---
_id: '1020'
abstract:
- lang: eng
text: Cellulose is the most abundant biopolymer on Earth. Cellulose fibers, such
as the one extracted form cotton or woodpulp, have been used by humankind for
hundreds of years to make textiles and paper. Here we show how, by engineering
light-matter interaction, we can optimize light scattering using exclusively cellulose
nanocrystals. The produced material is sustainable, biocompatible, and when compared
to ordinary microfiber-based paper, it shows enhanced scattering strength (×4),
yielding a transport mean free path as low as 3.5 μm in the visible light range.
The experimental results are in a good agreement with the theoretical predictions
obtained with a diffusive model for light propagation.
acknowledgement: This research was funded by the EPSRC (EP/M027961/1), the Leverhulme
Trust (RPG-2014-238), Royal Society (RG140457), the BBSRC David Phillips fellowship
(BB/K014617/1), and the European Research Council (ERC-2014-STG H2020 639088). All
data created during this research are provided in full in the results section and
Supporting Information. They are openly available from figshare and can be accessed
at ref 30.
article_processing_charge: No
author:
- first_name: Soraya
full_name: Caixeiro, Soraya
last_name: Caixeiro
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Olimpia
full_name: Onelli, Olimpia
last_name: Onelli
- first_name: Silvia
full_name: Vignolini, Silvia
last_name: Vignolini
- first_name: Riccardo
full_name: Sapienza, Riccardo
last_name: Sapienza
citation:
ama: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. Disordered cellulose
based nanostructures for enhanced light scattering. ACS Applied Materials and
Interfaces. 2017;9(9):7885-7890. doi:10.1021/acsami.6b15986
apa: Caixeiro, S., Peruzzo, M., Onelli, O., Vignolini, S., & Sapienza, R. (2017).
Disordered cellulose based nanostructures for enhanced light scattering. ACS
Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.6b15986
chicago: Caixeiro, Soraya, Matilda Peruzzo, Olimpia Onelli, Silvia Vignolini, and
Riccardo Sapienza. “Disordered Cellulose Based Nanostructures for Enhanced Light
Scattering.” ACS Applied Materials and Interfaces. American Chemical Society,
2017. https://doi.org/10.1021/acsami.6b15986.
ieee: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, and R. Sapienza, “Disordered
cellulose based nanostructures for enhanced light scattering,” ACS Applied
Materials and Interfaces, vol. 9, no. 9. American Chemical Society, pp. 7885–7890,
2017.
ista: Caixeiro S, Peruzzo M, Onelli O, Vignolini S, Sapienza R. 2017. Disordered
cellulose based nanostructures for enhanced light scattering. ACS Applied Materials
and Interfaces. 9(9), 7885–7890.
mla: Caixeiro, Soraya, et al. “Disordered Cellulose Based Nanostructures for Enhanced
Light Scattering.” ACS Applied Materials and Interfaces, vol. 9, no. 9,
American Chemical Society, 2017, pp. 7885–90, doi:10.1021/acsami.6b15986.
short: S. Caixeiro, M. Peruzzo, O. Onelli, S. Vignolini, R. Sapienza, ACS Applied
Materials and Interfaces 9 (2017) 7885–7890.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-03-08T00:00:00Z
date_updated: 2023-09-22T09:40:14Z
day: '08'
department:
- _id: JoFi
doi: 10.1021/acsami.6b15986
external_id:
isi:
- '000396186000002'
intvolume: ' 9'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01415
month: '03'
oa: 1
oa_version: Submitted Version
page: 7885 - 7890
publication: ACS Applied Materials and Interfaces
publication_identifier:
issn:
- '19448244'
publication_status: published
publisher: American Chemical Society
publist_id: '6372'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disordered cellulose based nanostructures for enhanced light scattering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2017'
...
---
_id: '1021'
abstract:
- lang: eng
text: Most flows in nature and engineering are turbulent because of their large
velocities and spatial scales. Laboratory experiments on rotating quasi-Keplerian
flows, for which the angular velocity decreases radially but the angular momentum
increases, are however laminar at Reynolds numbers exceeding one million. This
is in apparent contradiction to direct numerical simulations showing that in these
experiments turbulence transition is triggered by the axial boundaries. We here
show numerically that as the Reynolds number increases, turbulence becomes progressively
confined to the boundary layers and the flow in the bulk fully relaminarizes.
Our findings support that turbulence is unlikely to occur in isothermal constant-density
quasi-Keplerian flows.
article_processing_charge: No
author:
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Lopez Alonso JM, Avila M. Boundary layer turbulence in experiments on quasi
Keplerian flows. Journal of Fluid Mechanics. 2017;817:21-34. doi:10.1017/jfm.2017.109
apa: Lopez Alonso, J. M., & Avila, M. (2017). Boundary layer turbulence in experiments
on quasi Keplerian flows. Journal of Fluid Mechanics. Cambridge University
Press. https://doi.org/10.1017/jfm.2017.109
chicago: Lopez Alonso, Jose M, and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics. Cambridge University
Press, 2017. https://doi.org/10.1017/jfm.2017.109.
ieee: J. M. Lopez Alonso and M. Avila, “Boundary layer turbulence in experiments
on quasi Keplerian flows,” Journal of Fluid Mechanics, vol. 817. Cambridge
University Press, pp. 21–34, 2017.
ista: Lopez Alonso JM, Avila M. 2017. Boundary layer turbulence in experiments on
quasi Keplerian flows. Journal of Fluid Mechanics. 817, 21–34.
mla: Lopez Alonso, Jose M., and Marc Avila. “Boundary Layer Turbulence in Experiments
on Quasi Keplerian Flows.” Journal of Fluid Mechanics, vol. 817, Cambridge
University Press, 2017, pp. 21–34, doi:10.1017/jfm.2017.109.
short: J.M. Lopez Alonso, M. Avila, Journal of Fluid Mechanics 817 (2017) 21–34.
date_created: 2018-12-11T11:49:44Z
date_published: 2017-04-25T00:00:00Z
date_updated: 2023-09-22T09:39:46Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.109
external_id:
isi:
- '000398179100006'
intvolume: ' 817'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05527
month: '04'
oa: 1
oa_version: Submitted Version
page: 21 - 34
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6371'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary layer turbulence in experiments on quasi Keplerian flows
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 817
year: '2017'
...
---
_id: '1017'
abstract:
- lang: eng
text: The development of the vertebrate central nervous system is reliant on a complex
cascade of biological processes that include mitotic division, relocation of migrating
neurons, and the extension of dendritic and axonal processes. Each of these cellular
events requires the diverse functional repertoire of the microtubule cytoskeleton
for the generation of forces, assembly of macromolecular complexes and transport
of molecules and organelles. The tubulins are a multi-gene family that encode
for the constituents of microtubules, and have been implicated in a spectrum of
neurological disorders. Evidence is building that different tubulins tune the
functional properties of the microtubule cytoskeleton dependent on the cell type,
developmental profile and subcellular localisation. Here we review of the origins
of the functional specification of the tubulin gene family in the developing brain
at a transcriptional, translational, and post-transcriptional level. We remind
the reader that tubulins are not just loading controls for your average Western
blot.
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Ines
full_name: Leca, Ines
last_name: Leca
- first_name: Thomas
full_name: Gstrein, Thomas
last_name: Gstrein
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: David
full_name: Keays, David
last_name: Keays
citation:
ama: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. Tubulins and brain development:
The origins of functional specification. Molecular and Cellular Neuroscience.
2017;84:58-67. doi:10.1016/j.mcn.2017.03.002'
apa: 'Breuss, M., Leca, I., Gstrein, T., Hansen, A. H., & Keays, D. (2017).
Tubulins and brain development: The origins of functional specification. Molecular
and Cellular Neuroscience. Academic Press. https://doi.org/10.1016/j.mcn.2017.03.002'
chicago: 'Breuss, Martin, Ines Leca, Thomas Gstrein, Andi H Hansen, and David Keays.
“Tubulins and Brain Development: The Origins of Functional Specification.” Molecular
and Cellular Neuroscience. Academic Press, 2017. https://doi.org/10.1016/j.mcn.2017.03.002.'
ieee: 'M. Breuss, I. Leca, T. Gstrein, A. H. Hansen, and D. Keays, “Tubulins and
brain development: The origins of functional specification,” Molecular and
Cellular Neuroscience, vol. 84. Academic Press, pp. 58–67, 2017.'
ista: 'Breuss M, Leca I, Gstrein T, Hansen AH, Keays D. 2017. Tubulins and brain
development: The origins of functional specification. Molecular and Cellular Neuroscience.
84, 58–67.'
mla: 'Breuss, Martin, et al. “Tubulins and Brain Development: The Origins of Functional
Specification.” Molecular and Cellular Neuroscience, vol. 84, Academic
Press, 2017, pp. 58–67, doi:10.1016/j.mcn.2017.03.002.'
short: M. Breuss, I. Leca, T. Gstrein, A.H. Hansen, D. Keays, Molecular and Cellular
Neuroscience 84 (2017) 58–67.
date_created: 2018-12-11T11:49:42Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-22T09:42:15Z
day: '01'
ddc:
- '571'
department:
- _id: SiHi
doi: 10.1016/j.mcn.2017.03.002
external_id:
isi:
- '000415140700007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:19Z
date_updated: 2018-12-12T10:09:19Z
file_id: '4742'
file_name: IST-2017-806-v1+2_1-s2.0-S1044743116302500-main_1_.pdf
file_size: 1436377
relation: main_file
file_date_updated: 2018-12-12T10:09:19Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 58 - 67
publication: Molecular and Cellular Neuroscience
publication_identifier:
issn:
- '10447431'
publication_status: published
publisher: Academic Press
publist_id: '6377'
pubrep_id: '806'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tubulins and brain development: The origins of functional specification'
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: 84
year: '2017'
...
---
_id: '1015'
abstract:
- lang: eng
text: 'Vortices are commonly observed in the context of classical hydrodynamics:
from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon
such as a tornado, all classical vortices are characterized by an arbitrary circulation
value of the local velocity field. On the other hand the appearance of vortices
with quantized circulation represents one of the fundamental signatures of macroscopic
quantum phenomena. In two-dimensional superfluids quantized vortices play a key
role in determining finite-temperature properties, as the superfluid phase and
the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless
transition. Very recent experiments with two-dimensional superfluid fermions motivate
the present work: we present theoretical results based on the renormalization
group showing that the universal jump of the superfluid density and the critical
temperature crucially depend on the interaction strength, providing a strong benchmark
for forthcoming investigations.'
article_number: '45702'
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: Luca
full_name: Salasnich, Luca
last_name: Salasnich
citation:
ama: Bighin G, Salasnich L. Vortices and antivortices in two-dimensional ultracold
Fermi gases. Scientific Reports. 2017;7. doi:10.1038/srep45702
apa: Bighin, G., & Salasnich, L. (2017). Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep45702
chicago: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports. Nature Publishing Group, 2017.
https://doi.org/10.1038/srep45702.
ieee: G. Bighin and L. Salasnich, “Vortices and antivortices in two-dimensional
ultracold Fermi gases,” Scientific Reports, vol. 7. Nature Publishing Group,
2017.
ista: Bighin G, Salasnich L. 2017. Vortices and antivortices in two-dimensional
ultracold Fermi gases. Scientific Reports. 7, 45702.
mla: Bighin, Giacomo, and Luca Salasnich. “Vortices and Antivortices in Two-Dimensional
Ultracold Fermi Gases.” Scientific Reports, vol. 7, 45702, Nature Publishing
Group, 2017, doi:10.1038/srep45702.
short: G. Bighin, L. Salasnich, Scientific Reports 7 (2017).
date_created: 2018-12-11T11:49:42Z
date_published: 2017-04-04T00:00:00Z
date_updated: 2023-09-22T09:43:10Z
day: '04'
ddc:
- '539'
department:
- _id: MiLe
doi: 10.1038/srep45702
external_id:
isi:
- '000398148100001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:32Z
date_updated: 2018-12-12T10:12:32Z
file_id: '4950'
file_name: IST-2017-809-v1+1_srep45702.pdf
file_size: 478289
relation: main_file
file_date_updated: 2018-12-12T10:12:32Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6380'
pubrep_id: '809'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices and antivortices in two-dimensional ultracold Fermi gases
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: 7
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: '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: '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'
file:
- access_level: open_access
checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
- access_level: open_access
checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
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: '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: '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'
file_name: IST-2017-881-v1+1_s00429-017-1408-0.pdf
file_size: 4011126
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '8'
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'
file:
- access_level: open_access
checksum: a9370f27b1591773b7a0de299bc81c8c
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T07:36:18Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7045'
file_name: 2017_WIREs_Shigemoto.pdf
file_size: 1647787
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
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: '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'
file:
- access_level: open_access
checksum: f7c32dabf52e6d9e709d9203761e39fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:12Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5264'
file_name: IST-2018-974-v1+1_manuscript.pdf
file_size: 494268
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 207'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 653 - 668
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
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'
quality_controlled: '1'
scopus_import: '1'
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'
...
---
_id: '916'
abstract:
- lang: eng
text: We study the quadratic assignment problem, in computer vision also known as
graph matching. Two leading solvers for this problem optimize the Lagrange decomposition
duals with sub-gradient and dual ascent (also known as message passing) updates.
We explore this direction further and propose several additional Lagrangean relaxations
of the graph matching problem along with corresponding algorithms, which are all
based on a common dual ascent framework. Our extensive empirical evaluation gives
several theoretical insights and suggests a new state-of-the-art anytime solver
for the considered problem. Our improvement over state-of-the-art is particularly
visible on a new dataset with large-scale sparse problem instances containing
more than 500 graph nodes each.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Carsten
full_name: Abu Alhaija, Carsten
last_name: Abu Alhaija
- first_name: Dagmar
full_name: Kainmueller, Dagmar
last_name: Kainmueller
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study
of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol
2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747'
apa: 'Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy,
B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph
matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and
Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747'
chicago: Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller,
and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.
ieee: 'P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy,
“A study of lagrangean decompositions and dual ascent solvers for graph matching,”
presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States, 2017, vol. 2017, pp. 7062–7071.'
ista: 'Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A
study of lagrangean decompositions and dual ascent solvers for graph matching.
CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.'
mla: Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent
Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.
short: P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:,
IEEE, 2017, pp. 7062–7071.
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: 2018-12-11T11:49:11Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-26T15:41:40Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.747
ec_funded: 1
external_id:
isi:
- '000418371407018'
file:
- access_level: open_access
checksum: e38a2740daad1ea178465843b5072906
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:49:38Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5848'
file_name: 2017_CVPR_Swoboda2.pdf
file_size: 944332
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 7062-7071
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6525'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A study of lagrangean decompositions and dual ascent solvers for graph matching
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '915'
abstract:
- lang: eng
text: We propose a dual decomposition and linear program relaxation of the NP-hard
minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut
polytope, it is amenable to efficient optimization by message passing. Like other
polyhedral relaxations, it can be tightened efficiently by cutting planes. We
define an algorithm that alternates between message passing and efficient separation
of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art
algorithms based on linear programming, including algorithms written in the framework
of leading commercial software, as we show in experiments with large instances
of the problem from applications in computer vision, biomedical image analysis
and data mining.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bjoern
full_name: Andres, Bjoern
last_name: Andres
citation:
ama: 'Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut
problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530'
apa: 'Swoboda, P., & Andres, B. (2017). A message passing algorithm for the
minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR:
Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530'
chicago: Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the
Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.
ieee: 'P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost
multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition,
Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.'
ista: 'Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost
multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.'
mla: Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum
Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.
short: P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.
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: 2018-12-11T11:49:11Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-26T15:43:27Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.530
ec_funded: 1
external_id:
isi:
- '000418371405009'
file:
- access_level: open_access
checksum: 7e51dacefa693574581a32da3eff63dc
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:52:46Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5849'
file_name: Swoboda_A_Message_Passing_CVPR_2017_paper.pdf
file_size: 883264
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 4990-4999
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6526'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A message passing algorithm for the minimum cost multicut problem
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '917'
abstract:
- lang: eng
text: We propose a general dual ascent framework for Lagrangean decomposition
of combinatorial problems. Although methods of this type have shown their efficiency
for a number of problems, so far there was no general algorithm applicable to
multiple problem types. In this work, we propose such a general algorithm. It
depends on several parameters, which can be used to optimize its performance in
each particular setting. We demonstrate efficacy of our method on graph matching
and multicut problems, where it outperforms state-of-the-art solvers including
those based on subgradient optimization and off-the-shelf linear programming solvers.
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Jan
full_name: Kuske, Jan
last_name: Kuske
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean
decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526'
apa: 'Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework
for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.526'
chicago: Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework
for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017.
https://doi.org/10.1109/CVPR.2017.526.
ieee: 'P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean
decomposition of combinatorial problems,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.'
ista: 'Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean
decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition
vol. 2017, 4950–4960.'
mla: Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition
of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.
short: P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.
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: 2018-12-11T11:49:11Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2023-09-26T15:41:11Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/CVPR.2017.526
ec_funded: 1
external_id:
isi:
- '000418371405005'
file:
- access_level: open_access
checksum: 72fd291046bd8e5717961bd68f6b6f03
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T12:45:55Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5847'
file_name: 2017_CVPR_Swoboda.pdf
file_size: 898652
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 4950-4960
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6524'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dual ascent framework for Lagrangean decomposition of combinatorial problems
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '943'
abstract:
- lang: eng
text: Like many developing tissues, the vertebrate neural tube is patterned by antiparallel
morphogen gradients. To understand how these inputs are interpreted, we measured
morphogen signaling and target gene expression in mouse embryos and chick ex vivo
assays. From these data, we derived and validated a characteristic decoding map
that relates morphogen input to the positional identity of neural progenitors.
