---
_id: '384'
abstract:
- lang: eng
text: Can orthologous proteins differ in terms of their ability to be secreted?
To answer this question, we investigated the distribution of signal peptides within
the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons
revealed a large number of signal peptide gain and loss events, in which signal
peptides emerge or disappear in the course of evolution. Signal peptide losses
prevail over gains, an effect which is especially pronounced in the transition
from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate
decline in the number of signal peptide-containing proteins in endosymbionts cannot
be explained by the overall reduction of their genomes. Signal peptides can be
gained and lost either by acquisition/elimination of the corresponding N-terminal
regions or by gradual accumulation of mutations. The evolutionary dynamics of
signal peptides in bacterial proteins represents a powerful mechanism of functional
diversification.
acknowledgement: "his work was supported by the Deutsche Forschungsgemeinschaft (grant
\ number FR 1411/9-1). This work was supported by the German Research Foundation
(DFG) and the Technical University of Munich within the fund- ing programme Open
Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont
status of the organisms and Michael Galperin for\r\nuseful comments. T"
article_processing_charge: No
author:
- first_name: Peter
full_name: Hönigschmid, Peter
last_name: Hönigschmid
- first_name: Nadya
full_name: Bykova, Nadya
last_name: Bykova
- first_name: René
full_name: Schneider, René
last_name: Schneider
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Dmitrij
full_name: Frishman, Dmitrij
last_name: Frishman
citation:
ama: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay
between symbiotic relationships and patterns of signal peptide gain and loss.
Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049
apa: Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D.
(2018). Evolutionary interplay between symbiotic relationships and patterns of
signal peptide gain and loss. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evy049
chicago: Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij
Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns
of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford
University Press, 2018. https://doi.org/10.1093/gbe/evy049.
ieee: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University
Press, pp. 928–938, 2018.
ista: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss. Genome Biology and Evolution. 10(3), 928–938.
mla: Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships
and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution,
vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.
short: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome
Biology and Evolution 10 (2018) 928–938.
date_created: 2018-12-11T11:46:10Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:56:52Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1093/gbe/evy049
external_id:
isi:
- '000429483700022'
file:
- access_level: open_access
checksum: 458a7c2c2e79528567edfeb0f326cbe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:07Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4667'
file_name: IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf
file_size: 691602
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 928 - 938
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7445'
pubrep_id: '999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interplay between symbiotic relationships and patterns of signal
peptide gain and loss
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: 10
year: '2018'
...
---
_id: '563'
abstract:
- lang: eng
text: "In continuous populations with local migration, nearby pairs of individuals
have on average more similar genotypes\r\nthan geographically well separated pairs.
A barrier to gene flow distorts this classical pattern of isolation by distance.
Genetic similarity is decreased for sample pairs on different sides of the barrier
and increased for pairs on the same side near the barrier. Here, we introduce
an inference scheme that utilizes this signal to detect and estimate the strength
of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation
to model the effects of a barrier on the geographical spread of ancestry backwards
in time. This approach allows us to calculate the chance of recent coalescence
and probability of identity by descent. We introduce an inference scheme that
fits these theoretical results to the geographical covariance structure of bialleleic
genetic markers. It can estimate the strength of the barrier as well as several
demographic parameters. We investigate the power of our inference scheme to detect
barriers by applying it to a wide range of simulated data. We also showcase an
example application to a Antirrhinum majus (snapdragon) flower color hybrid zone,
where we do not detect any signal of a strong genome wide barrier to gene flow."
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: David
full_name: Field, David
last_name: Field
- 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: Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene
flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245.
doi:10.1534/genetics.117.300638
apa: Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating
barriers to gene flow from distorted isolation-by-distance patterns. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.117.300638
chicago: Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton.
“Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.”
Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.
ieee: H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers
to gene flow from distorted isolation-by-distance patterns,” Genetics,
vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.
ista: Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to
gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.
mla: Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted
Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society
of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.
short: H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:42:38Z
day: '01'
department:
- _id: NiBa
- _id: ChLa
doi: 10.1534/genetics.117.300638
external_id:
isi:
- '000426219600025'
intvolume: ' 208'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/205484v1
month: '03'
oa: 1
oa_version: Preprint
page: 1231-1245
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7251'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Estimating barriers to gene flow from distorted isolation-by-distance patterns
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '135'
abstract:
- lang: eng
text: The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by
combining particles with grids. To improve performance, the subsequent narrow
band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid
surface and a traditional grid‐based fluid simulation away from the surface. This
spatially‐limited FLIP simulation significantly reduces the number of particles
and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP
idea even further, by allowing a simulation to transition between a FLIP‐like
fluid simulation and a grid‐based simulation in arbitrary locations, not just
near the surface. This approach leads to even more savings in memory and computation,
because we can concentrate the particles only in areas where they are needed.
More importantly, this new method allows us to seamlessly transition to smooth
implicit surface geometry wherever the particle‐based simulation is unnecessary.
Consequently, our method leads to a practical algorithm for avoiding the noisy
surface artifacts associated with particle‐based liquid simulations, while simultaneously
maintaining the benefits of a FLIP simulation in regions of dynamic motion.
alternative_title:
- Eurographics
article_processing_charge: No
article_type: original
author:
- first_name: Takahiro
full_name: Sato, Takahiro
last_name: Sato
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
citation:
ama: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP
for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351
apa: Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended
narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley.
https://doi.org/10.1111/cgf.13351
chicago: Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi
Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics
Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.
ieee: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow
band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no.
2. Wiley, pp. 169–177, 2018.
ista: Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band
FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.
mla: Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.”
Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.
short: T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum
37 (2018) 169–177.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-05-22T00:00:00Z
date_updated: 2023-09-11T14:00:26Z
day: '22'
ddc:
- '006'
department:
- _id: ChWo
doi: 10.1111/cgf.13351
ec_funded: 1
external_id:
isi:
- '000434085600016'
file:
- access_level: open_access
checksum: 8edb90da8a72395eb5d970580e0925b6
content_type: application/pdf
creator: wojtan
date_created: 2020-10-08T08:38:23Z
date_updated: 2020-10-08T08:38:23Z
file_id: '8627'
file_name: exnbflip.pdf
file_size: 54309947
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:38:23Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 169 - 177
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: Computer Graphics Forum
publication_identifier:
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extended narrow band FLIP for liquid simulations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '316'
abstract:
- lang: eng
text: 'Self-incompatibility (SI) is a genetically based recognition system that
functions to prevent self-fertilization and mating among related plants. An enduring
puzzle in SI is how the high diversity observed in nature arises and is maintained.
Based on the underlying recognition mechanism, SI can be classified into two main
groups: self- and non-self recognition. Most work has focused on diversification
within self-recognition systems despite expected differences between the two groups
in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic
population genetic model and stochastic simulations to investigate how novel S-haplotypes
evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI
system. For this model the pathways for diversification involve either the maintenance
or breakdown of SI and can vary in the order of mutations of the female (SRNase)
and male (SLF) components. We show analytically that diversification can occur
with high inbreeding depression and self-pollination, but this varies with evolutionary
pathway and level of completeness (which determines the number of potential mating
partners in the population), and in general is more likely for lower haplotype
number. The conditions for diversification are broader in stochastic simulations
of finite population size. However, the number of haplotypes observed under high
inbreeding and moderate to high self-pollination is less than that commonly observed
in nature. Diversification was observed through pathways that maintain SI as well
as through self-compatible intermediates. Yet the lifespan of diversified haplotypes
was sensitive to their level of completeness. By examining diversification in
a non-self recognition SI system, this model extends our understanding of the
evolution and maintenance of haplotype diversity observed in a self recognition
system common in flowering plants.'
article_processing_charge: No
article_type: original
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.118.300748
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society
of America, 2018. https://doi.org/10.1534/genetics.118.300748.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary
pathways for the generation of new self-incompatibility haplotypes in a non-self
recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America,
pp. 861–883, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 209(3), 861–883.
mla: Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3,
Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018)
861–883.
