017.05.013
external_id:
isi:
- '000414113600003'
intvolume: ' 108'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05240
month: '11'
oa: 1
oa_version: Submitted Version
page: 662 - 688
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal de Mathématiques Pures et Appliquées
publication_identifier:
issn:
- '00217824'
publication_status: published
publisher: Elsevier
publist_id: '6928'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A note on the validity of Bogoliubov correction to mean field dynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 108
year: '2017'
...
---
_id: '737'
abstract:
- lang: eng
text: We generalize Brazas’ topology on the fundamental group to the whole universal
path space X˜ i.e., to the set of homotopy classes of all based paths. We develop
basic properties of the new notion and provide a complete comparison of the obtained
topology with the established topologies, in particular with the Lasso topology
and the CO topology, i.e., the topology that is induced by the compact-open topology.
It turns out that the new topology is the finest topology contained in the CO
topology, for which the action of the fundamental group on the universal path
space is a continuous group action.
article_processing_charge: No
author:
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
- first_name: Andreas
full_name: Zastrow, Andreas
last_name: Zastrow
citation:
ama: Virk Z, Zastrow A. A new topology on the universal path space. Topology
and its Applications. 2017;231:186-196. doi:10.1016/j.topol.2017.09.015
apa: Virk, Z., & Zastrow, A. (2017). A new topology on the universal path space.
Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2017.09.015
chicago: Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path
Space.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2017.09.015.
ieee: Z. Virk and A. Zastrow, “A new topology on the universal path space,” Topology
and its Applications, vol. 231. Elsevier, pp. 186–196, 2017.
ista: Virk Z, Zastrow A. 2017. A new topology on the universal path space. Topology
and its Applications. 231, 186–196.
mla: Virk, Ziga, and Andreas Zastrow. “A New Topology on the Universal Path Space.”
Topology and Its Applications, vol. 231, Elsevier, 2017, pp. 186–96, doi:10.1016/j.topol.2017.09.015.
short: Z. Virk, A. Zastrow, Topology and Its Applications 231 (2017) 186–196.
date_created: 2018-12-11T11:48:14Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-09-27T12:53:01Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.topol.2017.09.015
external_id:
isi:
- '000413889100012'
intvolume: ' 231'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
page: 186 - 196
publication: Topology and its Applications
publication_identifier:
issn:
- '01668641'
publication_status: published
publisher: Elsevier
publist_id: '6930'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new topology on the universal path space
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 231
year: '2017'
...
---
_id: '733'
abstract:
- lang: eng
text: Let A and B be two N by N deterministic Hermitian matrices and let U be an
N by N Haar distributed unitary matrix. It is well known that the spectral distribution
of the sum H = A + UBU∗ converges weakly to the free additive convolution of the
spectral distributions of A and B, as N tends to infinity. We establish the optimal
convergence rate in the bulk of the spectrum.
acknowledgement: Partially supported by ERC Advanced Grant RANMAT No. 338804, Hong
Kong RGC grant ECS 26301517, and the Göran Gustafsson Foundation
article_processing_charge: No
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Convergence rate for spectral distribution of addition
of random matrices. Advances in Mathematics. 2017;319:251-291. doi:10.1016/j.aim.2017.08.028
apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Convergence rate for spectral
distribution of addition of random matrices. Advances in Mathematics. Academic
Press. https://doi.org/10.1016/j.aim.2017.08.028
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Convergence Rate for Spectral
Distribution of Addition of Random Matrices.” Advances in Mathematics.
Academic Press, 2017. https://doi.org/10.1016/j.aim.2017.08.028.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Convergence rate for spectral distribution
of addition of random matrices,” Advances in Mathematics, vol. 319. Academic
Press, pp. 251–291, 2017.
ista: Bao Z, Erdös L, Schnelli K. 2017. Convergence rate for spectral distribution
of addition of random matrices. Advances in Mathematics. 319, 251–291.
mla: Bao, Zhigang, et al. “Convergence Rate for Spectral Distribution of Addition
of Random Matrices.” Advances in Mathematics, vol. 319, Academic Press,
2017, pp. 251–91, doi:10.1016/j.aim.2017.08.028.
short: Z. Bao, L. Erdös, K. Schnelli, Advances in Mathematics 319 (2017) 251–291.
date_created: 2018-12-11T11:48:13Z
date_published: 2017-10-15T00:00:00Z
date_updated: 2023-09-28T11:30:42Z
day: '15'
department:
- _id: LaEr
doi: 10.1016/j.aim.2017.08.028
ec_funded: 1
external_id:
isi:
- '000412150400010'
intvolume: ' 319'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.03076
month: '10'
oa: 1
oa_version: Submitted Version
page: 251 - 291
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Advances in Mathematics
publication_status: published
publisher: Academic Press
publist_id: '6935'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence rate for spectral distribution of addition of random matrices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 319
year: '2017'
...
---
_id: '840'
abstract:
- lang: eng
text: Heavy holes confined in quantum dots are predicted to be promising candidates
for the realization of spin qubits with long coherence times. Here we focus on
such heavy-hole states confined in germanium hut wires. By tuning the growth density
of the latter we can realize a T-like structure between two neighboring wires.
Such a structure allows the realization of a charge sensor, which is electrostatically
and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3
e. By integrating the T-like structure into a radiofrequency reflectometry setup,
single-shot measurements allowing the extraction of hole tunneling times are performed.
The extracted tunneling times of less than 10 μs are attributed to the small effective
mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.
acknowledged_ssus:
- _id: M-Shop
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in
germanium hut wires probed by single-shot reflectometry. Nano Letters.
2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627
apa: Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole
tunneling times in germanium hut wires probed by single-shot reflectometry. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros.
“Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling
times in germanium hut wires probed by single-shot reflectometry,” Nano Letters,
vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.
ista: Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times
in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9),
5706–5710.
mla: Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed
by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical
Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.
short: L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017)
5706–5710.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-10T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '10'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.7b02627
ec_funded: 1
external_id:
isi:
- '000411043500078'
file:
- access_level: open_access
checksum: 761371a0129b2aa442424b9561450ece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:33Z
date_updated: 2020-07-14T12:48:13Z
file_id: '4951'
file_name: IST-2017-865-v1+1_acs.nanolett.7b02627.pdf
file_size: 2449546
relation: main_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 5706 - 5710
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6808'
pubrep_id: '865'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '69'
relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry
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: 17
year: '2017'
...
---
_id: '914'
abstract:
- lang: eng
text: Infections with potentially lethal pathogens may negatively affect an individual’s
lifespan and decrease its reproductive value. The terminal investment hypothesis
predicts that individuals faced with a reduced survival should invest more into
reproduction instead of maintenance and growth. Several studies suggest that individuals
are indeed able to estimate their body condition and to increase their reproductive
effort with approaching death, while other studies gave ambiguous results. We
investigate whether queens of a perennial social insect (ant) are able to boost
their reproduction following infection with an obligate killing pathogen. Social
insect queens are special with regard to reproduction and aging, as they outlive
conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior,
fecundity increases with queen age. However, it remained unclear whether this
reflects negative reproductive senescence or terminal investment in response to
approaching death. Here, we test whether queens of C. obscurior react to infection
with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying
rate. We show that a fungal infection triggers a reinforced investment in reproduction
in queens. This adjustment of the reproductive rate by ant queens is consistent
with predictions of the terminal investment hypothesis and is reported for the
first time in a social insect.
acknowledgement: We thank two anonymous reviewers for helpful suggestions on the manuscript.
article_number: '170547'
article_processing_charge: No
author:
- first_name: Julia
full_name: Giehr, Julia
last_name: Giehr
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their
reproductive efforts after pathogen infection. Royal Society Open Science.
2017;4(7). doi:10.1098/rsos.170547
apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017).
Ant queens increase their reproductive efforts after pathogen infection. Royal
Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547
chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra
Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.”
Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547.
ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens
increase their reproductive efforts after pathogen infection,” Royal Society
Open Science, vol. 4, no. 7. Royal Society, The, 2017.
ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase
their reproductive efforts after pathogen infection. Royal Society Open Science.
4(7), 170547.
mla: Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after
Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547,
Royal Society, The, 2017, doi:10.1098/rsos.170547.
short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open
Science 4 (2017).
date_created: 2018-12-11T11:49:10Z
date_published: 2017-07-05T00:00:00Z
date_updated: 2023-09-26T15:45:47Z
day: '05'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rsos.170547
external_id:
isi:
- '000406670000025'
file:
- access_level: open_access
checksum: 351ae5e7a37e6e7d9295cd41146c4190
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:48:15Z
file_id: '4684'
file_name: IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf
file_size: 530412
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_identifier:
issn:
- '20545703'
publication_status: published
publisher: Royal Society, The
publist_id: '6527'
pubrep_id: '849'
quality_controlled: '1'
related_material:
record:
- id: '9853'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Ant queens increase their reproductive efforts after pathogen infection
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: 4
year: '2017'
...
---
_id: '910'
abstract:
- lang: eng
text: "Frequency-independent selection is generally considered as a force that acts
to reduce the genetic variation in evolving populations, yet rigorous arguments
for this idea are scarce. When selection fluctuates in time, it is unclear whether
frequency-independent selection may maintain genetic polymorphism without invoking
additional mechanisms. We show that constant frequency-independent selection with
arbitrary epistasis on a well-mixed haploid population eliminates genetic variation
if we assume linkage equilibrium between alleles. To this end, we introduce the
notion of frequency-independent selection at the level of alleles, which is sufficient
to prove our claim and contains the notion of frequency-independent selection
on haploids. When selection and recombination are weak but of the same order,
there may be strong linkage disequilibrium; numerical calculations show that stable
equilibria are highly unlikely. Using the example of a diallelic two-locus model,
we then demonstrate that frequency-independent selection that fluctuates in time
can maintain stable polymorphism if linkage disequilibrium changes its sign periodically.
We put our findings in the context of results from the existing literature and
point out those scenarios in which the possible role of frequency-independent
selection in maintaining genetic variation remains unclear.\r\n"
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novak S, Barton NH. When does frequency-independent selection maintain genetic
variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129
apa: Novak, S., & Barton, N. H. (2017). When does frequency-independent selection
maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129
chicago: Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics. Genetics Society of America,
2017. https://doi.org/10.1534/genetics.117.300129.
ieee: S. Novak and N. H. Barton, “When does frequency-independent selection maintain
genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America,
pp. 653–668, 2017.
ista: Novak S, Barton NH. 2017. When does frequency-independent selection maintain
genetic variation? Genetics. 207(2), 653–668.
mla: Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics
Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.
short: S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.
date_created: 2018-12-11T11:49:09Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-26T15:49:15Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300129
ec_funded: 1
external_id:
isi:
- '000412232600019'
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creator: system
date_created: 2018-12-12T10:17:12Z
date_updated: 2020-07-14T12:48:15Z
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file_name: IST-2018-974-v1+1_manuscript.pdf
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language:
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month: '10'
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oa_version: Submitted Version
page: 653 - 668
project:
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call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6533'
pubrep_id: '974'
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status: public
title: When does frequency-independent selection maintain genetic variation?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 207
year: '2017'
...