Analysis of the observed responses indicates that the underlying interpretation
strategy minimizes patterning errors in response to the joint input of noisy opposing
gradients. We reverse-engineered a transcriptional network that provides a mechanistic
basis for the observed cell fate decisions and accounts for the precision and
dynamics of pattern formation. Together, our data link opposing gradient dynamics
in a growing tissue to precise pattern formation.
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Yoji
full_name: Tabata, Yoji
last_name: Tabata
- first_name: Nathalie
full_name: Brandenberg, Nathalie
last_name: Brandenberg
- first_name: Matthias
full_name: Lutolf, Matthias
last_name: Lutolf
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing
neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383.
doi:10.1126/science.aam5887
apa: Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach,
T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from
antiparallel morphogen gradients. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aam5887
chicago: Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf,
Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of
Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.
ieee: M. P. Zagórski et al., “Decoding of position in the developing neural
tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345.
American Association for the Advancement of Science, pp. 1379–1383, 2017.
ista: Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe
J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel
morphogen gradients. Science. 356(6345), 1379–1383.
mla: Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural
Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345,
American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
short: M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach,
J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.
date_created: 2018-12-11T11:49:20Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2023-09-26T15:38:05Z
day: '30'
department:
- _id: AnKi
- _id: GaTk
doi: 10.1126/science.aam5887
ec_funded: 1
external_id:
isi:
- '000404351500036'
pmid:
- '28663499'
intvolume: ' 356'
isi: 1
issue: '6345'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1379 - 1383
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6474'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decoding of position in the developing neural tube from antiparallel morphogen
gradients
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 356
year: '2017'
...
---
_id: '939'
abstract:
- lang: eng
text: We reveal the existence of continuous families of guided single-mode solitons
in planar waveguides with weakly nonlinear active core and absorbing boundaries.
Stable propagation of TE and TM-polarized solitons is accompanied by attenuation
of all other modes, i.e., the waveguide features properties of conservative and
dissipative systems. If the linear spectrum of the waveguide possesses exceptional
points, which occurs in the case of TM polarization, an originally focusing (defocusing)
material nonlinearity may become effectively defocusing (focusing). This occurs
due to the geometric phase of the carried eigenmode when the surface impedance
encircles the exceptional point. In its turn, the change of the effective nonlinearity
ensures the existence of dark (bright) solitons in spite of focusing (defocusing)
Kerr nonlinearity of the core. The existence of an exceptional point can also
result in anomalous enhancement of the effective nonlinearity. In terms of practical
applications, the nonlinearity of the reported waveguide can be manipulated by
controlling the properties of the absorbing cladding.
article_number: '033905'
article_processing_charge: No
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: 'Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled
by an exceptional point and solitons. Physical Review Letters. 2017;119(3).
doi:10.1103/PhysRevLett.119.033905'
apa: 'Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries:
Nonlinearity controlled by an exceptional point and solitons. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905'
chicago: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries:
Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review
Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.'
ieee: 'B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity
controlled by an exceptional point and solitons,” Physical Review Letters,
vol. 119, no. 3. American Physical Society, 2017.'
ista: 'Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity
controlled by an exceptional point and solitons. Physical Review Letters. 119(3),
033905.'
mla: 'Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries:
Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review
Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.'
short: B. Midya, V. Konotop, Physical Review Letters 119 (2017).
date_created: 2018-12-11T11:49:18Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-09-26T15:39:46Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.119.033905
ec_funded: 1
external_id:
isi:
- '000405718200012'
intvolume: ' 119'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://arxiv.org/abs/1706.04085 '
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 Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
publist_id: '6481'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional
point and solitons'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 119
year: '2017'
...
---
_id: '9853'
abstract:
- lang: eng
text: Egg laying rates and infection loads of C. obscurior queens
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. Raw data from ant queens
increase their reproductive efforts after pathogen infection. 2017. doi:10.6084/m9.figshare.5117788.v1
apa: Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017).
Raw data from ant queens increase their reproductive efforts after pathogen infection.
The Royal Society. https://doi.org/10.6084/m9.figshare.5117788.v1
chicago: Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra
Schrempf. “Raw Data from Ant Queens Increase Their Reproductive Efforts after
Pathogen Infection.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5117788.v1.
ieee: J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Raw data from
ant queens increase their reproductive efforts after pathogen infection.” The
Royal Society, 2017.
ista: Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Raw data from ant
queens increase their reproductive efforts after pathogen infection, The Royal
Society, 10.6084/m9.figshare.5117788.v1.
mla: Giehr, Julia, et al. Raw Data from Ant Queens Increase Their Reproductive
Efforts after Pathogen Infection. The Royal Society, 2017, doi:10.6084/m9.figshare.5117788.v1.
short: J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, (2017).
date_created: 2021-08-10T06:57:57Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2023-09-26T15:45:47Z
day: '19'
department:
- _id: SyCr
doi: 10.6084/m9.figshare.5117788.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.5117788.v1
month: '06'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '914'
relation: used_in_publication
status: public
status: public
title: Raw data from ant queens increase their reproductive efforts after pathogen
infection
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '833'
abstract:
- lang: eng
text: We present an efficient algorithm to compute Euler characteristic curves of
gray scale images of arbitrary dimension. In various applications the Euler characteristic
curve is used as a descriptor of an image. Our algorithm is the first streaming
algorithm for Euler characteristic curves. The usage of streaming removes the
necessity to store the entire image in RAM. Experiments show that our implementation
handles terabyte scale images on commodity hardware. Due to lock-free parallelism,
it scales well with the number of processor cores. Additionally, we put the concept
of the Euler characteristic curve in the wider context of computational topology.
In particular, we explain the connection with persistence diagrams.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of
multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer;
2017:397-409. doi:10.1007/978-3-319-64689-3_32'
apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic
curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger
(Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of
Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32'
chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden,
and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32.
ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves
of multidimensional images,” presented at the CAIP: Computer Analysis of Images
and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.'
ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves
of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS,
vol. 10424, 397–409.'
mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol.
10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.
short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer,
2017, pp. 397–409.
conference:
end_date: 2017-08-24
location: Ystad, Sweden
name: 'CAIP: Computer Analysis of Images and Patterns'
start_date: 2017-08-22
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2023-09-26T16:10:03Z
day: '28'
department:
- _id: HeEd
doi: 10.1007/978-3-319-64689-3_32
editor:
- first_name: Michael
full_name: Felsberg, Michael
last_name: Felsberg
- first_name: Anders
full_name: Heyden, Anders
last_name: Heyden
- first_name: Norbert
full_name: Krüger, Norbert
last_name: Krüger
external_id:
isi:
- '000432085900032'
intvolume: ' 10424'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02045
month: '07'
oa: 1
oa_version: Submitted Version
page: 397 - 409
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6815'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Streaming algorithm for Euler characteristic curves of multidimensional images
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10424
year: '2017'
...
---
_id: '834'
abstract:
- lang: eng
text: 'Thermal and many-body localized phases are separated by a dynamical phase
transition of a new kind. We analyze the distribution of off-diagonal matrix elements
of local operators across this transition in two different models of disordered
spin chains. We show that the behavior of matrix elements can be used to characterize
the breakdown of thermalization and to extract the many-body Thouless energy.
We find that upon increasing the disorder strength the system enters a critical
region around the many-body localization transition. The properties of the system
in this region are: (i) the Thouless energy becomes smaller than the level spacing,
(ii) the matrix elements show critical dependence on the energy difference, and
(iii) the matrix elements, viewed as amplitudes of a fictitious wave function,
exhibit strong multifractality. This critical region decreases with the system
size, which we interpret as evidence for a diverging correlation length at the
many-body localization transition. Our findings show that the correlation length
becomes larger than the accessible system sizes in a broad range of disorder strength
values and shed light on the critical behavior near the many-body localization
transition.'
acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover,
and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS
Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of
this work were completed (supported in part by the National Science Foundation under
Grant No. NSF PHY11-25915)
article_number: '104201'
article_processing_charge: No
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Papic
full_name: Zlatko, Papic
last_name: Zlatko
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
citation:
ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the
many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201
apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality
across the many-body localization transition. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201
chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality
across the Many-Body Localization Transition.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.
ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality
across the many-body localization transition,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 10. American Physical Society,
2017.
ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across
the many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 96(10), 104201.
mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.
short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 96 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-09-06T00:00:00Z
date_updated: 2023-09-26T15:51:54Z
day: '06'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104201
external_id:
isi:
- '000409429300004'
intvolume: ' 96'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02389
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6814'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thouless energy and multifractality across the many-body localization transition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- 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: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
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: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '824'
abstract:
- lang: eng
text: 'In shear flows at transitional Reynolds numbers, localized patches of turbulence,
known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev.
Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic
solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds
number. Combining slicing methods for continuous symmetry reduction with Poincaré
sections for the first time in a shear flow setting, we compute and visualize
the unstable manifold of the lower-branch solution and show that it extends towards
the neighbourhood of the upper-branch solution. Surprisingly, this connection
even persists far above the bifurcation point and appears to mediate the first
stage of the puff generation: amplification of streamwise localized fluctuations.
When the state-space trajectories on the unstable manifold reach the vicinity
of the upper branch, corresponding fluctuations expand in space and eventually
take the usual shape of a puff.'
article_number: R1
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: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow.
Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516
apa: Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized
chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2017.516
chicago: Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press,
2017. https://doi.org/10.1017/jfm.2017.516.
ieee: N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos
in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University
Press, 2017.
ista: Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in
pipe flow. Journal of Fluid Mechanics. 827, R1.
mla: Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge
University Press, 2017, doi:10.1017/jfm.2017.516.
short: N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-18T00:00:00Z
date_updated: 2023-09-26T16:17:43Z
day: '18'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.516
external_id:
isi:
- '000408326300001'
intvolume: ' 827'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.10484
month: '08'
oa: 1
oa_version: Submitted Version
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6824'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic path to spatially localized chaos in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 827
year: '2017'
...
---
_id: '799'
abstract:
- lang: eng
text: Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly
distributing various membrane proteins to their destination. Polarly localized
auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported
between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular
trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA),
which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation
factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive
trafficking pathway have not been revealed fully. In a previous study, we have
identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective
3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular
PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF
GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for
TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized
PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2
as a crucial component of this BFA action at the level of TGN/EE. Furthermore,
ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF
GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF
component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.
article_number: 1801-1811
article_processing_charge: No
author:
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Yuki
full_name: Matsuura, Yuki
last_name: Matsuura
- first_name: Luca
full_name: Santuari, Luca
last_name: Santuari
- first_name: Hirotaka
full_name: Kouno, Hirotaka
last_name: Kouno
- first_name: Kohei
full_name: Arima, Kohei
last_name: Arima
- first_name: Christian
full_name: Hardtke, Christian
last_name: Hardtke
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
citation:
ama: Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in
brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in
Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118
apa: Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima,
K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana.
Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118
chicago: Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka
Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu
Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at
the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and
Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.
ieee: S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,”
Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.
ista: Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke
C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin
a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis
thaliana. Plant and Cell Physiology. 58(10), 1801–1811.
mla: Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive
Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.”
Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University
Press, 2017, doi:10.1093/pcp/pcx118.
short: S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima,
C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-08-21T00:00:00Z
date_updated: 2023-09-27T11:00:19Z
day: '21'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1093/pcp/pcx118
external_id:
isi:
- '000413220400019'
pmid:
- '29016942'
file:
- access_level: open_access
checksum: bd3e3a94d55416739cbb19624bb977f8
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:52:34Z
date_updated: 2020-07-14T12:48:06Z
file_id: '6333'
file_name: 2017_PlantCellPhysio_Kitakura.pdf
file_size: 1352913
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '6854'
pubrep_id: '1009'
quality_controlled: '1'
scopus_import: '1'
status: public
title: BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi
network/early endosome in Arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 58
year: '2017'
...
---
_id: '800'
abstract:
- lang: eng
text: Gamma oscillations (30–150 Hz) in neuronal networks are associated with the
processing and recall of information. We measured local field potentials in the
dentate gyrus of freely moving mice and found that gamma activity occurs in bursts,
which are highly heterogeneous in their spatial extensions, ranging from focal
to global coherent events. Synaptic communication among perisomatic-inhibitory
interneurons (PIIs) is thought to play an important role in the generation of
hippocampal gamma patterns. However, how neuronal circuits can generate synchronous
oscillations at different spatial scales is unknown. We analyzed paired recordings
in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron
synapses is distance dependent. Synaptic strength declines whereas the duration
of inhibitory signals increases with axonal distance among interconnected PIIs.
Using neuronal network modeling, we show that distance-dependent inhibition generates
multiple highly synchronous focal gamma bursts allowing the network to process
complex inputs in parallel in flexibly organized neuronal centers.
article_number: '758'
article_processing_charge: No
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Jonas
full_name: Sauer, Jonas
last_name: Sauer
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates
focality of gamma oscillations in the dentate gyrus. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-00936-3
apa: Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent
inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3
chicago: Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent
Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3.
ieee: M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition
facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications,
vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition
facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications.
8(1), 758.
mla: Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality
of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol.
8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3.
short: M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-10-02T00:00:00Z
date_updated: 2023-09-27T10:59:41Z
day: '02'
ddc:
- '571'
department:
- _id: PeJo
doi: 10.1038/s41467-017-00936-3
ec_funded: 1
external_id:
isi:
- '000412053100004'
file:
- access_level: open_access
checksum: 7e2c7621afd5f802338e92e8619f024d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:17Z
date_updated: 2020-07-14T12:48:07Z
file_id: '5135'
file_name: IST-2017-914-v1+1_s41467-017-00936-3.pdf
file_size: 4261832
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6853'
pubrep_id: '914'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distance-dependent inhibition facilitates focality of gamma oscillations in
the dentate gyrus
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: '803'
abstract:
- lang: eng
text: Eukaryotic cells store their chromosomes in a single nucleus. This is important
to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei)
are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble
their nucleus and release individualized chromosomes for segregation. How numerous
chromosomes subsequently reform a single nucleus has remained unclear. Using image-based
screening of human cells, we identified barrier-to-autointegration factor (BAF)
as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear
assembly does not require BAF?s association with inner nuclear membrane proteins
but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging
and in vitro reconstitution showed that BAF enriches around the mitotic chromosome
ensemble to induce a densely cross-bridged chromatin layer that is mechanically
stiff and limits membranes to the surface. Our study reveals that BAF-mediated
changes in chromosome mechanics underlie nuclear assembly with broad implications
for proper genome function.
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Matthias
full_name: Samwer, Matthias
last_name: Samwer
- first_name: Maximilian
full_name: Schneider, Maximilian
last_name: Schneider
- first_name: Rudolf
full_name: Hoefler, Rudolf
last_name: Hoefler
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Julian
full_name: Jude, Julian
last_name: Jude
- first_name: Johannes
full_name: Zuber, Johannes
last_name: Zuber
- first_name: Daniel
full_name: Gerlic, Daniel
last_name: Gerlic
citation:
ama: Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single
nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038
apa: Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber,
J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a
set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038
chicago: Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst,
Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single
Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038.
ieee: M. Samwer et al., “DNA cross-bridging shapes a single nucleus from
a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972,
2017.
ista: Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic
D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes.
Cell. 170(5), 956–972.
mla: Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a
Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp.
956–72, doi:10.1016/j.cell.2017.07.038.
short: M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber,
D. Gerlic, Cell 170 (2017) 956–972.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-08-24T00:00:00Z
date_updated: 2023-09-27T10:59:14Z
day: '24'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cell.2017.07.038
external_id:
isi:
- '000408372400014'
file:
- access_level: open_access
checksum: 64897b0c5373f22273f598e4672c60ff
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:45:40Z
date_updated: 2020-07-14T12:48:08Z
file_id: '5852'
file_name: 2017_Cell_Samwer.pdf
file_size: 17666637
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 170'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 956 - 972
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '6848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes
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: 170
year: '2017'
...
---
_id: '804'
abstract:
- lang: eng
text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
biological processes. However, precise biochemical or genetic manipulation of
these often complex structures is laborious and hampers experimental structure–function
studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
to generate and test hypotheses on saccharide function. Yet, currently used MD
force fields often overestimate the aggregation propensity of polysaccharides,
affecting the usability of those simulations. Here we tested MARTINI, a popular
coarse-grained (CG) force field for biological macromolecules, for its ability
to accurately represent molecular forces between saccharides. To this end, we
calculated a thermodynamic solution property, the second virial coefficient of
the osmotic pressure (B22). Comparison with light scattering experiments revealed
a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
at an imbalance of the nonbonded solute–solute, solute–water, and water–water
interactions. This finding also applies to smaller oligosaccharides which were
all found to aggregate in simulations even at moderate concentrations, well below
their solubility limit. Finally, we explored the influence of the Lennard-Jones
(LJ) interaction between saccharide molecules and propose a simple scaling of
the LJ interaction strength that makes MARTINI more reliable for the simulation
of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and
Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
author:
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Felix
full_name: Deluweit, Felix
last_name: Deluweit
- first_name: Roger
full_name: Scherrers, Roger
last_name: Scherrers
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
citation:
ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374
apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &
Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
simulations of polysaccharides. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374
chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation.