date_created: 2018-12-11T11:45:47Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:57:43Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1534/genetics.118.300748
ec_funded: 1
external_id:
isi:
- '000437171700017'
intvolume: ' 209'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/node/80098.abstract
month: '07'
oa: 1
oa_version: Preprint
page: 861-883
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genetics
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/
record:
- id: '9813'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '190'
abstract:
- lang: eng
text: The German cockroach, Blattella germanica, is a worldwide pest that infests
buildings, including homes, restaurants, and hospitals, often living in unsanitary
conditions. As a disease vector and producer of allergens, this species has major
health and economic impacts on humans. Factors contributing to the success of
the German cockroach include its resistance to a broad range of insecticides,
immunity to many pathogens, and its ability, as an extreme generalist omnivore,
to survive on most food sources. The recently published genome shows that B. germanica
has an exceptionally high number of protein coding genes. In this study, we investigate
the functions of the 93 significantly expanded gene families with the aim to better
understand the success of B. germanica as a major pest despite such inhospitable
conditions. We find major expansions in gene families with functions related to
the detoxification of insecticides and allelochemicals, defense against pathogens,
digestion, sensory perception, and gene regulation. These expansions might have
allowed B. germanica to develop multiple resistance mechanisms to insecticides
and pathogens, and enabled a broad, flexible diet, thus explaining its success
in unsanitary conditions and under recurrent chemical control. The findings and
resources presented here provide insights for better understanding molecular mechanisms
that will facilitate more effective cockroach control.
article_processing_charge: No
article_type: original
author:
- first_name: Mark
full_name: Harrison, Mark
last_name: Harrison
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Lucas
full_name: Kremer, Lucas
last_name: Kremer
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- 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: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Maria
full_name: Puilachs, Maria
last_name: Puilachs
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
citation:
ama: 'Harrison M, Arning N, Kremer L, et al. Expansions of key protein families
in the German cockroach highlight the molecular basis of its remarkable success
as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824'
apa: 'Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer,
E., … Schal, C. (2018). Expansions of key protein families in the German cockroach
highlight the molecular basis of its remarkable success as a global indoor pest.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution.
Wiley. https://doi.org/10.1002/jez.b.22824'
chicago: 'Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles,
Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families
in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success
as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.'
ieee: 'M. Harrison et al., “Expansions of key protein families in the German
cockroach highlight the molecular basis of its remarkable success as a global
indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution, vol. 330. Wiley, pp. 254–264, 2018.'
ista: 'Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans
AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein
families in the German cockroach highlight the molecular basis of its remarkable
success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 330, 254–264.'
mla: 'Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach
Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.”
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution,
vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.'
short: 'M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer,
A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental
Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.'
date_created: 2018-12-11T11:45:06Z
date_published: 2018-07-11T00:00:00Z
date_updated: 2023-09-11T13:59:54Z
day: '11'
department:
- _id: BeVi
doi: 10.1002/jez.b.22824
external_id:
isi:
- '000443231000002'
pmid:
- '29998472'
intvolume: ' 330'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824
month: '07'
oa: 1
oa_version: Submitted Version
page: 254-264
pmid: 1
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_status: published
publisher: Wiley
publist_id: '7730'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expansions of key protein families in the German cockroach highlight the molecular
basis of its remarkable success as a global indoor pest
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 330
year: '2018'
...
---
_id: '404'
abstract:
- lang: eng
text: "We construct martingale solutions to stochastic thin-film equations by introducing
a (spatial) semidiscretization and establishing convergence. The discrete scheme
allows for variants of the energy and entropy estimates in the continuous setting
as long as the discrete energy does not exceed certain threshold values depending
on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy
paths constant in time, arbitrary moments of coupled energy/entropy functionals
can be controlled. Having established Hölder regularity of approximate solutions,
the convergence proof is then based on compactness arguments---in particular on
Jakubowski's generalization of Skorokhod's theorem---weak convergence methods,
and recent tools on martingale convergence.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Günther
full_name: Grün, Günther
last_name: Grün
citation:
ama: Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796
apa: Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic
thin-film equations. SIAM Journal on Mathematical Analysis. Society for
Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796
chicago: Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to
Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.
ieee: J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic
thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no.
1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.
ista: Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film
equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.
mla: Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic
Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no.
1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.
short: J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.
date_created: 2018-12-11T11:46:17Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2023-09-11T13:59:22Z
day: '30'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1137/16M1098796
external_id:
isi:
- '000426630900015'
file:
- access_level: open_access
checksum: 89a8eae7c52bb356c04f52b44bff4b5a
content_type: application/pdf
creator: dernst
date_created: 2019-11-07T12:20:25Z
date_updated: 2020-07-14T12:46:22Z
file_id: '6992'
file_name: 2018_SIAM_Fischer.pdf
file_size: 557338
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 411 - 455
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7425'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Existence of positive solutions to stochastic thin-film equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-11T13:57:42Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '5780'
abstract:
- lang: eng
text: Bioluminescence is found across the entire tree of life, conferring a spectacular
set of visually oriented functions from attracting mates to scaring off predators.
Half a dozen different luciferins, molecules that emit light when enzymatically
oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis
has been described in full, which is found only in bacteria. Here, we report identification
of the fungal luciferase and three other key enzymes that together form the biosynthetic
cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite.
Introduction of the identified genes into the genome of the yeast Pichia pastoris
along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent
in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis
cycle and found that fungal bioluminescence emerged through a series of events
that included two independent gene duplications. The retention of the duplicated
enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication
was followed by functional sequence divergence of enzymes of at least one gene
in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence
proceeded through several closely related stepping stone nonluminescent biochemical
reactions with adaptive roles. The availability of a complete eukaryotic luciferin
biosynthesis pathway provides several applications in biomedicine and bioengineering.
article_processing_charge: No
author:
- first_name: Alexey A.
full_name: Kotlobay, Alexey A.
last_name: Kotlobay
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Yuliana A.
full_name: Mokrushina, Yuliana A.
last_name: Mokrushina
- first_name: Marina
full_name: Marcet-Houben, Marina
last_name: Marcet-Houben
- first_name: Ekaterina O.
full_name: Serebrovskaya, Ekaterina O.
last_name: Serebrovskaya
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Andrey Y.
full_name: Gorokhovatsky, Andrey Y.
last_name: Gorokhovatsky
- first_name: Andrey
full_name: Vvedensky, Andrey
last_name: Vvedensky
- first_name: Konstantin V.
full_name: Purtov, Konstantin V.
last_name: Purtov
- first_name: Valentin N.
full_name: Petushkov, Valentin N.
last_name: Petushkov
- first_name: Natalja S.
full_name: Rodionova, Natalja S.
last_name: Rodionova
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Liliia
full_name: Fakhranurova, Liliia
last_name: Fakhranurova
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Rustam
full_name: Ziganshin, Rustam
last_name: Ziganshin
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Zinaida M.
full_name: Kaskova, Zinaida M.
last_name: Kaskova
- first_name: Victoria
full_name: Shender, Victoria
last_name: Shender
- first_name: Maxim
full_name: Abakumov, Maxim
last_name: Abakumov
- first_name: Tatiana O.
full_name: Abakumova, Tatiana O.
last_name: Abakumova
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Fedor M.
full_name: Eroshkin, Fedor M.
last_name: Eroshkin
- first_name: Andrey G.
full_name: Zaraisky, Andrey G.
last_name: Zaraisky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Tatiana Y.
full_name: Mitiouchkina, Tatiana Y.
last_name: Mitiouchkina
- first_name: Eugene P.
full_name: Kopantzev, Eugene P.
last_name: Kopantzev
- first_name: Hans E.
full_name: Waldenmaier, Hans E.
last_name: Waldenmaier
- first_name: Anderson G.
full_name: Oliveira, Anderson G.
last_name: Oliveira
- first_name: Yuichi
full_name: Oba, Yuichi
last_name: Oba
- first_name: Ekaterina
full_name: Barsova, Ekaterina
last_name: Barsova
- first_name: Ekaterina A.
full_name: Bogdanova, Ekaterina A.
last_name: Bogdanova
- first_name: Toni
full_name: Gabaldón, Toni
last_name: Gabaldón
- first_name: Cassius V.
full_name: Stevani, Cassius V.
last_name: Stevani
- first_name: Sergey
full_name: Lukyanov, Sergey
last_name: Lukyanov
- first_name: Ivan V.
full_name: Smirnov, Ivan V.
last_name: Smirnov
- first_name: Josef I.
full_name: Gitelson, Josef I.
last_name: Gitelson
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
citation:
ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115
apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya,
E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115
chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben,
Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et
al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.
ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system
from fungi,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732,
2018.
ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO,
Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov
VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova
AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin
FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier
HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov
S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable
bioluminescent system from fungi. Proceedings of the National Academy of Sciences
of the United States of America. 115(50), 12728–12732.
mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from
Fungi.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32,
doi:10.1073/pnas.1803615115.
short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya,
N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov,
V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya,
R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova,
I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y.
Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova,
E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson,
F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences
of the United States of America 115 (2018) 12728–12732.
date_created: 2018-12-23T22:59:18Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-11T14:04:05Z
day: '11'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1073/pnas.1803615115
external_id:
isi:
- '000452866000068'
file:
- access_level: open_access
checksum: 46b2c12185eb2ddb598f4c7b4bd267bf
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T15:21:40Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5926'
file_name: 2018_PNAS_Kotlobay.pdf
file_size: 1271988
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 12728-12732
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encodable bioluminescent system from fungi
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '428'
abstract:
- lang: eng
text: The plant hormone gibberellic acid (GA) is a crucial regulator of growth and
development. The main paradigm of GA signaling puts forward transcriptional regulation
via the degradation of DELLA transcriptional repressors. GA has also been shown
to regulate tropic responses by modulation of the plasma membrane incidence of
PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular
and molecular mechanisms by which GA redirects protein trafficking and thus regulates
cell surface functionality. Photoconvertible reporters revealed that GA balances
the protein traffic between the vacuole degradation route and recycling back to
the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple
cargos, including PIN proteins, whereas high GA levels promote their recycling
to the plasma membrane. This GA effect requires components of the retromer complex,
such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated
protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates
the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton
is essential for the GA effect on trafficking. This GA cellular action occurs
through DELLA proteins that regulate the MT and retromer presumably via their
interaction partners Prefoldins (PFDs). Our study identified a branching of the
GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating
transcription, also target by a nontranscriptional mechanism the retromer complex
acting at the intersection of the degradation and recycling trafficking routes.
By this mechanism, GA can redirect receptors and transporters to the cell surface,
thus coregulating multiple processes, including PIN-dependent auxin fluxes during
tropic responses.
acknowledgement: "We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular
y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and
Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology,
Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central
European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for
Science), and Y. Gu (Penn State University) for making available the materials used
in this study;\r\n...funding from the European Research Council (ERC) under the
European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement
282300.\r\nCC BY NC ND"
article_processing_charge: No
author:
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Kaori
full_name: Tabata, Kaori
id: 7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0
last_name: Tabata
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets
the retromer complex to redirect protein trafficking to the plasma membrane. PNAS.
2018;115(14):3716-3721. doi:10.1073/pnas.1721760115
apa: Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc,
M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex
to redirect protein trafficking to the plasma membrane. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1721760115
chicago: Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi
Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the
Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS.
National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.
ieee: Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer
complex to redirect protein trafficking to the plasma membrane,” PNAS,
vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.
ista: Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml
J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect
protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.
mla: Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer
Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS,
vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.
short: Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc,
J. Friml, PNAS 115 (2018) 3716–3721.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-04-03T00:00:00Z
date_updated: 2023-09-11T14:06:34Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1721760115
ec_funded: 1
external_id:
isi:
- '000429012500073'
file:
- access_level: open_access
checksum: 1fcf7223fb8f99559cfa80bd6f24ce44
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:30:14Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5700'
file_name: 2018_PNAS_Salanenka.pdf
file_size: 1924101
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: ' 3716 - 3721'
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7395'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gibberellin DELLA signaling targets the retromer complex to redirect protein
trafficking to the plasma membrane
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '62'
abstract:
- lang: eng
text: Imaging is a dominant strategy for data collection in neuroscience, yielding
stacks of images that often scale to gigabytes of data for a single experiment.
Machine learning algorithms from computer vision can serve as a pair of virtual
eyes that tirelessly processes these images, automatically detecting and identifying
microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction
of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual
clues and requires no training. This approach generalizes across different modalities,
including serially-sectioned scanning electron microscopy (sSEM) of genetically
labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe)
microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue
volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets,
demonstrating the high biological fidelity of the pipeline’s reconstructions.
FLoRIN reconstructions are of sufficient quality for preliminary biological study,
for example examining the distribution and morphology of cells or extracting single
axons from functional data. Compared to existing supervised learning methods,
FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions
that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.
acknowledgement: 'Equipment was generously donated by the NVIDIA Corporation, and
made available by the National Science Foundation (NSF) through grant #CNS-1629914.
This research used resources of the Argonne Leadership Computing Facility, which
is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.'
article_number: '14247'
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Shabazi, Ali
last_name: Shabazi
- first_name: Jeffery
full_name: Kinnison, Jeffery
last_name: Kinnison
- first_name: Rafael
full_name: Vescovi, Rafael
last_name: Vescovi
- first_name: Ming
full_name: Du, Ming
last_name: Du
- first_name: Robert
full_name: Hill, Robert
last_name: Hill
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Marc
full_name: Takeno, Marc
last_name: Takeno
- first_name: Hongkui
full_name: Zeng, Hongkui
last_name: Zeng
- first_name: Nuno
full_name: Da Costa, Nuno
last_name: Da Costa
- first_name: Jaime
full_name: Grutzendler, Jaime
last_name: Grutzendler
- first_name: Narayanan
full_name: Kasthuri, Narayanan
last_name: Kasthuri
- first_name: Walter
full_name: Scheirer, Walter
last_name: Scheirer
citation:
ama: Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation
and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3
apa: Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer,
W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes.
Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3
chicago: Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian
A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018.
https://doi.org/10.1038/s41598-018-32628-3.
ieee: A. Shabazi et al., “Flexible learning-free segmentation and reconstruction
of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing
Group, 2018.
ista: Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H,
Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free
segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.
mla: Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction
of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing
Group, 2018, doi:10.1038/s41598-018-32628-3.
short: A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno,
H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:44:25Z
date_published: 2018-09-24T00:00:00Z
date_updated: 2023-09-11T14:02:55Z
day: '24'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-018-32628-3
external_id:
isi:
- '000445336600015'
file:
- access_level: open_access
checksum: 1a14ae0666b82fbaa04bef110e3f6bf2
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:22:24Z
date_updated: 2020-07-14T12:47:24Z
file_id: '5699'
file_name: 2018_ScientificReports_Shahbazi.pdf
file_size: 4141645
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7992'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41598-018-36220-7
scopus_import: '1'
status: public
title: Flexible learning-free segmentation and reconstruction of neural volumes
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: '2018'
...
---
_id: '437'
abstract:
- lang: eng
text: Dendritic cells (DCs) are sentinels of the adaptive immune system that reside
in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation
and up-regulate the chemokine receptor CCR7 that guides them along gradients of
its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs
present peripherally acquired antigen to naïve T cells, thereby triggering adaptive
immunity.
acknowledged_ssus:
- _id: SSU
acknowledgement: "This work was supported by grants of the European Research Council
(ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific
support units at IST Austria for excellent technical support.\r\nWe thank the scientific
\ support units at IST Austria for excellent technical support. "
article_processing_charge: Yes (via OA deal)
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Hans
full_name: Haecker, Hans
last_name: Haecker
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast
and efficient genetic engineering of hematopoietic precursor cells for the study
of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077.
doi:10.1002/eji.201747358
apa: Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &
Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor
cells for the study of dendritic cell migration. European Journal of Immunology.