American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.
ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13,
no. 10. American Chemical Society, pp. 5039–5053, 2017.
ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 13(10), 5039–5053.
mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory
and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
doi:10.1021/acs.jctc.7b00374.
short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2023-09-27T10:58:45Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
isi:
- '000412965700036'
intvolume: ' 13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
issn:
- '15499618'
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2017'
...
---
_id: '746'
abstract:
- lang: eng
text: Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated
in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at
the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored.
Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5
cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function,
and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using
single-molecule tracking, we found that mGluR5 was significantly more mobile at
synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface
co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of
synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression,
and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral
phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides
a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes
of FXS, unveiling novel targets for mGluR5-based therapeutics.
article_number: '1103'
article_processing_charge: No
author:
- first_name: Elisabetta
full_name: Aloisi, Elisabetta
last_name: Aloisi
- first_name: Katy
full_name: Le Corf, Katy
last_name: Le Corf
- first_name: Julien
full_name: Dupuis, Julien
last_name: Dupuis
- first_name: Pei
full_name: Zhang, Pei
last_name: Zhang
- first_name: Melanie
full_name: Ginger, Melanie
last_name: Ginger
- first_name: Virginie
full_name: Labrousse, Virginie
last_name: Labrousse
- first_name: Michela
full_name: Spatuzza, Michela
last_name: Spatuzza
- first_name: Matthias
full_name: Georg Haberl, Matthias
last_name: Georg Haberl
- first_name: Lara
full_name: Costa, Lara
last_name: Costa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Anke
full_name: Tappe Theodor, Anke
last_name: Tappe Theodor
- first_name: Fillippo
full_name: Drago, Fillippo
last_name: Drago
- first_name: Pier
full_name: Vincenzo Piazza, Pier
last_name: Vincenzo Piazza
- first_name: Christophe
full_name: Mulle, Christophe
last_name: Mulle
- first_name: Laurent
full_name: Groc, Laurent
last_name: Groc
- first_name: Lucia
full_name: Ciranna, Lucia
last_name: Ciranna
- first_name: Maria
full_name: Catania, Maria
last_name: Catania
- first_name: Andreas
full_name: Frick, Andreas
last_name: Frick
citation:
ama: Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke
synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature
Communications. 2017;8(1). doi:10.1038/s41467-017-01191-2
apa: Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V.,
… Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction
and cognitive defects in Fmr1 knockout mice. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/s41467-017-01191-2
chicago: Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger,
Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics
Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01191-2.
ieee: E. Aloisi et al., “Altered surface mGluR5 dynamics provoke synaptic
NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” Nature Communications,
vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M,
Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza
P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5
dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout
mice. Nature Communications. 8(1), 1103.
mla: Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic
NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” Nature Communications,
vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01191-2.
short: E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza,
M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo
Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications
8 (2017).
date_created: 2018-12-11T11:48:17Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-27T12:27:30Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1038/s41467-017-01191-2
external_id:
isi:
- '000413571300004'
file:
- access_level: open_access
checksum: 99ceee57549dc0461e3adfc037ec70a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:32Z
date_updated: 2020-07-14T12:47:58Z
file_id: '5287'
file_name: IST-2017-915-v1+1_s41467-017-01191-2.pdf
file_size: 1841650
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6921'
pubrep_id: '915'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive
defects in Fmr1 knockout mice
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: '749'
abstract:
- lang: eng
text: 'Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous
transmitter release and facilitation at synapses. However, Syt7 is strongly expressed
in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output
synapses of these neurons produce only minimal asynchronous release and show depression
rather than facilitation. To resolve this apparent contradiction, we examined
the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic
basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate
that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment,
and facilitation. In combination, these three effects ensure efficient transmitter
release during high-frequency activity and guarantee frequency independence of
inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency
of high-frequency inhibitory synaptic transmission'
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Rachel
full_name: Satterfield, Rachel
last_name: Satterfield
- first_name: Samuel
full_name: Young, Samuel
last_name: Young
- 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, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses.
Cell Reports. 2017;21(8):2082-2089. doi:10.1016/j.celrep.2017.10.122
apa: Chen, C., Satterfield, R., Young, S., & Jonas, P. M. (2017). Triple function
of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central
GABAergic synapses. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.10.122
chicago: Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple
Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission
at Central GABAergic Synapses.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.10.122.
ieee: C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses,”
Cell Reports, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017.
ista: Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin
7 ensures efficiency of high-frequency transmission at central GABAergic synapses.
Cell Reports. 21(8), 2082–2089.
mla: Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency
of High-Frequency Transmission at Central GABAergic Synapses.” Cell Reports,
vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:10.1016/j.celrep.2017.10.122.
short: C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089.
date_created: 2018-12-11T11:48:18Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2023-09-27T12:26:04Z
day: '21'
ddc:
- '570'
- '571'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2017.10.122
ec_funded: 1
external_id:
isi:
- '000416216700007'
file:
- access_level: open_access
checksum: a6afa3764909bf6edafa07982d8e1cee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:14Z
date_updated: 2020-07-14T12:47:59Z
file_id: '4737'
file_name: IST-2017-874-v1+1_PIIS2211124717316029.pdf
file_size: 2759195
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '8'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2082 - 2089
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
publication: Cell Reports
publication_identifier:
issn:
- '22111247'
publication_status: published
publisher: Cell Press
publist_id: '6907'
pubrep_id: '874'
quality_controlled: '1'
related_material:
record:
- id: '324'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission
at central GABAergic synapses
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: 21
year: '2017'
...
---
_id: '744'
abstract:
- lang: eng
text: In evolutionary game theory interactions between individuals are often assumed
obligatory. However, in many real-life situations, individuals can decide to opt
out of an interaction depending on the information they have about the opponent.
We consider a simple evolutionary game theoretic model to study such a scenario,
where at each encounter between two individuals the type of the opponent (cooperator/defector)
is known with some probability, and where each individual either accepts or opts
out of the interaction. If the type of the opponent is unknown, a trustful individual
accepts the interaction, whereas a suspicious individual opts out of the interaction.
If either of the two individuals opt out both individuals remain without an interaction.
We show that in the prisoners dilemma optional interactions along with suspicious
behaviour facilitates the emergence of trustful cooperation.
article_processing_charge: No
article_type: original
author:
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Priklopil T, Chatterjee K, Nowak M. Optional interactions and suspicious behaviour
facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical
Biology. 2017;433:64-72. doi:10.1016/j.jtbi.2017.08.025
apa: Priklopil, T., Chatterjee, K., & Nowak, M. (2017). Optional interactions
and suspicious behaviour facilitates trustful cooperation in prisoners dilemma.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2017.08.025
chicago: Priklopil, Tadeas, Krishnendu Chatterjee, and Martin Nowak. “Optional Interactions
and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.”
Journal of Theoretical Biology. Elsevier, 2017. https://doi.org/10.1016/j.jtbi.2017.08.025.
ieee: T. Priklopil, K. Chatterjee, and M. Nowak, “Optional interactions and suspicious
behaviour facilitates trustful cooperation in prisoners dilemma,” Journal
of Theoretical Biology, vol. 433. Elsevier, pp. 64–72, 2017.
ista: Priklopil T, Chatterjee K, Nowak M. 2017. Optional interactions and suspicious
behaviour facilitates trustful cooperation in prisoners dilemma. Journal of Theoretical
Biology. 433, 64–72.
mla: Priklopil, Tadeas, et al. “Optional Interactions and Suspicious Behaviour Facilitates
Trustful Cooperation in Prisoners Dilemma.” Journal of Theoretical Biology,
vol. 433, Elsevier, 2017, pp. 64–72, doi:10.1016/j.jtbi.2017.08.025.
short: T. Priklopil, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 433
(2017) 64–72.
date_created: 2018-12-11T11:48:16Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2023-09-27T12:29:02Z
day: '21'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1016/j.jtbi.2017.08.025
ec_funded: 1
external_id:
isi:
- '000412039800007'
pmid:
- '28867224'
file:
- access_level: open_access
checksum: 4b43af1615ebf1a861840cb03d8a320c
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T07:57:39Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7047'
file_name: 2017_JournTheoretBio_Priklopil.pdf
file_size: 537323
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 433'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 64 - 72
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: ' Journal of Theoretical Biology'
publication_identifier:
issn:
- '00225193'
publication_status: published
publisher: Elsevier
publist_id: '6923'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optional interactions and suspicious behaviour facilitates trustful cooperation
in prisoners dilemma
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: 433
year: '2017'
...
---
_id: '745'
abstract:
- lang: eng
text: 'Fluid flows in nature and applications are frequently subject to periodic
velocity modulations. Surprisingly, even for the generic case of flow through
a straight pipe, there is little consensus regarding the influence of pulsation
on the transition threshold to turbulence: while most studies predict a monotonically
increasing threshold with pulsation frequency (i.e. Womersley number, ), others
observe a decreasing threshold for identical parameters and only observe an increasing
threshold at low . In the present study we apply recent advances in the understanding
of transition in steady shear flows to pulsating pipe flow. For moderate pulsation
amplitudes we find that the first instability encountered is subcritical (i.e.
requiring finite amplitude disturbances) and gives rise to localized patches of
turbulence (''puffs'') analogous to steady pipe flow. By monitoring the impact
of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter
space. Transition in pulsatile flow can be separated into three regimes. At small
Womersley numbers the dynamics is dominated by the decay turbulence suffers during
the slower part of the cycle and hence transition is delayed significantly. As
shown in this regime thresholds closely agree with estimates based on a quasi-steady
flow assumption only taking puff decay rates into account. The transition point
predicted in the zero limit equals to the critical point for steady pipe flow
offset by the oscillation Reynolds number (i.e. the dimensionless oscillation
amplitude). In the high frequency limit on the other hand, puff lifetimes are
identical to those in steady pipe flow and hence the transition threshold appears
to be unaffected by flow pulsation. In the intermediate frequency regime the transition
threshold sharply drops (with increasing ) from the decay dominated (quasi-steady)
threshold to the steady pipe flow level.'
article_processing_charge: No
author:
- first_name: Duo
full_name: Xu, Duo
id: 3454D55E-F248-11E8-B48F-1D18A9856A87
last_name: Xu
- first_name: Sascha
full_name: Warnecke, Sascha
last_name: Warnecke
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Xingyu
full_name: Ma, Xingyu
id: 34BADBA6-F248-11E8-B48F-1D18A9856A87
last_name: Ma
orcid: 0000-0002-0179-9737
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Xu D, Warnecke S, Song B, Ma X, Hof B. Transition to turbulence in pulsating
pipe flow. Journal of Fluid Mechanics. 2017;831:418-432. doi:10.1017/jfm.2017.620
apa: Xu, D., Warnecke, S., Song, B., Ma, X., & Hof, B. (2017). Transition to
turbulence in pulsating pipe flow. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2017.620
chicago: Xu, Duo, Sascha Warnecke, Baofang Song, Xingyu Ma, and Björn Hof. “Transition
to Turbulence in Pulsating Pipe Flow.” Journal of Fluid Mechanics. Cambridge
University Press, 2017. https://doi.org/10.1017/jfm.2017.620.
ieee: D. Xu, S. Warnecke, B. Song, X. Ma, and B. Hof, “Transition to turbulence
in pulsating pipe flow,” Journal of Fluid Mechanics, vol. 831. Cambridge
University Press, pp. 418–432, 2017.
ista: Xu D, Warnecke S, Song B, Ma X, Hof B. 2017. Transition to turbulence in pulsating
pipe flow. Journal of Fluid Mechanics. 831, 418–432.
mla: Xu, Duo, et al. “Transition to Turbulence in Pulsating Pipe Flow.” Journal
of Fluid Mechanics, vol. 831, Cambridge University Press, 2017, pp. 418–32,
doi:10.1017/jfm.2017.620.
short: D. Xu, S. Warnecke, B. Song, X. Ma, B. Hof, Journal of Fluid Mechanics 831
(2017) 418–432.
date_created: 2018-12-11T11:48:17Z
date_published: 2017-11-25T00:00:00Z
date_updated: 2023-09-27T12:28:12Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.620
ec_funded: 1
external_id:
isi:
- '000412934800005'
intvolume: ' 831'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.03738
month: '11'
oa: 1
oa_version: Submitted Version
page: 418 - 432
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6922'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to turbulence in pulsating pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 831
year: '2017'
...
---
_id: '747'
abstract:
- lang: eng
text: Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts
multiple effects via B1 and B2 receptor activation. In the cardiovascular system,
bradykinin has cardioprotective and vasodilator properties. We investigated the
effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for
the parasympathetic cardiac regulation. BK produced a dose-dependent increase
in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist,
but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective
B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic
Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin
GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with
ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished
the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate,
antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response
to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase,
while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the
response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons,
which was prevented by the B2 receptor antagonist. In vivo studies indicate that
microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats
via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK
activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic
reticulum, and membrane depolarization; these effects are translated in vivo by
bradycardia.
article_processing_charge: No
article_type: original
author:
- first_name: Eugen
full_name: Brǎiloiu, Eugen
last_name: Brǎiloiu
- first_name: Matthew
full_name: Mcguire, Matthew
last_name: Mcguire
- first_name: Shadaria
full_name: Shuler, Shadaria
last_name: Shuler
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Jeffrey
full_name: Barr, Jeffrey
last_name: Barr
- first_name: Mary
full_name: Abood, Mary
last_name: Abood
- first_name: Gabriela
full_name: Brailoiu, Gabriela
last_name: Brailoiu
citation:
ama: Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by
bradykinin acting on nucleus ambiguus. Neuroscience. 2017;365:23-32. doi:10.1016/j.neuroscience.2017.09.034
apa: Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., &
Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on
nucleus ambiguus. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2017.09.034
chicago: Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey
Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by
Bradykinin Acting on Nucleus Ambiguus.” Neuroscience. Elsevier, 2017. https://doi.org/10.1016/j.neuroscience.2017.09.034.
ieee: E. Brǎiloiu et al., “Modulation of cardiac vagal tone by bradykinin
acting on nucleus ambiguus,” Neuroscience, vol. 365. Elsevier, pp. 23–32,
2017.
ista: Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017.
Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience.
365, 23–32.
mla: Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting
on Nucleus Ambiguus.” Neuroscience, vol. 365, Elsevier, 2017, pp. 23–32,
doi:10.1016/j.neuroscience.2017.09.034.
short: E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu,
Neuroscience 365 (2017) 23–32.
date_created: 2018-12-11T11:48:17Z
date_published: 2017-12-04T00:00:00Z
date_updated: 2023-09-27T12:26:59Z
day: '04'
department:
- _id: GaNo
doi: 10.1016/j.neuroscience.2017.09.034
external_id:
isi:
- '000415966200003'
pmid:
- '28951324'
intvolume: ' 365'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458
month: '12'
oa: 1
oa_version: Submitted Version
page: 23 - 32
pmid: 1
publication: Neuroscience
publication_identifier:
issn:
- '03064522'
publication_status: published
publisher: Elsevier
publist_id: '6911'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 365
year: '2017'
...
---
_id: '961'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes the first step in the emergence of multicellularity in
evolution, thereby allowing the differentiation of specialized cell types. In metazoan
development, cell-cell contact formation is thought to influence cell fate specification,
and cell fate specification has been implicated in cell-cell contact
formation. However, remarkably little is yet known about whether and how the
interaction and feedback between cell-cell contact formation and cell fate specification
affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and
mesendoderm cell fate specification during zebrafish gastrulation. We show that long
lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor
cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further
show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an
effective positive feedback loop between ppl cell-cell contact duration and cell fate
specification. Finally, by using a combination of theoretical modeling and experimentation,
we show that this feedback loop determines whether anterior axial mesendoderm cells
become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal
that the gene regulatory networks leading to cell fate diversification within the developing
embryo are controlled by the interdependent activities of cell-cell signaling and contact
formation.
acknowledgement: "Many people accompanied me during this trip: I would not have reached
my destination nor \r\nenjoyed the travelling without them. First of all, thanks
to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting
and incredibly competent people and thanks for \r\nall the good science I witnessed
\ and participated in. It has been a \r\nblast, an incredibly \r\nexciting
\ one! Thanks to JLo, for teaching me how to master my pipettes and
\ showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching
me basically everything \r\nabout zebrafish and being always there to advice,
\ sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the
critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing
kicker matches, and Keisuke, for showing me the light, and to the three of them
\r\ntogether for all the good laughs we\r\nhad. My start in Vienna would
\ have been a lot more \r\ndifficult without you guys. Also it would not
\ have been possible without Elena and Inês: \r\nthanks for helping setting
\ up this lab and for the dinners in Gugging. Thanks to Martin, for
\r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp,
\ for the interest and \r\nadvice, and to Michael, for the Viennise take on things.
Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend
in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel
for the enthusiasm and the neverending energy and for all your \r\nhelp over the
years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.
\ To Shayan, for being such a motivated student. To Matt, for helping
\ out\r\nwith coding \r\nand for finding punk solutions to data analysis problems.
Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla,
Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful
\ atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments
would have been much more difficult without your help. Special thanks to Katjia
\r\nfor setting up an amazing imaging facility and for building the best
\ team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith
all the late sortings and for helping with all \r\nthe technical problems. Thanks
to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald
Janovjak for being a present and helpful committee member over the years \r\nand
\ to Patrick Lemaire f\r\nor the helpful insight and extremely interesting
\ discussion we had \r\nabout the project. Also, this journey would not
\ have been the same without all the friends \r\nthat I met in Dresden and
then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne,
Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph,
\r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled
my days with \r\nfun and support. A special thank to my family, always close even
if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William,
\ e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri
di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe
crazy life of a scientist, the living apart for\r\nso long, never knowing when things
are going \r\nto happen. Thanks for being a great partner and my number one fan!"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
citation:
ama: 'Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish
gastrulation. 2017. doi:10.15479/AT:ISTA:th_825'
apa: 'Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop
during zebrafish gastrulation. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th_825'
chicago: 'Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017.
https://doi.org/10.15479/AT:ISTA:th_825.'
ieee: 'V. Barone, “Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.'
ista: 'Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation. Institute of Science and Technology Austria.'
mla: 'Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation. Institute of Science and Technology Austria,
2017, doi:10.15479/AT:ISTA:th_825.'
short: 'V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during
Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.'
date_created: 2018-12-11T11:49:25Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-27T14:16:45Z
day: '01'
ddc:
- '570'
- '590'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:th_825
file:
- access_level: closed
checksum: 242f88c87f2cf267bf05049fa26a687b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6205'
file_name: 2017_Barone_thesis_final.docx
file_size: 14497822
relation: source_file
- access_level: open_access
checksum: ba5b0613ed8bade73a409acdd880fb8a
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6206'
file_name: 2017_Barone_thesis_.pdf
file_size: 14995941
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6444'
pubrep_id: '825'
related_material:
record:
- id: '1100'
relation: part_of_dissertation
status: public
- id: '1537'
relation: part_of_dissertation
status: public
- id: '1912'
relation: part_of_dissertation
status: public
- id: '2926'
relation: part_of_dissertation
status: public
- id: '3246'
relation: part_of_dissertation
status: public
- id: '676'
relation: part_of_dissertation
status: public
- id: '735'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '734'
abstract:
- lang: eng
text: 'Social insect societies are long-standing models for understanding social
behaviour and evolution. Unlike other advanced biological societies (such as the
multicellular body), the component parts of social insect societies can be easily
deconstructed and manipulated. Recent methodological and theoretical innovations
have exploited this trait to address an expanded range of biological questions.
We illustrate the broadening range of biological insight coming from social insect
biology with four examples. These new frontiers promote open-minded, interdisciplinary
exploration of one of the richest and most complex of biological phenomena: sociality.'
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Kennedy, Patrick
last_name: Kennedy
- first_name: Gemma
full_name: Baron, Gemma
last_name: Baron
- first_name: Bitao
full_name: Qiu, Bitao
last_name: Qiu
- first_name: Dalial
full_name: Freitak, Dalial
last_name: Freitak
- first_name: Heikki
full_name: Helantera, Heikki
last_name: Helantera
- first_name: Edmund
full_name: Hunt, Edmund
last_name: Hunt
- first_name: Fabio
full_name: Manfredini, Fabio
last_name: Manfredini
- first_name: Thomas
full_name: O'Shea Wheller, Thomas
last_name: O'Shea Wheller
- first_name: Solenn
full_name: Patalano, Solenn
last_name: Patalano
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Takao
full_name: Sasaki, Takao
last_name: Sasaki
- first_name: Daisy
full_name: Taylor, Daisy
last_name: Taylor
- first_name: Christopher
full_name: Wyatt, Christopher
last_name: Wyatt
- first_name: Seirian
full_name: Sumner, Seirian
last_name: Sumner
citation:
ama: Kennedy P, Baron G, Qiu B, et al. Deconstructing superorganisms and societies
to address big questions in biology. Trends in Ecology and Evolution. 2017;32(11):861-872.
doi:10.1016/j.tree.2017.08.004
apa: Kennedy, P., Baron, G., Qiu, B., Freitak, D., Helantera, H., Hunt, E., … Sumner,
S. (2017). Deconstructing superorganisms and societies to address big questions
in biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2017.08.004
chicago: Kennedy, Patrick, Gemma Baron, Bitao Qiu, Dalial Freitak, Heikki Helantera,
Edmund Hunt, Fabio Manfredini, et al. “Deconstructing Superorganisms and Societies
to Address Big Questions in Biology.” Trends in Ecology and Evolution.
Cell Press, 2017. https://doi.org/10.1016/j.tree.2017.08.004.
ieee: P. Kennedy et al., “Deconstructing superorganisms and societies to
address big questions in biology,” Trends in Ecology and Evolution, vol.
32, no. 11. Cell Press, pp. 861–872, 2017.
ista: Kennedy P, Baron G, Qiu B, Freitak D, Helantera H, Hunt E, Manfredini F, O’Shea
Wheller T, Patalano S, Pull C, Sasaki T, Taylor D, Wyatt C, Sumner S. 2017. Deconstructing
superorganisms and societies to address big questions in biology. Trends in Ecology
and Evolution. 32(11), 861–872.
mla: Kennedy, Patrick, et al. “Deconstructing Superorganisms and Societies to Address
Big Questions in Biology.” Trends in Ecology and Evolution, vol. 32, no.
11, Cell Press, 2017, pp. 861–72, doi:10.1016/j.tree.2017.08.004.
short: P. Kennedy, G. Baron, B. Qiu, D. Freitak, H. Helantera, E. Hunt, F. Manfredini,
T. O’Shea Wheller, S. Patalano, C. Pull, T. Sasaki, D. Taylor, C. Wyatt, S. Sumner,
Trends in Ecology and Evolution 32 (2017) 861–872.
date_created: 2018-12-11T11:48:13Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-09-27T14:15:15Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1016/j.tree.2017.08.004
external_id:
isi:
- '000413231900011'
file:
- access_level: open_access
checksum: c8f49309ed9436201814fa7153d66a99
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:22:27Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7842'
file_name: 2017_TrendsEcology_Kennedy.pdf
file_size: 15018382
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 861 - 872
publication: Trends in Ecology and Evolution
publication_identifier:
issn:
- '01695347'
publication_status: published
publisher: Cell Press
publist_id: '6933'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Deconstructing superorganisms and societies to address big questions in biology
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2017'
...
---
_id: '819'
abstract:
- lang: eng
text: 'Contagious diseases must transmit from infectious to susceptible hosts in
order to reproduce. Whilst vectored pathogens can rely on intermediaries to find
new hosts for them, many infectious pathogens require close contact or direct
interaction between hosts for transmission. Hence, this means that conspecifics
are often the main source of infection for most animals and so, in theory, animals
should avoid conspecifics to reduce their risk of infection. Of course, in reality
animals must interact with one another, as a bare minimum, to mate. However, being
social provides many additional benefits and group living has become a taxonomically
diverse and widespread trait. How then do social animals overcome the issue of
increased disease? Over the last few decades, the social insects (ants, termites
and some bees and wasps) have become a model system for studying disease in social
animals. On paper, a social insect colony should be particularly susceptible to
disease, given that they often contain thousands of potential hosts that are closely
related and frequently interact, as well as exhibiting stable environmental conditions
that encourage microbial growth. Yet, disease outbreaks appear to be rare and
attempts to eradicate pest species using pathogens have failed time and again.
Evolutionary biologists investigating this observation have discovered that the
reduced disease susceptibility in social insects is, in part, due to collectively
performed disease defences of the workers. These defences act like a “social immune
system” for the colony, resulting in a per capita decrease in disease, termed
social immunity. Our understanding of social immunity, and its importance in relation
to the immunological defences of each insect, continues to grow, but there remain
many open questions. In this thesis I have studied disease defence in garden ants.
In the first data chapter, I use the invasive garden ant, Lasius neglectus, to
investigate how colonies mitigate lethal infections and prevent them from spreading
systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour
that uses endogenously produced acidic poison to kill diseased brood and to prevent
the pathogen from replicating. In the second experimental chapter, I continue
to study the use of poison in invasive garden ant colonies, finding that it is
sprayed prophylactically within the nest. However, this spraying has negative
effects on developing pupae when they have had their cocoons artificially removed.
Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon
spinning in this species. In the next experimental chapter, I investigated how
colony founding black garden ant queens (Lasius niger) prevent disease when a
co-foundress dies. I show that ant queens prophylactically perform undertaking
behaviours, similar to those performed by the workers in mature nests. When a
co-foundress was infected, these undertaking behaviours improved the survival
of the healthy queen. In the final data chapter, I explored how immunocompetence
(measured as antifungal activity) changes as incipient black garden ant colonies
grow and mature, from the solitary queen phase to colonies with several hundred
workers. Queen and worker antifungal activity varied throughout this time period,
but despite social immunity, did not decrease as colonies matured. In addition
to the above data chapters, this thesis includes two co-authored reviews. In the
first, we examine the state of the art in the field of social immunity and how
it might develop in the future. In the second, we identify several challenges
and open questions in the study of disease defence in animals. We highlight how
social insects offer a unique model to tackle some of these problems, as disease
defence can be studied from the cell to the society. '
acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely
spoilt to work in a lab with such good resources and I must thank the wonderful
Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help
and keeping the lab up and running. You guys will probably be the most missed once
I realise just how much work you have been saving me! For the same reason, I must
say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding
my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you
will be sorely missed now that I will have to take this task on myself. Of course,
I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing
and being a constant source of guidance and inspiration. You have given me the perfect
balance of independence and supervision. I cannot thank you enough for creating
such a great working environment and allowing me the freedom to follow my own research
questions. I have had so many exceptional opportunities – attending and presenting
at conferences all over the world, inviting me to write the ARE with you, going
to workshops in Panama and Switzerland, and even organising our own PhD course –
that I often think I must have had the best PhD in the world. You have taught me
so much and made me a scientist. I sincerely hope we get the chance to work together
again in the future. Thank you for everything. I must also thank my PhD Committee,
Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout
the duration of my PhD. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
citation:
ama: Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861
apa: Pull, C. (2017). Disease defence in garden ants. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861
chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science
and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861.
ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology
Austria, 2017.
ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology
Austria.
mla: Pull, Christopher. Disease Defence in Garden Ants. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.
short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-28T11:31:32Z
day: '26'
ddc:
- '576'
- '577'
- '578'
- '579'
- '590'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:th_861
file:
- access_level: closed
checksum: 4993cdd5382295758ecc3ecbd2a9aaff
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T07:53:04Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6199'
file_name: 2017_Thesis_Pull.docx
file_size: 18580400
relation: source_file
- access_level: open_access
checksum: ee2e3ebb5b53c154c866f5b052b25153
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T07:53:04Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6200'
file_name: 2017_Thesis_Pull.pdf
file_size: 14400681
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '122'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6830'
pubrep_id: '861'
related_material:
record:
- id: '616'
relation: part_of_dissertation
status: public
- id: '806'
relation: part_of_dissertation
status: public
- id: '734'
relation: part_of_dissertation
status: public
- id: '732'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Disease defence in garden ants
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '732'
abstract:
- lang: eng
text: 'Background: Social insects form densely crowded societies in environments
with high pathogen loads, but have evolved collective defences that mitigate the
impact of disease. However, colony-founding queens lack this protection and suffer
high rates of mortality. The impact of pathogens may be exacerbated in species
where queens found colonies together, as healthy individuals may contract pathogens
from infectious co-founders. Therefore, we tested whether ant queens avoid founding
colonies with pathogen-exposed conspecifics and how they might limit disease transmission
from infectious individuals. Results: Using Lasius Niger queens and a naturally
infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally
likely to found colonies with another pathogen-exposed or sham-treated queen.
However, when one queen died, the surviving individual performed biting, burial
and removal of the corpse. These undertaking behaviours were performed prophylactically,
i.e. targeted equally towards non-infected and infected corpses, as well as carried
out before infected corpses became infectious. Biting and burial reduced the risk
of the queens contracting and dying from disease from an infectious corpse of
a dead co-foundress. Conclusions: We show that co-founding ant queens express
undertaking behaviours that, in mature colonies, are performed exclusively by
workers. Such infection avoidance behaviours act before the queens can contract
the disease and will therefore improve the overall chance of colony founding success
in ant queens.'
article_number: '219'
article_processing_charge: Yes
article_type: original
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Cremer S. Co-founding ant queens prevent disease by performing prophylactic
undertaking behaviour. BMC Evolutionary Biology. 2017;17(1). doi:10.1186/s12862-017-1062-4
apa: Pull, C., & Cremer, S. (2017). Co-founding ant queens prevent disease by
performing prophylactic undertaking behaviour. BMC Evolutionary Biology.
BioMed Central. https://doi.org/10.1186/s12862-017-1062-4
chicago: Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease
by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology.
BioMed Central, 2017. https://doi.org/10.1186/s12862-017-1062-4.
ieee: C. Pull and S. Cremer, “Co-founding ant queens prevent disease by performing
prophylactic undertaking behaviour,” BMC Evolutionary Biology, vol. 17,
no. 1. BioMed Central, 2017.
ista: Pull C, Cremer S. 2017. Co-founding ant queens prevent disease by performing
prophylactic undertaking behaviour. BMC Evolutionary Biology. 17(1), 219.
mla: Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease
by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology,
vol. 17, no. 1, 219, BioMed Central, 2017, doi:10.1186/s12862-017-1062-4.
short: C. Pull, S. Cremer, BMC Evolutionary Biology 17 (2017).
date_created: 2018-12-11T11:48:12Z
date_published: 2017-10-13T00:00:00Z
date_updated: 2023-09-28T11:31:32Z
day: '13'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1186/s12862-017-1062-4
ec_funded: 1
external_id:
isi:
- '000412816800001'
file:
- access_level: open_access
checksum: 3e24a2cfd48f49f7b3643d08d30fb480
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:18Z
date_updated: 2020-07-14T12:47:55Z
file_id: '5271'
file_name: IST-2017-882-v1+1_12862_2017_Article_1062.pdf
file_size: 949857
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: BMC Evolutionary Biology
publication_identifier:
issn:
- '14712148'
publication_status: published
publisher: BioMed Central
publist_id: '6937'
pubrep_id: '882'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Co-founding ant queens prevent disease by performing prophylactic undertaking
behaviour
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: '726'
abstract:
- lang: eng
text: The morphogenesis of branched organs remains a subject of abiding interest.
Although much is known about the underlying signaling pathways, it remains unclear
how macroscopic features of branched organs, including their size, network topology,
and spatial patterning, are encoded. Here, we show that, in mouse mammary gland,
kidney, and human prostate, these features can be explained quantitatively within
a single unifying framework of branching and annihilating random walks. Based
on quantitative analyses of large-scale organ reconstructions and proliferation
kinetics measurements, we propose that morphogenesis follows from the proliferative
activity of equipotent tips that stochastically branch and randomly explore their
environment but compete neutrally for space, becoming proliferatively inactive
when in proximity with neighboring ducts. These results show that complex branched
epithelial structures develop as a self-organized process, reliant upon a strikingly
simple but generic rule, without recourse to a rigid and deterministic sequence
of genetically programmed events.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Colinda
full_name: Scheele, Colinda
last_name: Scheele
- first_name: Mohammad
full_name: Moad, Mohammad
last_name: Moad
- first_name: Nicholas
full_name: Drogo, Nicholas
last_name: Drogo
- first_name: Rakesh
full_name: Heer, Rakesh
last_name: Heer
- first_name: Rosemary
full_name: Sampogna, Rosemary
last_name: Sampogna
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
citation:
ama: Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis.
Cell. 2017;171(1):242-255. doi:10.1016/j.cell.2017.08.026
apa: Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., …
Simons, B. (2017). A unifying theory of branching morphogenesis. Cell.
Cell Press. https://doi.org/10.1016/j.cell.2017.08.026
chicago: Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh
Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory
of Branching Morphogenesis.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.08.026.
ieee: E. B. Hannezo et al., “A unifying theory of branching morphogenesis,”
Cell, vol. 171, no. 1. Cell Press, pp. 242–255, 2017.
ista: Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J,
Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255.
mla: Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.”
Cell, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:10.1016/j.cell.2017.08.026.
short: E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van
Rheenen, B. Simons, Cell 171 (2017) 242–255.
date_created: 2018-12-11T11:48:10Z
date_published: 2017-09-21T00:00:00Z
date_updated: 2023-09-28T11:34:17Z
day: '21'
ddc:
- '539'
department:
- _id: EdHa
doi: 10.1016/j.cell.2017.08.026
external_id:
isi:
- '000411331800024'
file:
- access_level: open_access
checksum: 7a036d93a9e2e597af9bb504d6133aca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:17Z
date_updated: 2020-07-14T12:47:55Z
file_id: '4870'
file_name: IST-2017-883-v1+1_PIIS0092867417309510.pdf
file_size: 12670204
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 171'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 242 - 255
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '6952'
pubrep_id: '883'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A unifying theory of branching morphogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 171
year: '2017'
...
---
_id: '548'
abstract:
- lang: eng
text: In this work maximum entropy distributions in the space of steady states of
metabolic networks are considered upon constraining the first and second moments
of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux
distributions, emerges upon considering control on the average growth (optimization)
and its fluctuations (heterogeneity). This is applied to the carbon catabolic
core of Escherichia coli where it quantifies the metabolic activity of slow growing
phenotypes and it provides a quantitative map with metabolic fluxes, opening the
possibility to detect coexistence from flux data. A preliminary analysis on data
for E. coli cultures in standard conditions shows degeneracy for the inferred
parameters that extend in the coexistence region.
alternative_title:
- Rapid Communications
article_number: '060401'
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. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
2017;96(6). doi:10.1103/PhysRevE.96.060401
apa: De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401
chicago: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by
Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical
Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.
ieee: D. De Martino, “Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes,” Physical Review E,
vol. 96, no. 6. American Physical Society, 2017.
ista: De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining
growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6),
060401.
mla: De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining
Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E,
vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401.
short: D. De Martino, Physical Review E 96 (2017).
date_created: 2018-12-11T11:47:06Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2023-10-10T13:29:38Z
day: '21'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.96.060401
ec_funded: 1
intvolume: ' 96'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1707.00320
month: '12'
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
publication_identifier:
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
publist_id: '7266'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum entropy modeling of metabolic networks by constraining growth-rate
moments predicts coexistence of phenotypes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '673'
abstract:
- lang: eng
text: We present a numerical study of wavy supercritical cylindrical Couette flow
between counter-rotating cylinders in which the wavy pattern propagates either
prograde with the inner cylinder or retrograde opposite the rotation of the inner
cylinder. The wave propagation reversals from prograde to retrograde and vice
versa occur at distinct values of the inner cylinder Reynolds number when the
associated frequency of the wavy instability vanishes. The reversal occurs for
both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation
reversal only occurs for sufficiently strong counter-rotation. The flow pattern
reversal appears to be intrinsic in the system as either periodic boundary conditions
or fixed end wall boundary conditions for different system sizes always result
in the wave propagation reversal. We present a detailed bifurcation sequence and
parameter space diagram with respect to retrograde behavior of wavy flows. The
retrograde propagation of the instability occurs when the inner Reynolds number
is about two times the outer Reynolds number. The mechanism for the retrograde
propagation is associated with the inviscidly unstable region near the inner cylinder
and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal
behavior, global mean angular velocity, and torque of the flow with the wavy pattern
are explored.
article_number: '053103'
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Richard
full_name: Lueptow, Richard
last_name: Lueptow
citation:
ama: Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide
gap counter rotating cylindrical Couette flow. Physical Review E. 2017;95(5).
doi:10.1103/PhysRevE.95.053103
apa: Altmeyer, S., & Lueptow, R. (2017). Wave propagation reversal for wavy
vortices in wide gap counter rotating cylindrical Couette flow. Physical Review
E. American Physical Society. https://doi.org/10.1103/PhysRevE.95.053103
chicago: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for
Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical
Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.95.053103.
ieee: S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in
wide gap counter rotating cylindrical Couette flow,” Physical Review E,
vol. 95, no. 5. American Physical Society, 2017.
ista: Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in
wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5),
053103.
mla: Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy
Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review
E, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:10.1103/PhysRevE.95.053103.
short: S. Altmeyer, R. Lueptow, Physical Review E 95 (2017).
date_created: 2018-12-11T11:47:50Z
date_published: 2017-05-10T00:00:00Z
date_updated: 2023-10-10T13:30:03Z
day: '10'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.95.053103
intvolume: ' 95'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/physics/0505164.pdf
month: '05'
oa: 1
oa_version: Submitted Version
publication: Physical Review E
publication_identifier:
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
publist_id: '7049'
scopus_import: '1'
status: public
title: Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical
Couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...
---
_id: '447'
abstract:
- lang: eng
text: We consider last passage percolation (LPP) models with exponentially distributed
random variables, which are linked to the totally asymmetric simple exclusion
process (TASEP). The competition interface for LPP was introduced and studied
in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process
had a rarefaction fan. Here we consider situations with a shock and determine
the law of the fluctuations of the competition interface around its deter- ministic
law of large number position. We also study the multipoint distribution of the
LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015).
article_processing_charge: No
article_type: original
author:
- first_name: Patrik
full_name: Ferrari, Patrik
last_name: Ferrari
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Ferrari P, Nejjar P. Fluctuations of the competition interface in presence
of shocks. Revista Latino-Americana de Probabilidade e Estatística. 2017;9:299-325.
doi:10.30757/ALEA.v14-17
apa: Ferrari, P., & Nejjar, P. (2017). Fluctuations of the competition interface
in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística.
Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v14-17
chicago: Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface
in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística.
Instituto Nacional de Matematica Pura e Aplicada, 2017. https://doi.org/10.30757/ALEA.v14-17.
ieee: P. Ferrari and P. Nejjar, “Fluctuations of the competition interface in presence
of shocks,” Revista Latino-Americana de Probabilidade e Estatística, vol.
9. Instituto Nacional de Matematica Pura e Aplicada, pp. 299–325, 2017.
ista: Ferrari P, Nejjar P. 2017. Fluctuations of the competition interface in presence
of shocks. Revista Latino-Americana de Probabilidade e Estatística. 9, 299–325.
mla: Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface
in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística,
vol. 9, Instituto Nacional de Matematica Pura e Aplicada, 2017, pp. 299–325, doi:10.30757/ALEA.v14-17.
short: P. Ferrari, P. Nejjar, Revista Latino-Americana de Probabilidade e Estatística
9 (2017) 299–325.
date_created: 2018-12-11T11:46:31Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2023-10-10T13:10:32Z
day: '23'
department:
- _id: LaEr
- _id: JaMa
doi: 10.30757/ALEA.v14-17
ec_funded: 1
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://alea.impa.br/articles/v14/14-17.pdf
month: '03'
oa: 1
oa_version: Submitted Version
page: 299 - 325
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Revista Latino-Americana de Probabilidade e Estatística
publication_status: published
publisher: Instituto Nacional de Matematica Pura e Aplicada
publist_id: '7376'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuations of the competition interface in presence of shocks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '557'
abstract:
- lang: eng
text: PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful
therapeutic for the rescue and regeneration of these cells after optic nerve damage.
However, early after damage, RGCs undergo atrophic changes, including gene silencing.
It is not known if these changes will deleteriously affect transduction and transgene
expression, or if the therapeutic protein can influence reactivation of the endogenous
genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter,
and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant
blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At
times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received
an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful
transduction was monitored by expression of the tdTomato reporter. Immunostaining
was used to localize tdTomato expression in select cell types. RESULTS. Successful
transduction of RGCs was achieved at all time points after ONC using AAV2 expressing
Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter.
ONC promoted an increase in the transduction of cell types in the inner nuclear
layer, including Müller cells and rod bipolar neurons. There was minimal evidence
of transduction of amacrine cells and astrocytes in the inner retina or optic
nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous
genes can be subsequently activated. Optic nerve damage may change retinal architecture
to allow greater penetration of an AAV2 virus to transduce several additional
cell types in the inner nuclear layer.
article_processing_charge: No
author:
- first_name: Robert
full_name: Nickells, Robert
last_name: Nickells
- first_name: Heather
full_name: Schmitt, Heather
last_name: Schmitt
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Cassandra
full_name: Schlamp, Cassandra
last_name: Schlamp
citation:
ama: Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the
mouse retina after optic nerve injury. Investigative Ophthalmology and Visual
Science. 2017;58(14):6091-6104. doi:10.1167/iovs.17-22634
apa: Nickells, R., Schmitt, H., Maes, M. E., & Schlamp, C. (2017). AAV2 mediated
transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology
and Visual Science. Association for Research in Vision and Ophthalmology.
https://doi.org/10.1167/iovs.17-22634
chicago: Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp.
“AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative
Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology,
2017. https://doi.org/10.1167/iovs.17-22634.
ieee: R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction
of the mouse retina after optic nerve injury,” Investigative Ophthalmology
and Visual Science, vol. 58, no. 14. Association for Research in Vision and
Ophthalmology, pp. 6091–6104, 2017.
ista: Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction
of the mouse retina after optic nerve injury. Investigative Ophthalmology and
Visual Science. 58(14), 6091–6104.
mla: Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after
Optic Nerve Injury.” Investigative Ophthalmology and Visual Science, vol.
58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104,
doi:10.1167/iovs.17-22634.
short: R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology
and Visual Science 58 (2017) 6091–6104.
date_created: 2018-12-11T11:47:10Z
date_published: 2017-12-14T00:00:00Z
date_updated: 2023-10-10T14:06:18Z
day: '14'
ddc:
- '576'
department:
- _id: SaSi
doi: 10.1167/iovs.17-22634
file:
- access_level: open_access
checksum: d7a7b6f1fa9211a04e5e65634a0265d9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:53Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5311'
file_name: IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf
file_size: 2955559
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
intvolume: ' 58'
issue: '14'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 6091 - 6104
publication: Investigative Ophthalmology and Visual Science
publication_identifier:
issn:
- '01460404'
publication_status: published
publisher: Association for Research in Vision and Ophthalmology
publist_id: '7254'
pubrep_id: '920'
quality_controlled: '1'
scopus_import: '1'
status: public
title: AAV2 mediated transduction of the mouse retina after optic nerve injury
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '997'
abstract:
- lang: eng
text: Recently it was shown that molecules rotating in superfluid helium can be
described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301
(2017)). Here we demonstrate that in the experimentally realized regime the angulon
can be seen as a point charge on a 2-sphere interacting with a gauge field of
a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields
of the angulon problem emerge in the real coordinate space, as opposed to the
momentum space or some effective parameter space. Furthermore, we find a topological
transition associated with making the monopole abelian, which takes place in the
vicinity of the previously reported angulon instabilities. These results pave
the way for studying topological phenomena in experiments on molecules trapped
in superfluid helium nanodroplets, as well as on other realizations of orbital
impurity problems.
article_number: '235301'
article_processing_charge: No
article_type: original
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Deuchert A, Lemeshko M. Emergence of non-abelian magnetic monopoles
in a quantum impurity problem. Physical Review Letters. 2017;119(23). doi:10.1103/PhysRevLett.119.235301
apa: Yakaboylu, E., Deuchert, A., & Lemeshko, M. (2017). Emergence of non-abelian
magnetic monopoles in a quantum impurity problem. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.119.235301
chicago: Yakaboylu, Enderalp, Andreas Deuchert, and Mikhail Lemeshko. “Emergence
of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.235301.
ieee: E. Yakaboylu, A. Deuchert, and M. Lemeshko, “Emergence of non-abelian magnetic
monopoles in a quantum impurity problem,” Physical Review Letters, vol.
119, no. 23. American Physical Society, 2017.
ista: Yakaboylu E, Deuchert A, Lemeshko M. 2017. Emergence of non-abelian magnetic
monopoles in a quantum impurity problem. Physical Review Letters. 119(23), 235301.
mla: Yakaboylu, Enderalp, et al. “Emergence of Non-Abelian Magnetic Monopoles in
a Quantum Impurity Problem.” Physical Review Letters, vol. 119, no. 23,
235301, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.235301.
short: E. Yakaboylu, A. Deuchert, M. Lemeshko, Physical Review Letters 119 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2023-10-10T13:31:54Z
day: '06'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevLett.119.235301
ec_funded: 1
external_id:
arxiv:
- '1705.05162'
isi:
- '000417132100007'
intvolume: ' 119'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05162
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
publist_id: '6401'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of non-abelian magnetic monopoles in a quantum impurity problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '911'
abstract:
- lang: eng
text: We develop a probabilistic technique for colorizing grayscale natural images.
In light of the intrinsic uncertainty of this task, the proposed probabilistic
framework has numerous desirable properties. In particular, our model is able
to produce multiple plausible and vivid colorizations for a given grayscale image
and is one of the first colorization models to provide a proper stochastic sampling
scheme. Moreover, our training procedure is supported by a rigorous theoretical
framework that does not require any ad hoc heuristics and allows for efficient
modeling and learning of the joint pixel color distribution.We demonstrate strong
quantitative and qualitative experimental results on the CIFAR-10 dataset and
the challenging ILSVRC 2012 dataset.
article_processing_charge: No
author:
- first_name: Amélie
full_name: Royer, Amélie
id: 3811D890-F248-11E8-B48F-1D18A9856A87
last_name: Royer
orcid: 0000-0002-8407-0705
- 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: 'Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA
Press; 2017:85.1-85.12. doi:10.5244/c.31.85'
apa: 'Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization
(p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London,
United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85'
chicago: Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic
Image Colorization,” 85.1-85.12. BMVA Press, 2017. https://doi.org/10.5244/c.31.85.
ieee: 'A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,”
presented at the BMVC: British Machine Vision Conference, London, United Kingdom,
2017, p. 85.1-85.12.'
ista: 'Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization.
BMVC: British Machine Vision Conference, 85.1-85.12.'
mla: Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press,
2017, p. 85.1-85.12, doi:10.5244/c.31.85.
short: A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.
conference:
end_date: 2017-09-07
location: London, United Kingdom
name: 'BMVC: British Machine Vision Conference'
start_date: 2017-09-04
date_created: 2018-12-11T11:49:09Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-10-16T10:04:02Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.5244/c.31.85
ec_funded: 1
external_id:
arxiv:
- '1705.04258'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T07:14:33Z
date_updated: 2020-08-10T07:14:33Z
file_id: '8224'
file_name: 2017_BMVC_Royer.pdf
file_size: 1625363
relation: main_file
success: 1
file_date_updated: 2020-08-10T07:14:33Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 85.1-85.12
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
eisbn:
- 190172560X
publication_status: published
publisher: BMVA Press
publist_id: '6532'
quality_controlled: '1'
related_material:
record:
- id: '8390'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Probabilistic image colorization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '627'
abstract:
- lang: eng
text: Beige adipocytes are a new type of recruitable brownish adipocytes, with highly
mitochondrial membrane uncoupling protein 1 expression and thermogenesis. Beige
adipocytes were found among white adipocytes, especially in subcutaneous white
adipose tissue (sWAT). Therefore, beige adipocytes may be involved in the regulation
of energy metabolism and fat deposition. Transient receptor potential melastatin
8 (TRPM8), a Ca2+-permeable non-selective cation channel, plays vital roles in
the regulation of various cellular functions. It has been reported that TRPM8
activation enhanced the thermogenic function of brown adiposytes. However, the
involvement of TRPM8 in the thermogenic function of WAT remains unexplored. Our
data revealed that TRPM8 was expressed in mouse white adipocytes at mRNA, protein
and functional levels. The mRNA expression of Trpm8 was significantly increased
in the differentiated white adipocytes than pre-adipocytes. Moreover, activation
of TRPM8 by menthol enhanced the expression of thermogenic genes in cultured white
aidpocytes. And menthol-induced increases of the thermogenic genes in white adipocytes
was inhibited by either KT5720 (a protein kinase A inhibitor) or BAPTA-AM. In
addition, high fat diet (HFD)-induced obesity in mice was significantly recovered
by co-treatment with menthol. Dietary menthol enhanced WAT "browning"
and improved glucose metabolism in HFD-induced obesity mice as well. Therefore,
we concluded that TRPM8 might be involved in WAT "browning" by increasing
the expression levels of genes related to thermogenesis and energy metabolism.
And dietary menthol could be a novel approach for combating human obesity and
related metabolic diseases.
article_processing_charge: No
author:
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
- first_name: Ming-Zhu
full_name: Zhai, Ming-Zhu
id: 34009CFA-F248-11E8-B48F-1D18A9856A87
last_name: Zhai
- first_name: Dong
full_name: Yan, Dong
last_name: Yan
- first_name: Da
full_name: Li, Da
last_name: Li
- first_name: Chen
full_name: Li, Chen
last_name: Li
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Lizu
full_name: Xiao, Lizu
last_name: Xiao
- first_name: Donglin
full_name: Xiong, Donglin
last_name: Xiong
- first_name: Qiwen
full_name: Deng, Qiwen
last_name: Deng
- first_name: Wuping
full_name: Sun, Wuping
last_name: Sun
citation:
ama: Jiang C, Zhai M-Z, Yan D, et al. Dietary menthol-induced TRPM8 activation enhances
WAT “browning” and ameliorates diet-induced obesity. Oncotarget. 2017;8(43):75114-75126.
doi:10.18632/oncotarget.20540
apa: Jiang, C., Zhai, M.-Z., Yan, D., Li, D., Li, C., Zhang, Y., … Sun, W. (2017).
Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates
diet-induced obesity. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20540
chicago: Jiang, Changyu, Ming-Zhu Zhai, Dong Yan, Da Li, Chen Li, Yonghong Zhang,
Lizu Xiao, Donglin Xiong, Qiwen Deng, and Wuping Sun. “Dietary Menthol-Induced
TRPM8 Activation Enhances WAT ‘Browning’ and Ameliorates Diet-Induced Obesity.”
Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20540.
ieee: C. Jiang et al., “Dietary menthol-induced TRPM8 activation enhances
WAT ‘browning’ and ameliorates diet-induced obesity,” Oncotarget, vol.
8, no. 43. Impact Journals, pp. 75114–75126, 2017.
ista: Jiang C, Zhai M-Z, Yan D, Li D, Li C, Zhang Y, Xiao L, Xiong D, Deng Q, Sun
W. 2017. Dietary menthol-induced TRPM8 activation enhances WAT “browning” and
ameliorates diet-induced obesity. Oncotarget. 8(43), 75114–75126.
mla: Jiang, Changyu, et al. “Dietary Menthol-Induced TRPM8 Activation Enhances WAT
‘Browning’ and Ameliorates Diet-Induced Obesity.” Oncotarget, vol. 8, no.