Wiley-Blackwell. https://doi.org/10.1002/eji.201747358
chicago: Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild,
Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.
ieee: A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M.
K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells
for the study of dendritic cell migration,” European Journal of Immunology,
vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.
ista: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018.
Fast and efficient genetic engineering of hematopoietic precursor cells for the
study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.
mla: Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.
short: A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K.
Sixt, European Journal of Immunology 48 (2018) 1074–1077.
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-09-11T14:01:18Z
day: '13'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1002/eji.201747358
ec_funded: 1
external_id:
isi:
- '000434963700016'
file:
- access_level: open_access
checksum: 9d5b74cd016505aeb9a4c2d33bbedaeb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5044'
file_name: IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf
file_size: 590106
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1074 - 1077
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7386'
pubrep_id: '1067'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and efficient genetic engineering of hematopoietic precursor cells for
the study of dendritic cell migration
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: 48
year: '2018'
...
---
_id: '617'
abstract:
- lang: eng
text: Insects are exposed to a variety of potential pathogens in their environment,
many of which can severely impact fitness and health. Consequently, hosts have
evolved resistance and tolerance strategies to suppress or cope with infections.
Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads,
and hosts utilizing tolerance reduce harmful fitness effects per pathogen load.
To understand variation in, and selective pressures on, resistance and tolerance,
we asked to what degree they are shaped by host genetic background, whether plasticity
in these responses depends upon dietary environment, and whether there are interactions
between these two factors. Females from ten wild-type Drosophila melanogaster
genotypes were kept on high- or low-protein (yeast) diets and infected with one
of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila.
We measured host resistance as the inverse of bacterial load in the early infection
phase. The relationship (slope) between fly fecundity and individual-level bacteria
load provided our fecundity tolerance measure. Genotype and dietary yeast determined
host fecundity and strongly affected survival after infection with pathogenic
P. entomophila. There was considerable genetic variation in host resistance, a
commonly found phenomenon resulting from for example varying resistance costs
or frequency-dependent selection. Despite this variation and the reproductive
cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes.
The absence of genetic variation in tolerance may suggest that at this early infection
stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are
not expressed under these infection conditions.
acknowledgement: 'We would like to thank Susann Wicke for performing the genome-wide
SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara
Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical
help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the
Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for
their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG)
priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR
872/1-1). '
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival,
and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
2018;31(1):159-171. doi:10.1111/jeb.13211
apa: Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect
resistance, survival, and fecundity but not fecundity tolerance. Journal of
Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect
Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of
Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.
ieee: M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary
Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.
ista: Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance,
survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology.
31(1), 159–171.
mla: Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity
but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31,
no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.
short: M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018)
159–171.
date_created: 2018-12-11T11:47:31Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T14:06:04Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/jeb.13211
external_id:
isi:
- '000419307000014'
pmid:
- '29150962'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jeb.13211
month: '01'
oa: 1
oa_version: Published Version
page: 159 - 171
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '7187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotype and diet affect resistance, survival, and fecundity but not fecundity
tolerance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 31
year: '2018'
...
---
_id: '5888'
abstract:
- lang: eng
text: "Despite the remarkable number of scientific breakthroughs of the last 100
years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum
disorder, intellectual disability) remains a great challenge. Recent advancements
in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists
to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given
the few hundred risk genes that have been discovered,\r\nthe etiological variability
and the heterogeneous clinical presentation, the need for genotype — along with
phenotype-\r\nbased diagnosis of individual patients has become a requisite. In
this review we look at recent advancements in\r\ngenomic analysis and their translation
into clinical practice."
article_number: '100'
article_processing_charge: No
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an
avenue to personalized medicine. Experimental & Molecular Medicine.
2018;50(8). doi:10.1038/s12276-018-0129-7'
apa: 'Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental
disorders: an avenue to personalized medicine. Experimental & Molecular
Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7'
chicago: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.'
ieee: 'D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders:
an avenue to personalized medicine,” Experimental & Molecular Medicine,
vol. 50, no. 8. Springer Nature, 2018.'
ista: 'Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders:
an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8),
100.'
mla: 'Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental
Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular
Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.'
short: D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50
(2018).
date_created: 2019-01-27T22:59:11Z
date_published: 2018-08-07T00:00:00Z
date_updated: 2023-09-11T14:04:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1038/s12276-018-0129-7
external_id:
isi:
- '000441266700006'
pmid:
- '30089840'
file:
- access_level: open_access
checksum: 4498301c8c53097c9a1a8ef990936eb5
content_type: application/pdf
creator: dernst
date_created: 2019-01-28T15:18:02Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5893'
file_name: 2018_EMM_Tarlungeanu.pdf
file_size: 1237482
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Experimental & Molecular Medicine
publication_identifier:
issn:
- 2092-6413
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomics in neurodevelopmental disorders: an avenue to personalized medicine'
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: 50
year: '2018'
...
---
_id: '295'
abstract:
- lang: eng
text: We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional
anyon gas. Our bounds are extensive in the particle number, as for fermions, and
linear in the statistics parameter (Formula presented.). The lower bounds extend
to Lieb–Thirring inequalities for all anyons except bosons.
acknowledgement: Financial support from the Swedish Research Council, grant no. 2013-4734
(D. L.), the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No 694227, R. S.), and by
the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully
acknowledged.
article_processing_charge: No
author:
- first_name: Douglas
full_name: Lundholm, Douglas
last_name: Lundholm
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in
Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y
apa: Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons.
Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y
chicago: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.
ieee: D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters
in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.
ista: Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters
in Mathematical Physics. 108(11), 2523–2541.
mla: Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.”
Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp.
2523–41, doi:10.1007/s11005-018-1091-y.
short: D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.
date_created: 2018-12-11T11:45:40Z
date_published: 2018-05-11T00:00:00Z
date_updated: 2023-09-11T14:01:57Z
day: '11'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11005-018-1091-y
ec_funded: 1
external_id:
arxiv:
- '1712.06218'
isi:
- '000446491500008'
file:
- access_level: open_access
checksum: 8beb9632fa41bbd19452f55f31286a31
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:14:17Z
date_updated: 2020-07-14T12:45:55Z
file_id: '5698'
file_name: 2018_LettMathPhys_Lundholm.pdf
file_size: 551996
relation: main_file
file_date_updated: 2020-07-14T12:45:55Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
issue: '11'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2523-2541
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: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '7586'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fermionic behavior of ideal anyons
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: 108
year: '2018'
...
---
_id: '555'
abstract:
- lang: eng
text: Conventional wisdom has it that proteins fold and assemble into definite structures,
and that this defines their function. Glycosaminoglycans (GAGs) are different.
In most cases the structures they form have a low degree of order, even when interacting
with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity,
charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich
matrices. By integrating soft matter physics concepts (e.g. polymer brushes and
phase separation) with our molecular understanding of GAG–protein interactions,
we can better comprehend how GAG-rich matrices assemble, what their properties
are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix
enveloping neurons — as a relevant example, we propose that microphase separation
determines the holey PNN anatomy that is pivotal to PNN functions.
acknowledgement: "This work was supported by the European Research Council [Starting
Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation
[MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering
and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1,
to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15,
to JCFK] and the European Union, the Operational Programme Research, Development
and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’
[CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis
Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on
GAG–protein interactions.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Ralf
full_name: Richter, Ralf
last_name: Richter
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Anthony
full_name: Day, Anthony
last_name: Day
- first_name: Jessica
full_name: Kwok, Jessica
last_name: Kwok
citation:
ama: 'Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology.