43, Impact Journals, 2017, pp. 75114–26, doi:10.18632/oncotarget.20540.
short: C. Jiang, M.-Z. Zhai, D. Yan, D. Li, C. Li, Y. Zhang, L. Xiao, D. Xiong,
Q. Deng, W. Sun, Oncotarget 8 (2017) 75114–75126.
date_created: 2018-12-11T11:47:34Z
date_published: 2017-08-24T00:00:00Z
date_updated: 2023-10-17T08:56:37Z
day: '24'
ddc:
- '571'
department:
- _id: RySh
doi: 10.18632/oncotarget.20540
file:
- access_level: open_access
checksum: 2219e5348bbfe1aac2725aa620c33280
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:15Z
date_updated: 2020-07-14T12:47:26Z
file_id: '5201'
file_name: IST-2017-907-v1+1_20540-294640-4-PB.pdf
file_size: 6101606
relation: main_file
file_date_updated: 2020-07-14T12:47:26Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '43'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 75114 - 75126
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
publist_id: '7167'
pubrep_id: '907'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates
diet-induced obesity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '1007'
abstract:
- lang: eng
text: 'A nonlinear system possesses an invariance with respect to a set of transformations
if its output dynamics remain invariant when transforming the input, and adjusting
the initial condition accordingly. Most research has focused on invariances with
respect to time-independent pointwise transformations like translational-invariance
(u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0).
In this article, we introduce the concept of s0-invariances with respect to continuous
input transformations exponentially growing/decaying over time. We show that s0-invariant
systems not only encompass linear time-invariant (LTI) systems with transfer functions
having an irreducible zero at s0 in R, but also that the input/output relationship
of nonlinear s0-invariant systems possesses properties well known from their linear
counterparts. Furthermore, we extend the concept of s0-invariances to second-
and higher-order s0-invariances, corresponding to invariances with respect to
transformations of the time-derivatives of the input, and encompassing LTI systems
with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant
systems realize – under mild conditions – nth-order nonlinear differential operators:
when excited by an input of a characteristic functional form, the system’s output
converges to a constant value only depending on the nth (nonlinear) derivative
of the input.'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Eduardo
full_name: Sontag, Eduardo
last_name: Sontag
citation:
ama: Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica.
2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030
apa: Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances.
Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030
chicago: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input
Invariances.” Automatica. International Federation of Automatic Control,
2017. https://doi.org/10.1016/j.automatica.2017.03.030.
ieee: M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,”
Automatica, vol. 81C. International Federation of Automatic Control, pp.
46–55, 2017.
ista: Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances.
Automatica. 81C, 46–55.
mla: Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.”
Automatica, vol. 81C, International Federation of Automatic Control, 2017,
pp. 46–55, doi:10.1016/j.automatica.2017.03.030.
short: M. Lang, E. Sontag, Automatica 81C (2017) 46–55.
date_created: 2018-12-11T11:49:39Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-10-17T08:51:18Z
day: '01'
ddc:
- '000'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.automatica.2017.03.030
ec_funded: 1
external_id:
isi:
- '000403513900006'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:29Z
date_updated: 2018-12-12T10:11:29Z
file_id: '4884'
file_name: IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf
file_size: 1401954
relation: main_file
file_date_updated: 2018-12-12T10:11:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 46 - 55
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Automatica
publication_identifier:
issn:
- 0005-1098
publication_status: published
publisher: International Federation of Automatic Control
publist_id: '6391'
pubrep_id: '813'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zeros of nonlinear systems with input invariances
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81C
year: '2017'
...
---
_id: '1108'
abstract:
- lang: eng
text: In this work we study the learnability of stochastic processes with respect
to the conditional risk, i.e. the existence of a learning algorithm that improves
its next-step performance with the amount of observed data. We introduce a notion
of pairwise discrepancy between conditional distributions at different times steps
and show how certain properties of these discrepancies can be used to construct
a successful learning algorithm. Our main results are two theorems that establish
criteria for learnability for many classes of stochastic processes, including
all special cases studied previously in the literature.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alexander
full_name: Zimin, Alexander
id: 37099E9C-F248-11E8-B48F-1D18A9856A87
last_name: Zimin
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Zimin A, Lampert C. Learning theory for conditional risk minimization. In:
Vol 54. ML Research Press; 2017:213-222.'
apa: 'Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk
minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence
and Statistics, Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional
Risk Minimization,” 54:213–22. ML Research Press, 2017.
ieee: 'A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,”
presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale,
FL, United States, 2017, vol. 54, pp. 213–222.'
ista: 'Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization.
AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.'
mla: Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional
Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22.
short: A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2018-12-11T11:50:11Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-10-17T10:01:12Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
isi:
- '000509368500024'
intvolume: ' 54'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf
month: '04'
oa: 1
oa_version: Submitted Version
page: 213 - 222
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: ML Research Press
publist_id: '6261'
quality_controlled: '1'
status: public
title: Learning theory for conditional risk minimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '909'
abstract:
- lang: eng
text: We study the lengths of curves passing through a fixed number of points on
the boundary of a convex shape in the plane. We show that, for any convex shape
K, there exist four points on the boundary of K such that the length of any curve
passing through these points is at least half of the perimeter of K. It is also
shown that the same statement does not remain valid with the additional constraint
that the points are extreme points of K. Moreover, the factor ½ cannot
be achieved with any fixed number of extreme points. We conclude the paper with
a few other inequalities related to the perimeter of a convex shape.
article_processing_charge: No
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Vladislav
full_name: Vysotsky, Vladislav
last_name: Vysotsky
citation:
ama: Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points
of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596.
doi:10.4169/amer.math.monthly.124.7.588
apa: Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through
boundary points of a planar convex shape. The American Mathematical Monthly.
Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588
chicago: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing
through Boundary Points of a Planar Convex Shape.” The American Mathematical
Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588.
ieee: A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary
points of a planar convex shape,” The American Mathematical Monthly, vol.
124, no. 7. Mathematical Association of America, pp. 588–596, 2017.
ista: Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary
points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.
mla: Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing
through Boundary Points of a Planar Convex Shape.” The American Mathematical
Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96,
doi:10.4169/amer.math.monthly.124.7.588.
short: A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.
date_created: 2018-12-11T11:49:09Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-17T11:24:57Z
day: '01'
department:
- _id: HeEd
doi: 10.4169/amer.math.monthly.124.7.588
ec_funded: 1
external_id:
arxiv:
- '1605.07997'
isi:
- '000413947300002'
intvolume: ' 124'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07997
month: '01'
oa: 1
oa_version: Submitted Version
page: 588 - 596
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: The American Mathematical Monthly
publication_identifier:
issn:
- '00029890'
publication_status: published
publisher: Mathematical Association of America
publist_id: '6534'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the lengths of curves passing through boundary points of a planar convex
shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2017'
...
---
_id: '431'
abstract:
- lang: eng
text: 'Parallel implementations of stochastic gradient descent (SGD) have received
significant research attention, thanks to its excellent scalability properties.
A fundamental barrier when parallelizing SGD is the high bandwidth cost of communicating
gradient updates between nodes; consequently, several lossy compresion heuristics
have been proposed, by which nodes only communicate quantized gradients. Although
effective in practice, these heuristics do not always converge. In this paper,
we propose Quantized SGD (QSGD), a family of compression schemes with convergence
guarantees and good practical performance. QSGD allows the user to smoothly trade
off communication bandwidth and convergence time: nodes can adjust the number
of bits sent per iteration, at the cost of possibly higher variance. We show that
this trade-off is inherent, in the sense that improving it past some threshold
would violate information-theoretic lower bounds. QSGD guarantees convergence
for convex and non-convex objectives, under asynchrony, and can be extended to
stochastic variance-reduced techniques. When applied to training deep neural networks
for image classification and automated speech recognition, QSGD leads to significant
reductions in end-to-end training time. For instance, on 16GPUs, we can train
the ResNet-152 network to full accuracy on ImageNet 1.8 × faster than the full-precision
variant. '
alternative_title:
- Advances in Neural Information Processing Systems
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: Demjan
full_name: Grubic, Demjan
last_name: Grubic
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Ryota
full_name: Tomioka, Ryota
last_name: Tomioka
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. QSGD: Communication-efficient
SGD via gradient quantization and encoding. In: Vol 2017. Neural Information Processing
Systems Foundation; 2017:1710-1721.'
apa: 'Alistarh, D.-A., Grubic, D., Li, J., Tomioka, R., & Vojnović, M. (2017).
QSGD: Communication-efficient SGD via gradient quantization and encoding (Vol.
2017, pp. 1710–1721). Presented at the NIPS: Neural Information Processing System,
Long Beach, CA, United States: Neural Information Processing Systems Foundation.'
chicago: 'Alistarh, Dan-Adrian, Demjan Grubic, Jerry Li, Ryota Tomioka, and Milan
Vojnović. “QSGD: Communication-Efficient SGD via Gradient Quantization and Encoding,”
2017:1710–21. Neural Information Processing Systems Foundation, 2017.'
ieee: 'D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, and M. Vojnović, “QSGD: Communication-efficient
SGD via gradient quantization and encoding,” presented at the NIPS: Neural Information
Processing System, Long Beach, CA, United States, 2017, vol. 2017, pp. 1710–1721.'
ista: 'Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. 2017. QSGD: Communication-efficient
SGD via gradient quantization and encoding. NIPS: Neural Information Processing
System, Advances in Neural Information Processing Systems, vol. 2017, 1710–1721.'
mla: 'Alistarh, Dan-Adrian, et al. QSGD: Communication-Efficient SGD via Gradient
Quantization and Encoding. Vol. 2017, Neural Information Processing Systems
Foundation, 2017, pp. 1710–21.'
short: D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, M. Vojnović, in:, Neural Information
Processing Systems Foundation, 2017, pp. 1710–1721.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NIPS: Neural Information Processing System'
start_date: 2017-12-04
date_created: 2018-12-11T11:46:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-17T11:48:03Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1610.02132'
intvolume: ' 2017'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02132
month: '01'
oa: 1
oa_version: Submitted Version
page: 1710-1721
publication_identifier:
issn:
- '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '7392'
quality_controlled: '1'
status: public
title: 'QSGD: Communication-efficient SGD via gradient quantization and encoding'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2017
year: '2017'
...
---
_id: '549'
abstract:
- lang: eng
text: Model checking is usually based on a comprehensive traversal of the state
space. Causality-based model checking is a radically different approach that instead
analyzes the cause-effect relationships in a program. We give an overview on a
new class of model checking algorithms that capture the causal relationships in
a special data structure called concurrent traces. Concurrent traces identify
key events in an execution history and link them through their cause-effect relationships.
The model checker builds a tableau of concurrent traces, where the case splits
represent different causal explanations of a hypothetical error. Causality-based
model checking has been implemented in the ARCTOR tool, and applied to previously
intractable multi-threaded benchmarks.
alternative_title:
- EPTCS
article_processing_charge: No
author:
- first_name: Bernd
full_name: Finkbeiner, Bernd
last_name: Finkbeiner
- first_name: Andrey
full_name: Kupriyanov, Andrey
id: 2C311BF8-F248-11E8-B48F-1D18A9856A87
last_name: Kupriyanov
citation:
ama: 'Finkbeiner B, Kupriyanov A. Causality-based model checking. In: Electronic
Proceedings in Theoretical Computer Science. Vol 259. Open Publishing Association;
2017:31-38. doi:10.4204/EPTCS.259.3'
apa: 'Finkbeiner, B., & Kupriyanov, A. (2017). Causality-based model checking.
In Electronic Proceedings in Theoretical Computer Science (Vol. 259, pp.
31–38). Uppsala, Sweden: Open Publishing Association. https://doi.org/10.4204/EPTCS.259.3'
chicago: Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.”
In Electronic Proceedings in Theoretical Computer Science, 259:31–38. Open
Publishing Association, 2017. https://doi.org/10.4204/EPTCS.259.3.
ieee: B. Finkbeiner and A. Kupriyanov, “Causality-based model checking,” in Electronic
Proceedings in Theoretical Computer Science, Uppsala, Sweden, 2017, vol. 259,
pp. 31–38.
ista: 'Finkbeiner B, Kupriyanov A. 2017. Causality-based model checking. Electronic
Proceedings in Theoretical Computer Science. CREST: Causal Reasoning for Embedded
and Safety-Critical Systems Technologies, EPTCS, vol. 259, 31–38.'
mla: Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.”
Electronic Proceedings in Theoretical Computer Science, vol. 259, Open
Publishing Association, 2017, pp. 31–38, doi:10.4204/EPTCS.259.3.
short: B. Finkbeiner, A. Kupriyanov, in:, Electronic Proceedings in Theoretical
Computer Science, Open Publishing Association, 2017, pp. 31–38.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies'
start_date: 2017-04-29
date_created: 2018-12-11T11:47:07Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2023-10-17T12:02:46Z
day: '10'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4204/EPTCS.259.3
file:
- access_level: open_access
checksum: 6274f6c0da3376a7b079180d81568518
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:21Z
date_updated: 2020-07-14T12:47:00Z
file_id: '4939'
file_name: IST-2018-925-v1+1_1710.03391v1.pdf
file_size: 209294
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 259'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.03391v1
month: '10'
oa: 1
oa_version: Submitted Version
page: 31 - 38
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: Electronic Proceedings in Theoretical Computer Science
publication_identifier:
issn:
- 2075-2180
publication_status: published
publisher: Open Publishing Association
publist_id: '7264'
pubrep_id: '925'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Causality-based model checking
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2017'
...
---
_id: '999'
abstract:
- lang: eng
text: 'In multi-task learning, a learner is given a collection of prediction tasks
and needs to solve all of them. In contrast to previous work, which required that
annotated training data must be available for all tasks, we consider a new setting,
in which for some tasks, potentially most of them, only unlabeled training data
is provided. Consequently, to solve all tasks, information must be transferred
between tasks with labels and tasks without labels. Focusing on an instance-based
transfer method we analyze two variants of this setting: when the set of labeled
tasks is fixed, and when it can be actively selected by the learner. We state
and prove a generalization bound that covers both scenarios and derive from it
an algorithm for making the choice of labeled tasks (in the active case) and for
transferring information between the tasks in a principled way. We also illustrate
the effectiveness of the algorithm on synthetic and real data. '
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Multi-task learning with labeled and unlabeled tasks.
In: Vol 70. ML Research Press; 2017:2807-2816.'
apa: 'Pentina, A., & Lampert, C. (2017). Multi-task learning with labeled and
unlabeled tasks (Vol. 70, pp. 2807–2816). Presented at the ICML: International
Conference on Machine Learning, Sydney, Australia: ML Research Press.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Multi-Task Learning with Labeled
and Unlabeled Tasks,” 70:2807–16. ML Research Press, 2017.
ieee: 'A. Pentina and C. Lampert, “Multi-task learning with labeled and unlabeled
tasks,” presented at the ICML: International Conference on Machine Learning, Sydney,
Australia, 2017, vol. 70, pp. 2807–2816.'
ista: 'Pentina A, Lampert C. 2017. Multi-task learning with labeled and unlabeled
tasks. ICML: International Conference on Machine Learning, PMLR, vol. 70, 2807–2816.'
mla: Pentina, Anastasia, and Christoph Lampert. Multi-Task Learning with Labeled
and Unlabeled Tasks. Vol. 70, ML Research Press, 2017, pp. 2807–16.
short: A. Pentina, C. Lampert, in:, ML Research Press, 2017, pp. 2807–2816.
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: 2017-06-08T00:00:00Z
date_updated: 2023-10-17T11:53:32Z
day: '08'
department:
- _id: ChLa
ec_funded: 1
external_id:
isi:
- '000683309502093'
intvolume: ' 70'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.06518
month: '06'
oa: 1
oa_version: Submitted Version
page: 2807 - 2816
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- '9781510855144'
publication_status: published
publisher: ML Research Press
publist_id: '6399'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multi-task learning with labeled and unlabeled tasks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '459'
abstract:
- lang: eng
text: The social insects bees, wasps, ants, and termites are species-rich, occur
in many habitats, and often constitute a large part of the biomass. Many are also
invasive, including species of termites, the red imported fire ant, and the Argentine
ant. While invasive social insects have been a problem in Southern Europe for
some time, Central Europa was free of invasive ant species until recently because
most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus,
a close relative of the common black garden ant, arrive in Germany. First described
in 1990 based on individuals collected in Budapest, the species has since been
detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species
is spread with soil during construction work or plantings, and L. neglectus therefore
is often found in parks and botanical gardens. Another invasive ant now spreading
in southern Germany is Formica fuscocinerea, which occurs along rivers, including
in the sandy floodplains of the river Isar. As is typical of pioneer species,
F. fuscocinerea quickly becomes extremely abundant and therefore causes problems
for example on playgrounds in Munich. All invasive ant species are characterized
by cooperation across nests, leading to strongly interconnected, very large super-colonies.
The resulting dominance results in the extinction of native ant species as well
as other arthropod species and thus in the reduction of biodiversity.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische
Fauna verändern. Rundgespräche Forum Ökologie. 2017;46:105-116.'
apa: 'Cremer, S. (2017). Invasive Ameisen in Europa: Wie sie sich ausbreiten und
die heimische Fauna verändern. Rundgespräche Forum Ökologie. Verlag Dr.