2018;50:65-74. doi:10.1016/j.sbi.2017.12.002'
apa: 'Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans
in extracellular matrix organisation: Are concepts from soft matter physics key
to understanding the formation of perineuronal nets? Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002'
chicago: 'Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans
in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key
to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural
Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.'
ieee: 'R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets?,” Current Opinion in Structural Biology,
vol. 50. Elsevier, pp. 65–74, 2018.'
ista: 'Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular
matrix organisation: Are concepts from soft matter physics key to understanding
the formation of perineuronal nets? Current Opinion in Structural Biology. 50,
65–74.'
mla: 'Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation:
Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal
Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018,
pp. 65–74, doi:10.1016/j.sbi.2017.12.002.'
short: R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural
Biology 50 (2018) 65–74.
date_created: 2018-12-11T11:47:09Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-11T14:07:03Z
day: '01'
department:
- _id: MaLo
doi: 10.1016/j.sbi.2017.12.002
external_id:
isi:
- '000443661300011'
intvolume: ' 50'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.whiterose.ac.uk/125524/
month: '06'
oa: 1
oa_version: Submitted Version
page: 65 - 74
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '7259'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Glycosaminoglycans in extracellular matrix organisation: Are concepts from
soft matter physics key to understanding the formation of perineuronal nets?'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '448'
abstract:
- lang: eng
text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
signatures of termite eusociality by comparing the genomes and transcriptomes
of three termites and the cockroach against the background of 16 other eusocial
and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
and perception of pheromones confirm the importance of chemical communication
in the termites. These are accompanied by major changes in gene regulation and
the molecular evolution of caste determination. Many of these results parallel
molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
solutions are remarkably different, thus revealing a striking case of convergence
in one of the major evolutionary transitions in biological complexity.
acknowledgement: We thank O. Niehuis for allowing use of the unpublished E. danica
genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J.
Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks
Charles Darwin University (Australia), especially S. Garnett and the Horticulture
and Aquaculture team, for providing logistic support to collect C. secundus. The
Parks and Wildlife Commission, Northern Territory, the Department of the Environment,
Water, Heritage and the Arts gave permission to collect (Permit number 36401) and
export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider
and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B.
J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and
M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251
and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds,
and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US
Department of Housing and Urban Development (NCHHU-0017-13), the National Science
Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National
Institute of Environmental Health Sciences (P30ES025128) to the Center for Human
Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported
by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).
article_processing_charge: No
author:
- first_name: Mark
full_name: Harrison, Mark
last_name: Harrison
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Hugh
full_name: Robertson, Hugh
last_name: Robertson
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Tristan
full_name: Bitard Feildel, Tristan
last_name: Bitard Feildel
- first_name: Hsu
full_name: Chao, Hsu
last_name: Chao
- first_name: Christopher
full_name: Childers, Christopher
last_name: Childers
- first_name: Huyen
full_name: Dinh, Huyen
last_name: Dinh
- first_name: Harshavardhan
full_name: Doddapaneni, Harshavardhan
last_name: Doddapaneni
- first_name: Shannon
full_name: Dugan, Shannon
last_name: Dugan
- first_name: Johannes
full_name: Gowin, Johannes
last_name: Gowin
- first_name: Carolin
full_name: Greiner, Carolin
last_name: Greiner
- first_name: Yi
full_name: Han, Yi
last_name: Han
- first_name: Haofu
full_name: Hu, Haofu
last_name: Hu
- first_name: Daniel
full_name: Hughes, Daniel
last_name: Hughes
- 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: Karsten
full_name: Kemena, Karsten
last_name: Kemena
- first_name: Lukas
full_name: Kremer, Lukas
last_name: Kremer
- first_name: Sandra
full_name: Lee, Sandra
last_name: Lee
- first_name: Alberto
full_name: López Ezquerra, Alberto
last_name: López Ezquerra
- first_name: Ludovic
full_name: Mallet, Ludovic
last_name: Mallet
- first_name: Jose
full_name: Monroy Kuhn, Jose
last_name: Monroy Kuhn
- first_name: Annabell
full_name: Moser, Annabell
last_name: Moser
- first_name: Shwetha
full_name: Murali, Shwetha
last_name: Murali
- first_name: Donna
full_name: Muzny, Donna
last_name: Muzny
- first_name: Saria
full_name: Otani, Saria
last_name: Otani
- first_name: Maria
full_name: Piulachs, Maria
last_name: Piulachs
- first_name: Monica
full_name: Poelchau, Monica
last_name: Poelchau
- first_name: Jiaxin
full_name: Qu, Jiaxin
last_name: Qu
- first_name: Florentine
full_name: Schaub, Florentine
last_name: Schaub
- first_name: Ayako
full_name: Wada Katsumata, Ayako
last_name: Wada Katsumata
- first_name: Kim
full_name: Worley, Kim
last_name: Worley
- first_name: Qiaolin
full_name: Xie, Qiaolin
last_name: Xie
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Michael
full_name: Poulsen, Michael
last_name: Poulsen
- first_name: Richard
full_name: Gibbs, Richard
last_name: Gibbs
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
citation:
ama: Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal
molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566.
doi:10.1038/s41559-017-0459-1
apa: Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T.,
Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular
basis of termite eusociality. Nature Ecology and Evolution. Springer Nature.
https://doi.org/10.1038/s41559-017-0459-1
chicago: Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan
Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes
Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution.
Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.
ieee: M. Harrison et al., “Hemimetabolous genomes reveal molecular basis
of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer
Nature, pp. 557–566, 2018.
ista: Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H,
Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes
D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy
Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub
F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards
S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular
basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.
mla: Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite
Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature,
2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.
short: M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H.
Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y.
Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra,
L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs,
M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla,
M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer,
Nature Ecology and Evolution 2 (2018) 557–566.
date_created: 2018-12-11T11:46:32Z
date_published: 2018-02-05T00:00:00Z
date_updated: 2023-09-11T14:10:57Z
day: '05'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1038/s41559-017-0459-1
external_id:
isi:
- '000426559600026'
file:
- access_level: open_access
checksum: 874953136ac125e65f37971d3cabc5b7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:08Z
date_updated: 2020-07-14T12:46:30Z
file_id: '4731'
file_name: IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf
file_size: 3730583
relation: main_file
file_date_updated: 2020-07-14T12:46:30Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 557-566
publication: Nature Ecology and Evolution
publication_status: published
publisher: Springer Nature
publist_id: '7375'
pubrep_id: '969'
quality_controlled: '1'
related_material:
record:
- id: '9841'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Hemimetabolous genomes reveal molecular basis of termite eusociality
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: 2
year: '2018'
...
---
_id: '723'
abstract:
- lang: eng
text: Escaping local optima is one of the major obstacles to function optimisation.
Using the metaphor of a fitness landscape, local optima correspond to hills separated
by fitness valleys that have to be overcome. We define a class of fitness valleys
of tunable difficulty by considering their length, representing the Hamming path
between the two optima and their depth, the drop in fitness. For this function
class we present a runtime comparison between stochastic search algorithms using
different search strategies. The (1+1) EA is a simple and well-studied evolutionary
algorithm that has to jump across the valley to a point of higher fitness because
it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm
and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population
genetics, are both able to cross the fitness valley by accepting worsening moves.
We show that the runtime of the (1+1) EA depends critically on the length of the
valley while the runtimes of the non-elitist algorithms depend crucially on the
depth of the valley. Moreover, we show that both SSWM and Metropolis can also
efficiently optimise a rugged function consisting of consecutive valleys.
article_processing_charge: No
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape
local optima in black box optimisation when non elitism outperforms elitism. Algorithmica.
2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
apa: Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B.
(2018). How to escape local optima in black box optimisation when non elitism
outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora
Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism
Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.
ieee: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How
to escape local optima in black box optimisation when non elitism outperforms
elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.
ista: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to
escape local optima in black box optimisation when non elitism outperforms elitism.
Algorithmica. 80(5), 1604–1633.
mla: Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation
When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer,
2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
short: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica
80 (2018) 1604–1633.
date_created: 2018-12-11T11:48:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:11:35Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-017-0369-2
ec_funded: 1
external_id:
isi:
- '000428239300010'
file:
- access_level: open_access
checksum: 7d92f5d7be81e387edeec4f06442791c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:14Z
date_updated: 2020-07-14T12:47:54Z
file_id: '4674'
file_name: IST-2018-1014-v1+1_2018_Paixao_Escape.pdf
file_size: 691245
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 80'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1604 - 1633
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6957'
pubrep_id: '1014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to escape local optima in black box optimisation when non elitism outperforms
elitism
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: 80
year: '2018'
...
---
_id: '321'
abstract:
- lang: eng
text: The twelve papers in this special section focus on learning systems with shared
information for computer vision and multimedia communication analysis. In the
real world, a realistic setting for computer vision or multimedia recognition
problems is that we have some classes containing lots of training data and many
classes containing a small amount of training data. Therefore, how to use frequent
classes to help learning rare classes for which it is harder to collect the training
data is an open question. Learning with shared information is an emerging topic
in machine learning, computer vision and multimedia analysis. There are different
levels of components that can be shared during concept modeling and machine learning
stages, such as sharing generic object parts, sharing attributes, sharing transformations,
sharing regularization parameters and sharing training examples, etc. Regarding
the specific methods, multi-task learning, transfer learning and deep learning
can be seen as using different strategies to share information. These learning
with shared information methods are very effective in solving real-world large-scale
problems.
article_processing_charge: No
article_type: original
author:
- first_name: Trevor
full_name: Darrell, Trevor
last_name: Darrell
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Nico
full_name: Sebe, Nico
last_name: Sebe
- first_name: Ying
full_name: Wu, Ying
last_name: Wu
- first_name: Yan
full_name: Yan, Yan
last_name: Yan
citation:
ama: Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the
special section on learning with Shared information for computer vision and multimedia
analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence.
2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998
apa: Darrell, T., Lampert, C., Sebe, N., Wu, Y., & Yan, Y. (2018). Guest editors’
introduction to the special section on learning with Shared information for computer
vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine
Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998
chicago: Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest
Editors’ Introduction to the Special Section on Learning with Shared Information
for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998.
ieee: T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction
to the special section on learning with Shared information for computer vision
and multimedia analysis,” IEEE Transactions on Pattern Analysis and Machine
Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.
ista: Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction
to the special section on learning with Shared information for computer vision
and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence.
40(5), 1029–1031.
mla: Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section
on Learning with Shared Information for Computer Vision and Multimedia Analysis.”
IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40,
no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.
short: T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern
Analysis and Machine Intelligence 40 (2018) 1029–1031.
date_created: 2018-12-11T11:45:48Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:07:54Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1109/TPAMI.2018.2804998
external_id:
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month: '05'
oa: 1
oa_version: Published Version
page: 1029 - 1031
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '7544'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guest editors' introduction to the special section on learning with Shared
information for computer vision and multimedia analysis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '9841'
abstract:
- lang: eng
text: Around 150 million years ago, eusocial termites evolved from within the cockroaches,
50 million years before eusocial Hymenoptera, such as bees and ants, appeared.
Here, we report the 2-Gb genome of the German cockroach, Blattella germanica,
and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary
signatures of termite eusociality by comparing the genomes and transcriptomes
of three termites and the cockroach against the background of 16 other eusocial
and non-eusocial insects. Dramatic adaptive changes in genes underlying the production
and perception of pheromones confirm the importance of chemical communication
in the termites. These are accompanied by major changes in gene regulation and
the molecular evolution of caste determination. Many of these results parallel
molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific
solutions are remarkably different, thus revealing a striking case of convergence
in one of the major evolutionary transitions in biological complexity.
article_processing_charge: No
author:
- first_name: Mark C.
full_name: Harrison, Mark C.
last_name: Harrison
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Hugh M.
full_name: Robertson, Hugh M.
last_name: Robertson
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Tristan
full_name: Bitard-Feildel, Tristan
last_name: Bitard-Feildel
- first_name: Hsu
full_name: Chao, Hsu
last_name: Chao
- first_name: Christopher P.
full_name: Childers, Christopher P.
last_name: Childers
- first_name: Huyen
full_name: Dinh, Huyen
last_name: Dinh
- first_name: Harshavardhan
full_name: Doddapaneni, Harshavardhan
last_name: Doddapaneni
- first_name: Shannon
full_name: Dugan, Shannon
last_name: Dugan
- first_name: Johannes
full_name: Gowin, Johannes
last_name: Gowin
- first_name: Carolin
full_name: Greiner, Carolin
last_name: Greiner
- first_name: Yi
full_name: Han, Yi
last_name: Han
- first_name: Haofu
full_name: Hu, Haofu
last_name: Hu
- first_name: Daniel S. T.
full_name: Hughes, Daniel S. T.
last_name: Hughes
- 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: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Lukas P. M.
full_name: Kremer, Lukas P. M.
last_name: Kremer
- first_name: Sandra L.
full_name: Lee, Sandra L.
last_name: Lee
- first_name: Alberto
full_name: Lopez-Ezquerra, Alberto
last_name: Lopez-Ezquerra
- first_name: Ludovic
full_name: Mallet, Ludovic
last_name: Mallet
- first_name: Jose M.
full_name: Monroy-Kuhn, Jose M.
last_name: Monroy-Kuhn
- first_name: Annabell
full_name: Moser, Annabell
last_name: Moser
- first_name: Shwetha C.
full_name: Murali, Shwetha C.
last_name: Murali
- first_name: Donna M.
full_name: Muzny, Donna M.
last_name: Muzny
- first_name: Saria
full_name: Otani, Saria
last_name: Otani
- first_name: Maria-Dolors
full_name: Piulachs, Maria-Dolors
last_name: Piulachs
- first_name: Monica
full_name: Poelchau, Monica
last_name: Poelchau
- first_name: Jiaxin
full_name: Qu, Jiaxin
last_name: Qu
- first_name: Florentine
full_name: Schaub, Florentine
last_name: Schaub
- first_name: Ayako
full_name: Wada-Katsumata, Ayako
last_name: Wada-Katsumata
- first_name: Kim C.
full_name: Worley, Kim C.
last_name: Worley
- first_name: Qiaolin
full_name: Xie, Qiaolin
last_name: Xie
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Michael
full_name: Poulsen, Michael
last_name: Poulsen
- first_name: Richard A.
full_name: Gibbs, Richard A.
last_name: Gibbs
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Judith
full_name: Korb, Judith
last_name: Korb
- first_name: Erich
full_name: Bornberg-Bauer, Erich
last_name: Bornberg-Bauer
citation:
ama: 'Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes
reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r'
apa: 'Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel,
T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal
molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r'
chicago: 'Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning,
Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from:
Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad,
2018. https://doi.org/10.5061/dryad.51d4r.'
ieee: 'M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular
basis of termite eusociality.” Dryad, 2018.'
ista: 'Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao
H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu
H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet
L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau
M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs
RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from:
Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.'
mla: 'Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular
Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r.'
short: M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel,
H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner,
Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee,
A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny,
S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C.
Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles,
J. Korb, E. Bornberg-Bauer, (2018).
date_created: 2021-08-09T13:13:48Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-11T14:10:56Z
day: '12'
department:
- _id: BeVi
doi: 10.5061/dryad.51d4r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.51d4r
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '448'
relation: used_in_publication
status: public
status: public
title: 'Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '32'
abstract:
- lang: eng
text: The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between
neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified
the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in
vivo during the peak of myelination by targeting the GluA2 subunit. Expression
of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered
proliferation of OPCs and reduced their differentiation into oligodendrocytes.
Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit
(C-tail), a modification designed to affect the interaction between GluA2 and
AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs,
decreased the differentiation of OPCs without affecting their proliferation. These
findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs,
as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in
the mouse corpus callosum, are important for balancing the response of OPCs to
proliferation and differentiation cues. In the brain, oligodendrocyte precursor
cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from
neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC
synapses alters proliferation and differentiation of OPCs. This expands the traditional
view of synaptic transmission by suggesting neurons also use synapses to modulate
behavior of glia.
acknowledgement: This work was supported by Deutsche Forschungsgemeinschaft (DFG)
grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience
(CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the
Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the
DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported
by the Tistou & Charlotte Kerstan Foundation.
article_processing_charge: No
author:
- first_name: Ting
full_name: Chen, Ting
last_name: Chen
- first_name: Bartosz
full_name: Kula, Bartosz
last_name: Kula
- first_name: Balint
full_name: Nagy, Balint
id: 30F830CE-02D1-11E9-9BAA-DAF4881429F2
last_name: Nagy
orcid: 0000-0002-4002-4686
- first_name: Ruxandra
full_name: Barzan, Ruxandra
last_name: Barzan
- first_name: Andrea
full_name: Gall, Andrea
last_name: Gall
- first_name: Ingrid
full_name: Ehrlich, Ingrid
last_name: Ehrlich
- first_name: Maria
full_name: Kukley, Maria
last_name: Kukley
citation:
ama: Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor
cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell
Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066
apa: Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley,
M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation
and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2018.09.066
chicago: Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid
Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell
Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell
Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.
ieee: T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell
proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell
Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.
ista: Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo
regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.
mla: Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation
and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports,
vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.
short: T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell
Reports 25 (2018) 852–861.e7.
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-11T14:13:32Z
day: '23'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2018.09.066
external_id:
isi:
- '000448219500005'
file:
- access_level: open_access
checksum: d9f74277fd57176e04732707d575cf08
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:42:57Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5703'
file_name: 2018_CellReports_Chen.pdf
file_size: 4461997
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 852 - 861.e7
publication: Cell Reports
publication_status: published
publisher: Elsevier
publist_id: '8023'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2
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: 25
year: '2018'
...
---
_id: '5672'
abstract:
- lang: eng
text: The release of IgM is the first line of an antibody response and precedes
the generation of high affinity IgG in germinal centers. Once secreted by freshly
activated plasmablasts, IgM is released into the efferent lymph of reactive lymph
nodes as early as 3 d after immunization. As pentameric IgM has an enormous size
of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through
the densely lymphocyte-packed environment of a lymph node parenchyma in order
to reach its exit. In this issue of JEM, Thierry et al. show that, in order to
reach the blood stream, IgM molecules take a specific micro-anatomical route via
lymph node conduits.
article_processing_charge: No
author:
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine.
2018;215(12):2959-2961. doi:10.1084/jem.20181934
apa: Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental
Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934
chicago: Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.
ieee: A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental
Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.
ista: Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine.
215(12), 2959–2961.
mla: Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61,
doi:10.1084/jem.20181934.
short: A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-11-20T00:00:00Z
date_updated: 2023-09-11T14:12:06Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20181934
external_id:
isi:
- '000451920600002'
file:
- access_level: open_access
checksum: 687beea1d64c213f4cb9e3c29ec11a14
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creator: dernst
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isi: 1
issue: '12'
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month: '11'
oa: 1
oa_version: Published Version
page: 2959-2961
publication: Journal of Experimental Medicine
publication_identifier:
issn:
- '00221007'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: IgM's exit route
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 215
year: '2018'
...
---
_id: '458'
abstract:
- lang: eng
text: We consider congruences of straight lines in a plane with the combinatorics
of the square grid, with all elementary quadrilaterals possessing an incircle.
It is shown that all the vertices of such nets (we call them incircular or IC-nets)
lie on confocal conics. Our main new results are on checkerboard IC-nets in the
plane. These are congruences of straight lines in the plane with the combinatorics
of the square grid, combinatorially colored as a checkerboard, such that all black
coordinate quadrilaterals possess inscribed circles. We show how this larger class
of IC-nets appears quite naturally in Laguerre geometry of oriented planes and
spheres and leads to new remarkable incidence theorems. Most of our results are
valid in hyperbolic and spherical geometries as well. We present also generalizations
in spaces of higher dimension, called checkerboard IS-nets. The construction of
these nets is based on a new 9 inspheres incidence theorem.
acknowledgement: DFG Collaborative Research Center TRR 109 “Discretization in Geometry
and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexander
full_name: Bobenko, Alexander
last_name: Bobenko
citation:
ama: Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292
apa: Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/7292
chicago: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal
Conics.” Transactions of the American Mathematical Society. American Mathematical
Society, 2018. https://doi.org/10.1090/tran/7292.
ieee: A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions
of the American Mathematical Society, vol. 370, no. 4. American Mathematical
Society, pp. 2825–2854, 2018.
ista: Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 370(4), 2825–2854.
mla: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.”
Transactions of the American Mathematical Society, vol. 370, no. 4, American
Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292.
short: A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society
370 (2018) 2825–2854.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-11T14:19:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/7292
ec_funded: 1
external_id:
isi:
- '000423197800019'
intvolume: ' 370'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.04637
month: '04'
oa: 1
oa_version: Preprint
page: 2825 - 2854
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '7363'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incircular nets and confocal conics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 370
year: '2018'
...
---
_id: '5788'
abstract:
- lang: eng
text: In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner or payoff of the game. Such
games are central in formal verification since they model the interaction between
a non-terminating system and its environment. We study bidding games in which
the players bid for the right to move the token. Two bidding rules have been defined.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the “bank” rather than the
other player. While poorman reachability games have been studied before, we present,
for the first time, results on infinite-duration poorman games. A central quantity
in these games is the ratio between the two players’ initial budgets. The questions
we study concern a necessary and sufficient ratio with which a player can achieve
a goal. For reachability objectives, such threshold ratios are known to exist
for both bidding rules. We show that the properties of poorman reachability games
extend to complex qualitative objectives such as parity, similarly to the Richman
case. Our most interesting results concern quantitative poorman games, namely
poorman mean-payoff games, where we construct optimal strategies depending on
the initial ratio, by showing a connection with random-turn based games. The connection
in itself is interesting, because it does not hold for reachability poorman games.
We also solve the complexity problems that arise in poorman bidding games.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games.
In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2'
apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration
poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International
Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2'
chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration
Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.
ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding
games,” presented at the 14th International Conference on Web and Internet Economics,
WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.
ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding
games. 14th International Conference on Web and Internet Economics, WINE, LNCS,
vol. 11316, 21–36.
mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316,
Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.
conference:
end_date: 2018-12-17
location: Oxford, UK
name: 14th International Conference on Web and Internet Economics, WINE
start_date: 2018-12-15
date_created: 2018-12-30T22:59:14Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-12T07:44:01Z
day: '21'
department:
- _id: ToHe
doi: 10.1007/978-3-030-04612-5_2
external_id:
arxiv:
- '1804.04372'
isi:
- '000865933000002'
intvolume: ' 11316'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04372
month: '11'
oa: 1
oa_version: Preprint
page: 21-36
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
isbn:
- '9783030046118'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infinite-duration poorman-bidding games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11316
year: '2018'
...
---
_id: '150'
abstract:
- lang: eng
text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1,
has a critical role during the formation of the HIV-1 virus particle. During virus
assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle,
which holds together the Gag hexamer and facilitates the formation of a curved
immature hexagonal lattice underneath the viral membrane2,3. Upon completion of
assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in
which the immature lattice is broken down; the liberated CA domain of Gag then
re-assembles into the mature conical capsid that encloses the viral genome and
associated enzymes. Folding and proteolysis of the six-helix bundle are crucial
rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle
is an established target of HIV-1 inhibitors4,5. Here, using a combination of
structural and functional analyses, we show that inositol hexakisphosphate (InsP6,
also known as IP6) facilitates the formation of the six-helix bundle and assembly
of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of
lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks
an alternative binding site, where IP6 interaction promotes the assembly of the
mature capsid lattice. These studies identify IP6 as a naturally occurring small
molecule that promotes both assembly and maturation of HIV-1.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Kaneil K
full_name: Zadrozny, Kaneil K
last_name: Zadrozny
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Terri D
full_name: Lyddon, Terri D
last_name: Lyddon
- first_name: Clifton L
full_name: Ricana, Clifton L
last_name: Ricana
- first_name: Jonathan M
full_name: Wagner, Jonathan M
last_name: Wagner
- first_name: Juan R
full_name: Perilla, Juan R
last_name: Perilla
- first_name: Pornillos Barbie K
full_name: Ganser, Pornillos Barbie K
last_name: Ganser
- first_name: Marc C
full_name: Johnson, Marc C
last_name: Johnson
- first_name: Owen
full_name: Pornillos, Owen
last_name: Pornillos
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
citation:
ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors
for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4
apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C.