Friedrich Pfeil.'
chicago: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und
Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie. Verlag Dr.
Friedrich Pfeil, 2017.'
ieee: 'S. Cremer, “Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische
Fauna verändern,” Rundgespräche Forum Ökologie, vol. 46. Verlag Dr. Friedrich
Pfeil, pp. 105–116, 2017.'
ista: 'Cremer S. 2017. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die
heimische Fauna verändern. Rundgespräche Forum Ökologie. 46, 105–116.'
mla: 'Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die
Heimische Fauna Verändern.” Rundgespräche Forum Ökologie, vol. 46, Verlag
Dr. Friedrich Pfeil, 2017, pp. 105–16.'
short: S. Cremer, Rundgespräche Forum Ökologie 46 (2017) 105–116.
date_created: 2018-12-11T11:46:35Z
date_published: 2017-04-04T00:00:00Z
date_updated: 2023-10-17T12:28:13Z
day: '04'
ddc:
- '592'
department:
- _id: SyCr
file:
- access_level: open_access
checksum: 4919baf9050415ca151fe22497379f78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:52Z
date_updated: 2020-07-14T12:46:32Z
file_id: '5175'
file_name: IST-2018-962-v1+1_044676698_07_Cremer__Invasive_Ameisen_in_Europa_...__BY-ND_.pdf
file_size: 1711131
relation: main_file
file_date_updated: 2020-07-14T12:46:32Z
has_accepted_license: '1'
intvolume: ' 46'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 105 - 116
publication: Rundgespräche Forum Ökologie
publication_identifier:
issn:
- 2366-2875
publication_status: published
publisher: Verlag Dr. Friedrich Pfeil
publist_id: '7362'
pubrep_id: '962'
quality_controlled: '1'
status: public
title: 'Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna
verändern'
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2017'
...
---
_id: '432'
abstract:
- lang: eng
text: 'Recently there has been significant interest in training machine-learning
models at low precision: by reducing precision, one can reduce computation and
communication by one order of magnitude. We examine training at reduced precision,
both from a theoretical and practical perspective, and ask: is it possible to
train models at end-to-end low precision with provable guarantees? Can this lead
to consistent order-of-magnitude speedups? We mainly focus on linear models, and
the answer is yes for linear models. We develop a simple framework called ZipML
based on one simple but novel strategy called double sampling. Our ZipML framework
is able to execute training at low precision with no bias, guaranteeing convergence,
whereas naive quanti- zation would introduce significant bias. We val- idate our
framework across a range of applica- tions, and show that it enables an FPGA proto-
type that is up to 6.5 × faster than an implemen- tation using full 32-bit precision.
We further de- velop a variance-optimal stochastic quantization strategy and show
that it can make a significant difference in a variety of settings. When applied
to linear models together with double sampling, we save up to another 1.7 × in
data movement compared with uniform quantization. When training deep networks
with quantized models, we achieve higher accuracy than the state-of-the- art XNOR-Net. '
alternative_title:
- PMLR Press
article_processing_charge: No
author:
- first_name: Hantian
full_name: Zhang, Hantian
last_name: Zhang
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- 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: Ji
full_name: Liu, Ji
last_name: Liu
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. ZipML: Training linear
models with end-to-end low precision, and a little bit of deep learning. In: Proceedings
of Machine Learning Research. Vol 70. ML Research Press; 2017:4035-4043.'
apa: 'Zhang, H., Li, J., Kara, K., Alistarh, D.-A., Liu, J., & Zhang, C. (2017).
ZipML: Training linear models with end-to-end low precision, and a little bit
of deep learning. In Proceedings of Machine Learning Research (Vol. 70,
pp. 4035–4043). Sydney, Australia: ML Research Press.'
chicago: 'Zhang, Hantian, Jerry Li, Kaan Kara, Dan-Adrian Alistarh, Ji Liu, and
Ce Zhang. “ZipML: Training Linear Models with End-to-End Low Precision, and a
Little Bit of Deep Learning.” In Proceedings of Machine Learning Research,
70:4035–43. ML Research Press, 2017.'
ieee: 'H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, and C. Zhang, “ZipML: Training
linear models with end-to-end low precision, and a little bit of deep learning,”
in Proceedings of Machine Learning Research, Sydney, Australia, 2017, vol.
70, pp. 4035–4043.'
ista: 'Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. 2017. ZipML: Training
linear models with end-to-end low precision, and a little bit of deep learning.
Proceedings of Machine Learning Research. ICML: International Conference on
Machine Learning, PMLR Press, vol. 70, 4035–4043.'
mla: 'Zhang, Hantian, et al. “ZipML: Training Linear Models with End-to-End Low
Precision, and a Little Bit of Deep Learning.” Proceedings of Machine Learning
Research, vol. 70, ML Research Press, 2017, pp. 4035–43.'
short: H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, C. Zhang, in:, Proceedings
of Machine Learning Research, ML Research Press, 2017, pp. 4035–4043.
conference:
end_date: 2017-08-11
location: Sydney, Australia
name: 'ICML: International Conference on Machine Learning'
start_date: 2017-08-06
date_created: 2018-12-11T11:46:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-17T12:31:15Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
file:
- access_level: open_access
checksum: 86156ba7f4318e47cef3eb9092593c10
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:23:58Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5869'
file_name: 2017_ICML_Zhang.pdf
file_size: 849345
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 4035 - 4043
publication: Proceedings of Machine Learning Research
publication_identifier:
isbn:
- 978-151085514-4
publication_status: published
publisher: ML Research Press
publist_id: '7391'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'ZipML: Training linear models with end-to-end low precision, and a little
bit of deep learning'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: ' 70'
year: '2017'
...
---
_id: '274'
abstract:
- lang: eng
text: We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x))
of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm
of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with
high probability assuming the existence of an oracle that produces samples from
the Gibbs distribution for a given parameter value in [0,β]. The current best
known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average
where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in
{0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show
that the same complexity can be achieved if exact oracles are replaced with approximate
sampling oracles that are within O(ε2qlnn) variation distance from exact oracles.
Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model
of computation.
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. A faster approximation algorithm for the Gibbs partition function.
In: Proceedings of the 31st Conference On Learning Theory. Vol 75. ML Research
Press; 2017:228-249.'
apa: Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition
function. In Proceedings of the 31st Conference On Learning Theory (Vol.
75, pp. 228–249). ML Research Press.
chicago: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition
Function.” In Proceedings of the 31st Conference On Learning Theory, 75:228–49.
ML Research Press, 2017.
ieee: V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,”
in Proceedings of the 31st Conference On Learning Theory, 2017, vol. 75,
pp. 228–249.
ista: 'Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition
function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual
Conference on Learning Theory vol. 75, 228–249.'
mla: Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition
Function.” Proceedings of the 31st Conference On Learning Theory, vol.
75, ML Research Press, 2017, pp. 228–49.
short: V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory,
ML Research Press, 2017, pp. 228–249.
conference:
end_date: 2018-07-09
name: 'COLT: Annual Conference on Learning Theory '
start_date: 2018-07-06
date_created: 2018-12-11T11:45:33Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-10-17T12:32:13Z
day: '27'
ddc:
- '510'
department:
- _id: VlKo
ec_funded: 1
external_id:
arxiv:
- '1608.04223'
file:
- access_level: open_access
checksum: 89db06a0e8083524449cb59b56bf4e5b
content_type: application/pdf
creator: dernst
date_created: 2020-05-12T09:23:27Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7820'
file_name: 2018_PMLR_Kolmogorov.pdf
file_size: 408974
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 75'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 228-249
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings of the 31st Conference On Learning Theory
publication_status: published
publisher: ML Research Press
publist_id: '7628'
quality_controlled: '1'
status: public
title: A faster approximation algorithm for the Gibbs partition function
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2017'
...
---
_id: '1030'
abstract:
- lang: ger
text: Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung
IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt
wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche
Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte
Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die
Bibliothek auf eine erfolgreiche Implementierung zurückblicken.
- lang: eng
text: "IST Austria was looking for a new library system until 2014 when the research
institute decided\r\nto implement Koha. The library first activated basic functions
of the open-source product and\r\nthen brought additional tools into operation.
The high flexibility of the system allows customized\r\nsolutions for different
institutions. Although the library faced some challenges, it can now look\r\nback
on a successful implementation."
article_processing_charge: No
article_type: original
author:
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1).
doi:10.11588/ip.2017.1.35227
apa: Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. Verein
Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227
chicago: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein
Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.
ieee: M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3,
no. 1. Verein Informationspraxis , 2017.
ista: Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).
mla: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3,
no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227.
short: M. Villányi, Informationspraxis 3 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-18T07:49:29Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.11588/ip.2017.1.35227
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:20Z
date_updated: 2018-12-12T10:08:20Z
file_id: '4680'
file_name: IST-2017-799-v1+1_35227-112025-1-PB.pdf
file_size: 201163
relation: main_file
file_date_updated: 2018-12-12T10:08:20Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
popular_science: '1'
publication: Informationspraxis
publication_identifier:
issn:
- 2297-3249
publication_status: published
publisher: 'Verein Informationspraxis '
publist_id: '6360'
pubrep_id: '799'
status: public
title: Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht
der IST Austria Library
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2017'
...
---
_id: '12193'
abstract:
- lang: eng
text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed
during animal development. However, whether developmental methylation reprogramming
during the sporophytic life cycle of flowering plants regulates genes is presently
unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation
(RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates
gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing
of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results
establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific
epigenetic signature that controls gene expression and contributes to cellular
function in flowering plants.
acknowledgement: We thank Daniel Zilberman for intellectual contributions to this
work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten
Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript,
Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method,
Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector,
Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics
support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant
Calder) for their assistance with microscopy. This work was funded by a Biotechnology
and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431)
to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to
J.W.
article_processing_charge: No
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: James D.
full_name: Higgins, James D.
last_name: Higgins
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5
apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D.,
& Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis
in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5
chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers,
James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates
Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.
ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research,
pp. 130–137, 2017.
ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017.
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature
Genetics. 50(1), 130–137.
mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis
in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017,
pp. 130–37, doi:10.1038/s41588-017-0008-5.
short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-10-18T07:21:53Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
external_id:
pmid:
- '29255257'
intvolume: ' 50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: None
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_id: '1194'
abstract:
- lang: eng
text: 'Termination is one of the basic liveness properties, and we study the termination
problem for probabilistic programs with real-valued variables. Previous works
focused on the qualitative problem that asks whether an input program terminates
with probability~1 (almost-sure termination). A powerful approach for this qualitative
problem is the notion of ranking supermartingales with respect to a given set
of invariants. The quantitative problem (probabilistic termination) asks for bounds
on the termination probability. A fundamental and conceptual drawback of the existing
approaches to address probabilistic termination is that even though the supermartingales
consider the probabilistic behavior of the programs, the invariants are obtained
completely ignoring the probabilistic aspect. In this work we address the probabilistic
termination problem for linear-arithmetic probabilistic programs with nondeterminism.
We define the notion of {\em stochastic invariants}, which are constraints along
with a probability bound that the constraints hold. We introduce a concept of
{\em repulsing supermartingales}. First, we show that repulsing supermartingales
can be used to obtain bounds on the probability of the stochastic invariants.
Second, we show the effectiveness of repulsing supermartingales in the following
three ways: (1)~With a combination of ranking and repulsing supermartingales we
can compute lower bounds on the probability of termination; (2)~repulsing supermartingales
provide witnesses for refutation of almost-sure termination; and (3)~with a combination
of ranking and repulsing supermartingales we can establish persistence properties
of probabilistic programs. We also present results on related computational problems
and an experimental evaluation of our approach on academic examples. '
alternative_title:
- ACM SIGPLAN Notices
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: Djordje
full_name: Zikelic, Djordje
last_name: Zikelic
citation:
ama: 'Chatterjee K, Novotný P, Zikelic D. Stochastic invariants for probabilistic
termination. In: Vol 52. ACM; 2017:145-160. doi:10.1145/3009837.3009873'
apa: 'Chatterjee, K., Novotný, P., & Zikelic, D. (2017). Stochastic invariants
for probabilistic termination (Vol. 52, pp. 145–160). Presented at the POPL: Principles
of Programming Languages, Paris, France: ACM. https://doi.org/10.1145/3009837.3009873'
chicago: Chatterjee, Krishnendu, Petr Novotný, and Djordje Zikelic. “Stochastic
Invariants for Probabilistic Termination,” 52:145–60. ACM, 2017. https://doi.org/10.1145/3009837.3009873.
ieee: 'K. Chatterjee, P. Novotný, and D. Zikelic, “Stochastic invariants for probabilistic
termination,” presented at the POPL: Principles of Programming Languages, Paris,
France, 2017, vol. 52, no. 1, pp. 145–160.'
ista: 'Chatterjee K, Novotný P, Zikelic D. 2017. Stochastic invariants for probabilistic
termination. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol.
52, 145–160.'
mla: Chatterjee, Krishnendu, et al. Stochastic Invariants for Probabilistic Termination.
Vol. 52, no. 1, ACM, 2017, pp. 145–60, doi:10.1145/3009837.3009873.
short: K. Chatterjee, P. Novotný, D. Zikelic, in:, ACM, 2017, pp. 145–160.
conference:
end_date: 2017-01-21
location: Paris, France
name: 'POPL: Principles of Programming Languages'
start_date: 2017-01-15
date_created: 2018-12-11T11:50:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-11-30T10:55:36Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3009837.3009873
ec_funded: 1
external_id:
isi:
- '000408311200013'
intvolume: ' 52'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.01063
month: '01'
oa: 1
oa_version: Submitted Version
page: 145 - 160
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _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
publication_identifier:
issn:
- '07308566'
publication_status: published
publisher: ACM
publist_id: '6157'
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stochastic invariants for probabilistic termination
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 52
year: '2017'
...
---
_id: '545'
abstract:
- lang: eng
text: Development of vascular tissue is a remarkable example of intercellular communication
and coordinated development involving hormonal signaling and tissue polarity.
Thus far, studies on vascular patterning and regeneration have been conducted
mainly in trees—woody plants—with a well-developed layer of vascular cambium and
secondary tissues. Trees are difficult to use as genetic models, i.e., due to
long generation time, unstable environmental conditions, and lack of available
mutants and transgenic lines. Therefore, the use of the main genetic model plant
Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic
lines, provides a unique opportunity to address molecular mechanism of vascular
tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis
can serve as a model to understand the growth of mighty trees and interconnect
a tree physiology with molecular genetics and cell biology of Arabidopsis.
alternative_title:
- Agricultural and Biological Sciences
author:
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Mazur E, Friml J. Vascular tissue development and regeneration in the model
plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering.
InTech; 2017:113-140. doi:10.5772/intechopen.69712'
apa: Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration
in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp.
113–140). InTech. https://doi.org/10.5772/intechopen.69712
chicago: Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration
in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana
Jurić, 113–40. Plant Engineering. InTech, 2017. https://doi.org/10.5772/intechopen.69712.
ieee: E. Mazur and J. Friml, “Vascular tissue development and regeneration in the
model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. InTech, 2017,
pp. 113–140.
ista: 'Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the
model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences,
, 113–140.'
mla: Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in
the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić,
InTech, 2017, pp. 113–40, doi:10.5772/intechopen.69712.
short: E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017,
pp. 113–140.
date_created: 2018-12-11T11:47:05Z
date_published: 2017-11-17T00:00:00Z
date_updated: 2024-02-12T12:03:42Z
day: '17'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.5772/intechopen.69712
ec_funded: 1
editor:
- first_name: Snježana
full_name: Jurić, Snježana
last_name: Jurić
file:
- access_level: open_access
checksum: e1f05e5850dfd9f9434d2d373ca61941
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:49Z
date_updated: 2020-07-14T12:46:58Z
file_id: '4969'
file_name: IST-2018-929-v1+1_56106.pdf
file_size: 7443683
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 113 - 140
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Engineering
publication_status: published
publisher: InTech
publist_id: '7269'
pubrep_id: '929'
quality_controlled: '1'
related_material:
record:
- id: '1274'
relation: earlier_version
status: public
series_title: Plant Engineering
status: public
title: Vascular tissue development and regeneration in the model plant arabidopsis
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: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '621'
abstract:
- lang: eng
text: The mammalian cerebral cortex is responsible for higher cognitive functions
such as perception, consciousness, and acquiring and processing information. The
neocortex is organized into six distinct laminae, each composed of a rich diversity
of cell types which assemble into highly complex cortical circuits. Radial glia
progenitors (RGPs) are responsible for producing all neocortical neurons and certain
glia lineages. Here, we discuss recent discoveries emerging from clonal lineage
analysis at the single RGP cell level that provide us with an inaugural quantitative
framework of RGP lineage progression. We further discuss the importance of the
relative contribution of intrinsic gene functions and non-cell-autonomous or community
effects in regulating RGP proliferation behavior and lineage progression.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Beattie RJ, Hippenmeyer S. Mechanisms of radial glia progenitor cell lineage
progression. FEBS letters. 2017;591(24):3993-4008. doi:10.1002/1873-3468.12906
apa: Beattie, R. J., & Hippenmeyer, S. (2017). Mechanisms of radial glia progenitor
cell lineage progression. FEBS Letters. Wiley-Blackwell. https://doi.org/10.1002/1873-3468.12906
chicago: Beattie, Robert J, and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor
Cell Lineage Progression.” FEBS Letters. Wiley-Blackwell, 2017. https://doi.org/10.1002/1873-3468.12906.
ieee: R. J. Beattie and S. Hippenmeyer, “Mechanisms of radial glia progenitor cell
lineage progression,” FEBS letters, vol. 591, no. 24. Wiley-Blackwell,
pp. 3993–4008, 2017.
ista: Beattie RJ, Hippenmeyer S. 2017. Mechanisms of radial glia progenitor cell
lineage progression. FEBS letters. 591(24), 3993–4008.
mla: Beattie, Robert J., and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor
Cell Lineage Progression.” FEBS Letters, vol. 591, no. 24, Wiley-Blackwell,
2017, pp. 3993–4008, doi:10.1002/1873-3468.12906.
short: R.J. Beattie, S. Hippenmeyer, FEBS Letters 591 (2017) 3993–4008.
date_created: 2018-12-11T11:47:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-14T12:02:08Z
day: '01'
ddc:
- '571'
- '610'
department:
- _id: SiHi
doi: 10.1002/1873-3468.12906
ec_funded: 1
external_id:
pmid:
- '29121403'
file:
- access_level: open_access
checksum: a46dadc84e0c28d389dd3e9e954464db
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:24Z
date_updated: 2020-07-14T12:47:24Z
file_id: '5211'
file_name: IST-2018-928-v1+1_Beattie_et_al-2017-FEBS_Letters.pdf
file_size: 644149
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 591'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3993 - 4008
pmid: 1
project:
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: FEBS letters
publication_identifier:
issn:
- '00145793'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7183'
pubrep_id: '928'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms of radial glia progenitor cell lineage progression
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 591
year: '2017'
...
---
_id: '5562'
abstract:
- lang: eng
text: "This data was collected as part of the study [1]. It consists of preprocessed
multi-electrode array recording from 160 salamander retinal ganglion cells responding
to 297 repeats of a 19 s natural movie. The data is available in two formats:
(1) a .mat file containing an array with dimensions “number of repeats” x “number
of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data
represented as an array with dimensions “number of neurons” x “number of samples”,
where the number of samples is equal to the product of the number of repeats and
timebins within a repeat. The time dimension is divided into 20 ms time windows,
and the array is binary indicating whether a given cell elicited at least one
spike in a given time window during a particular repeat. See the reference below
for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre
O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior
in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."
article_processing_charge: No
author:
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode
array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61
apa: Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry,
M. (2017). Multi-electrode array recording from salamander retinal ganglion cells.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61
chicago: Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek,
and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion
Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.
ieee: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode
array recording from salamander retinal ganglion cells.” Institute of Science
and Technology Austria, 2017.
ista: Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode
array recording from salamander retinal ganglion cells, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:61.
mla: Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal
Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.
short: O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).
datarep_id: '61'
date_created: 2018-12-12T12:31:33Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2024-02-21T13:46:14Z
day: '27'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:61
file:
- access_level: open_access
checksum: e620eff260646f57b479a69492c8b765
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:03:04Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5622'
file_name: IST-2017-61-v1+1_bint_fishmovie32_100.mat
file_size: 1336936
relation: main_file
- access_level: open_access
checksum: de83f9b81ea0aae3cddfc3ed982e0759
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:05Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5623'
file_name: IST-2017-61-v1+2_bint_fishmovie32_100.zip
file_size: 1897543
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
keyword:
- multi-electrode recording
- retinal ganglion cells
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '2257'
relation: research_paper
status: public
status: public
title: Multi-electrode array recording from salamander retinal ganglion cells
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5561'
abstract:
- lang: eng
text: 'Graph matching problems as described in "Active Graph Matching for Automatic
Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug,
Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2
hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text
format used by the feature matching solver described in "Feature Correspondence
via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir
Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. '
acknowledgement: We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.
article_processing_charge: No
author:
- first_name: Dagmar
full_name: Kainmueller, Dagmar
last_name: Kainmueller
- first_name: Florian
full_name: Jug, Florian
last_name: Jug
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Gene
full_name: Meyers, Gene
last_name: Meyers
citation:
ama: Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating
C. Elegans. 2017. doi:10.15479/AT:ISTA:57
apa: Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching
problems for annotating C. Elegans. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:57
chicago: Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph
Matching Problems for Annotating C. Elegans.” Institute of Science and Technology
Austria, 2017. https://doi.org/10.15479/AT:ISTA:57.
ieee: D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems
for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.
ista: Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for
annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57.
mla: Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:57.
short: D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017).
datarep_id: '57'
date_created: 2018-12-12T12:31:32Z
date_published: 2017-02-13T00:00:00Z
date_updated: 2024-02-21T13:46:31Z
day: '13'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:57
file:
- access_level: open_access
checksum: 3dc3e1306a66028a34181ebef2923139
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:54Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5614'
file_name: IST-2017-57-v1+1_wormMatchingProblems.zip
file_size: 327042819
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
keyword:
- graph matching
- feature matching
- QAP
- MAP-inference
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Graph matching problems for annotating C. Elegans
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5563'
abstract:
- lang: eng
text: "MATLAB code and processed datasets available for reproducing the results
in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.\r\n*equal contributions"
article_processing_charge: No
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
citation:
ama: Lukacisin M. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties
of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”
2017. doi:10.15479/AT:ISTA:64
apa: Lukacisin, M. (2017). MATLAB analysis code for “Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:64
chicago: Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:64.
ieee: M. Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties
of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’”
Institute of Science and Technology Austria, 2017.
ista: Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:64.
mla: Lukacisin, Martin. MATLAB Analysis Code for “Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:64.
short: M. Lukacisin, (2017).
datarep_id: '64'
date_created: 2018-12-12T12:31:33Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2024-02-21T13:46:47Z
day: '20'
ddc:
- '571'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:64
file:
- access_level: open_access
checksum: ee697f2b1ade4dc14d6ac0334dd832ab
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:37Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5602'
file_name: IST-2016-45-v1+1_PaperCode.zip
file_size: 296722548
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '839'
abstract:
- lang: eng
text: 'This thesis describes a brittle fracture simulation method for visual effects
applications. Building upon a symmetric Galerkin boundary element method, we first
compute stress intensity factors following the theory of linear elastic fracture
mechanics. We then use these stress intensities to simulate the motion of a propagating
crack front at a significantly higher resolution than the overall deformation
of the breaking object. Allowing for spatial variations of the material''s toughness
during crack propagation produces visually realistic, highly-detailed fracture
surfaces. Furthermore, we introduce approximations for stress intensities and
crack opening displacements, resulting in both practical speed-up and theoretically
superior runtime complexity compared to previous methods. While we choose a quasi-static
approach to fracture mechanics, ignoring dynamic deformations, we also couple
our fracture simulation framework to a standard rigid-body dynamics solver, enabling
visual effects artists to simulate both large scale motion, as well as fracturing
due to collision forces in a combined system. As fractures inside of an object
grow, their geometry must be represented both in the coarse boundary element mesh,
as well as at the desired fine output resolution. Using a boundary element method,
we avoid complicated volumetric meshing operations. Instead we describe a simple
set of surface meshing operations that allow us to progressively add cracks to
the mesh of an object and still re-use all previously computed entries of the
linear boundary element system matrix. On the high resolution level, we opt for
an implicit surface representation. We then describe how to capture fracture surfaces
during crack propagation, as well as separate the individual fragments resulting
from the fracture process, based on this implicit representation. We show results
obtained with our method, either solving the full boundary element system in every
time step, or alternatively using our fast approximations. These results demonstrate
that both of these methods perform well in basic test cases and produce realistic
fracture surfaces. Furthermore we show that our fast approximations substantially
out-perform the standard approach in more demanding scenarios. Finally, these
two methods naturally combine, using the full solution while the problem size
is manageably small and switching to the fast approximations later on. The resulting
hybrid method gives the user a direct way to choose between speed and accuracy
of the simulation. '
acknowledgement: "ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all,
let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for
supporting me throughout my PhD. Obviously, none of this work would\r\nhave been
possible without you.\r\nFurthermore, Thank You to all the people who have contributed
to this work in various\r\nways, in particular Martin Schanz and his group for providing
and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and
Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions
during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel,
and all the members – past and present – of his\r\nand Chris’ research groups at
IST Austria for always providing honest and insightful\r\nfeedback throughout many
joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang
Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs
only virtual objects have been harmed in the process of creating this work, I would\r\nlike
to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo”
models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg
for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different
ways.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
citation:
ama: Hahn D. Brittle fracture simulation with boundary elements for computer graphics.
2017. doi:10.15479/AT:ISTA:th_855
apa: Hahn, D. (2017). Brittle fracture simulation with boundary elements for
computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855
chicago: Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer
Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855.
ieee: D. Hahn, “Brittle fracture simulation with boundary elements for computer
graphics,” Institute of Science and Technology Austria, 2017.
ista: Hahn D. 2017. Brittle fracture simulation with boundary elements for computer
graphics. Institute of Science and Technology Austria.
mla: Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer
Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855.
short: D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer
Graphics, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2024-02-21T13:48:02Z
day: '14'
ddc:
- '004'
- '005'
- '006'
- '531'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_855
ec_funded: 1
file:
- access_level: open_access
checksum: 6c1ae8c90bfaba5e089417fefbc4a272
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:46Z
date_updated: 2020-07-14T12:48:13Z
file_id: '5100'
file_name: IST-2017-855-v1+1_thesis_online_pdfA.pdf
file_size: 14596191
relation: main_file
- access_level: closed
checksum: 421672f68d563b029869c5cf1713f919
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:40:30Z
date_updated: 2020-07-14T12:48:13Z
file_id: '6207'
file_name: 2017_thesis_Hahn_source.zip
file_size: 15060566
relation: source_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6809'
pubrep_id: '855'
related_material:
record:
- id: '1362'
relation: part_of_dissertation
status: public
- id: '1633'
relation: part_of_dissertation
status: public
- id: '5568'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Brittle fracture simulation with boundary elements for computer graphics
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '614'
abstract:
- lang: eng
text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated
WZ sex chromosomes. However, in most lineages outside of the division Ditrysia,
as well as in the sister order Trichoptera, females lack a W chromosome. The W
is therefore thought to have been acquired secondarily. Here we compare the genomes
of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three
models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex
chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment
of a B chromosome). We show that the gene content of the Z is highly conserved
across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes
moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome
fusion). Our comparative genomics analysis therefore supports the secondary acquisition
of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme
stability of well-differentiated sex chromosomes.'
article_number: '1486'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z
chromosome suggests a non canonical origin of the W. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01663-5
apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation
of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5
chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation
of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.
ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the
Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W. Nature Communications.
8(1), 1486.
mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome
Suggests a Non Canonical Origin of the W.” Nature Communications, vol.
8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.
short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1038/s41467-017-01663-5
external_id:
pmid:
- '29133797'
file:
- access_level: open_access
checksum: 4da2651303c8afc2f7fc419be42a2433
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T15:55:50Z
date_updated: 2020-07-14T12:47:20Z
file_id: '7562'
file_name: 2017_NatureComm_Fraisse.pdf
file_size: 1201520
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7190'
pubrep_id: '910'
quality_controlled: '1'
related_material:
record:
- id: '7163'
relation: popular_science
status: public
scopus_import: 1
status: public
title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical
origin of the W
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '5564'
abstract:
- lang: eng
text: Compressed Fastq files with whole-genome sequencing data of IS-wt strain D
and clones from four evolved populations (A11, C08, C10, D08). Information on
this data collection is available in the Methods Section of the primary publication.
article_processing_charge: No
author:
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
- 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: Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects
determine the adaptive potential of a gene under selection.” 2017. doi:10.15479/AT:ISTA:65
apa: Steinrück, M., & Guet, C. C. (2017). Fastq files for “Complex chromosomal
neighborhood effects determine the adaptive potential of a gene under selection.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:65
chicago: Steinrück, Magdalena, and Calin C Guet. “Fastq Files for ‘Complex Chromosomal
Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:65.
ieee: M. Steinrück and C. C. Guet, “Fastq files for ‘Complex chromosomal neighborhood
effects determine the adaptive potential of a gene under selection.’” Institute
of Science and Technology Austria, 2017.
ista: Steinrück M, Guet CC. 2017. Fastq files for ‘Complex chromosomal neighborhood
effects determine the adaptive potential of a gene under selection’, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:65.
mla: Steinrück, Magdalena, and Calin C. Guet. Fastq Files for “Complex Chromosomal
Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:65.
short: M. Steinrück, C.C. Guet, (2017).
datarep_id: '65'
date_created: 2018-12-12T12:31:33Z
date_published: 2017-04-11T00:00:00Z
date_updated: 2024-02-21T13:47:28Z
day: '11'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:65
file:
- access_level: open_access
checksum: 31a0c01d022721073241a23d192cc37e
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:18Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5627'
file_name: IST-2017-65-v1+1_D_anc_1.fastq.zip
file_size: 1225959109
relation: main_file
- access_level: open_access
checksum: d8f26f83ce7e7e45436121f9c6cd9b83
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:30Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5628'
file_name: IST-2017-65-v1+1_D_anc_2.fastq.zip
file_size: 1422656107
relation: main_file
- access_level: open_access
checksum: e07b99bcfe55b5f132ca03b8b48c8cbc
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:33Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5629'
file_name: IST-2017-65-v1+2_D_A11_1.fastq.zip
file_size: 565014975
relation: main_file
- access_level: open_access
checksum: eda86143d5f32d844b54f8530041e32b
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:42Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5630'
file_name: IST-2017-65-v1+3_D_A11_2.fastq.zip
file_size: 564490030
relation: main_file
- access_level: open_access
checksum: 906d44f950c1626d9b99f34fbf89cb12
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:46Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5631'
file_name: IST-2017-65-v1+4_D_C10_1.fastq.zip
file_size: 875430169
relation: main_file
- access_level: open_access
checksum: 6ca14a032a79e0c787106bdf635725c9
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:54Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5632'
file_name: IST-2017-65-v1+6_D_C08_2.fastq.zip
file_size: 638298201
relation: main_file
- access_level: open_access
checksum: 66ab16ddb5ba64b2e263ef746ebf2893
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:01Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5633'
file_name: IST-2017-65-v1+5_D_C10_2.fastq.zip
file_size: 894702866
relation: main_file
- access_level: open_access
checksum: 82607970174f8d37773b7d3acc712195
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:07Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5634'
file_name: IST-2017-65-v1+7_D_C08_1.fastq.zip
file_size: 623648989
relation: main_file
- access_level: open_access
checksum: 225c30b243268c7dda9d6f8327933252
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:11Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5635'
file_name: IST-2017-65-v1+8_D_D08_1.fastq.zip
file_size: 259359583
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '704'
relation: research_paper
status: public
status: public
title: Fastq files for "Complex chromosomal neighborhood effects determine the adaptive
potential of a gene under selection"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5568'
abstract:
- lang: eng
text: Includes source codes, test cases, and example data used in the thesis Brittle
Fracture Simulation with Boundary Elements for Computer Graphics. Also includes
pre-built binaries of the HyENA library, but not sources - please contact the
HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
citation:
ama: 'Hahn D. Source codes: Brittle fracture simulation with boundary elements for
computer graphics. 2017. doi:10.15479/AT:ISTA:73'
apa: 'Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements
for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:73'
chicago: 'Hahn, David. “Source Codes: Brittle Fracture Simulation with Boundary
Elements for Computer Graphics.” Institute of Science and Technology Austria,
2017. https://doi.org/10.15479/AT:ISTA:73.'
ieee: 'D. Hahn, “Source codes: Brittle fracture simulation with boundary elements
for computer graphics.” Institute of Science and Technology Austria, 2017.'
ista: 'Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements
for computer graphics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:73.'
mla: 'Hahn, David. Source Codes: Brittle Fracture Simulation with Boundary Elements
for Computer Graphics. Institute of Science and Technology Austria, 2017,
doi:10.15479/AT:ISTA:73.'
short: D. Hahn, (2017).
datarep_id: '73'
date_created: 2018-12-12T12:31:35Z
date_published: 2017-08-16T00:00:00Z
date_updated: 2024-02-21T13:48:02Z
day: '16'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:73
ec_funded: 1
file:
- access_level: open_access
checksum: 2323a755842a3399cbc47d76545fc9a0
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:57Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5615'
file_name: IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip
file_size: 199353471
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
keyword:
- Boundary elements
- brittle fracture
- computer graphics
- fracture simulation
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '839'
relation: research_paper
status: public
status: public
title: 'Source codes: Brittle fracture simulation with boundary elements for computer
graphics'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '7163'
abstract:
- lang: eng
text: The de novo genome assemblies generated for this study, and the associated
metadata.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163
apa: Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:7163
chicago: Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of
the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163.
ieee: C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.’” Institute of Science
and Technology Austria, 2017.
ista: Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W’, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:7163.
mla: Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the
Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute
of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.
short: C. Fraisse, (2017).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2019-12-09T23:03:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/AT:ISTA:7163
file:
- access_level: open_access
checksum: 3cae8a2e3cbf8703399b9c483aaba7f3
content_type: application/zip
creator: cfraisse
date_created: 2019-12-10T08:46:46Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7164'
file_name: Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip
file_size: 841375478
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '614'
relation: research_paper
status: public
status: public
title: Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome
suggests a non canonical origin of the W"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...