L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1.
Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4
chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon,
Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly
Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.
ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,”
Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.
ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla
JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are
assembly co-factors for HIV-1. Nature. 560(7719), 509–512.
mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.”
Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512,
doi:10.1038/s41586-018-0396-4.
short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M.
Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature
560 (2018) 509–512.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-08-29T00:00:00Z
date_updated: 2023-09-12T07:44:37Z
day: '29'
department:
- _id: FlSc
doi: 10.1038/s41586-018-0396-4
external_id:
isi:
- '000442483400046'
pmid:
- '30158708'
intvolume: ' 560'
isi: 1
issue: '7719'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/
month: '08'
oa: 1
oa_version: Submitted Version
page: 509–512
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-018-0505-4
scopus_import: '1'
status: public
title: Inositol phosphates are assembly co-factors for HIV-1
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 560
year: '2018'
...
---
_id: '303'
abstract:
- lang: eng
text: The theory of tropical series, that we develop here, firstly appeared in the
study of the growth of pluriharmonic functions. Motivated by waves in sandpile
models we introduce a dynamic on the set of tropical series, and it is experimentally
observed that this dynamic obeys a power law. So, this paper serves as a compilation
of results we need for other articles and also introduces several objects interesting
by themselves.
acknowledgement: The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility
grant 168647. Support from the Basic Research Program of the National Research University
Higher School of Economics is gratefully acknowledged. The second author, Mikhail
Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science
Foundation as well as by the National Center of Competence in Research SwissMAP
of the Swiss National Science Foundation.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on
them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849.
doi:10.3934/dcds.2018120
apa: Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and
wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A.
AIMS. https://doi.org/10.3934/dcds.2018120
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series
and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series
A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.
ieee: N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic
on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38,
no. 6. AIMS, pp. 2827–2849, 2018.
ista: Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic
on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and
Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A,
vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.
short: N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series
A 38 (2018) 2827–2849.
date_created: 2018-12-11T11:45:43Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-12T07:45:37Z
day: '01'
department:
- _id: TaHa
doi: 10.3934/dcds.2018120
external_id:
arxiv:
- '1706.03062'
isi:
- '000438818400007'
intvolume: ' 38'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.03062
month: '06'
oa: 1
oa_version: Submitted Version
page: 2827 - 2849
publication: Discrete and Continuous Dynamical Systems- Series A
publication_status: published
publisher: AIMS
publist_id: '7576'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to tropical series and wave dynamic on them
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2018'
...
---
_id: '14202'
abstract:
- lang: eng
text: "Approximating a probability density in a tractable manner is a central task\r\nin
Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves
tractability by choosing a relatively simple variational family.\r\nBorrowing
ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost}
VI by replacing the selection of a single density with a\r\ngreedily constructed
mixture of densities. In order to guarantee convergence,\r\nprevious works impose
stringent assumptions that require significant effort for\r\npractitioners. Specifically,
they require a custom implementation of the greedy\r\nstep (called the LMO) for
every probabilistic model with respect to an\r\nunnatural variational family of
truncated distributions. Our work fixes these\r\nissues with novel theoretical
and algorithmic insights. On the theoretical\r\nside, we show that boosting VI
satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence
of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the
LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces
the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow
for black box implementation of the boosting\r\nsubroutine. Finally, we present
a stopping criterion drawn from the duality gap\r\nin the classic FW analyses
and exhaustive experiments to illustrate the\r\nusefulness of our theoretical
and algorithmic contributions."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gideon
full_name: Dresdner, Gideon
last_name: Dresdner
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Isabel
full_name: Valera, Isabel
last_name: Valera
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box
variational inference. In: Advances in Neural Information Processing Systems.
Vol 31. Neural Information Processing Systems Foundation; 2018.'
apa: 'Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018).
Boosting black box variational inference. In Advances in Neural Information
Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing
Systems Foundation.'
chicago: Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and
Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural
Information Processing Systems, Vol. 31. Neural Information Processing Systems
Foundation, 2018.
ieee: F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting
black box variational inference,” in Advances in Neural Information Processing
Systems, Montreal, Canada, 2018, vol. 31.
ista: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black
box variational inference. Advances in Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 31.'
mla: Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances
in Neural Information Processing Systems, vol. 31, Neural Information Processing
Systems Foundation, 2018.
short: F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances
in Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2018.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2018-12-03
date_created: 2023-08-22T14:15:40Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T07:38:24Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02185'
intvolume: ' 31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02185
month: '06'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
isbn:
- '9781510884472'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boosting black box variational inference
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '14201'
abstract:
- lang: eng
text: "Variational inference is a popular technique to approximate a possibly\r\nintractable
Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational
inference has been proposed as a new paradigm to approximate the\r\nposterior
by a mixture of densities by greedily adding components to the\r\nmixture. However,
as is the case with many other variational inference\r\nalgorithms, its theoretical
properties have not been studied. In the present\r\nwork, we study the convergence
properties of this approach from a modern\r\noptimization viewpoint by establishing
connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel
theoretical insights regarding the\r\nsufficient conditions for convergence, explicit
rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works
for variational\r\ninference has been on tractability, our work is especially
important as a much\r\nneeded attempt to bridge the gap between probabilistic
models and their\r\ncorresponding theoretical properties."
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Joydeep
full_name: Ghosh, Joydeep
last_name: Ghosh
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference:
An optimization perspective. In: Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.'
apa: 'Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational
inference: An optimization perspective. In Proceedings of the 21st International
Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472).
Playa Blanca, Lanzarote: ML Research Press.'
chicago: 'Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch.
“Boosting Variational Inference: An Optimization Perspective.” In Proceedings
of the 21st International Conference on Artificial Intelligence and Statistics,
84:464–72. ML Research Press, 2018.'
ieee: 'F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference:
An optimization perspective,” in Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018,
vol. 84, pp. 464–472.'
ista: 'Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference:
An optimization perspective. Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence
and Statistics, PMLR, vol. 84, 464–472.'
mla: 'Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization
Perspective.” Proceedings of the 21st International Conference on Artificial
Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.'
short: F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st
International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2018, pp. 464–472.
conference:
end_date: 2018-04-11
location: Playa Blanca, Lanzarote
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2018-04-09
date_created: 2023-08-22T14:15:20Z
date_published: 2018-04-15T00:00:00Z
date_updated: 2023-09-13T07:52:40Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1708.01733'
intvolume: ' 84'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01733
month: '04'
oa: 1
oa_version: Preprint
page: 464-472
publication: Proceedings of the 21st International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Boosting variational inference: An optimization perspective'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...
---
_id: '14198'
abstract:
- lang: eng
text: "High-dimensional time series are common in many domains. Since human\r\ncognition
is not optimized to work well in high-dimensional spaces, these areas\r\ncould
benefit from interpretable low-dimensional representations. However, most\r\nrepresentation
learning algorithms for time series data are difficult to\r\ninterpret. This is
due to non-intuitive mappings from data features to salient\r\nproperties of the
representation and non-smoothness over time. To address this\r\nproblem, we propose
a new representation learning framework building on ideas\r\nfrom interpretable
discrete dimensionality reduction and deep generative\r\nmodeling. This framework
allows us to learn discrete representations of time\r\nseries, which give rise
to smooth and interpretable embeddings with superior\r\nclustering performance.
We introduce a new way to overcome the\r\nnon-differentiability in discrete representation
learning and present a\r\ngradient-based version of the traditional self-organizing
map algorithm that is\r\nmore performant than the original. Furthermore, to allow
for a probabilistic\r\ninterpretation of our method, we integrate a Markov model
in the representation\r\nspace. This model uncovers the temporal transition structure,
improves\r\nclustering performance even further and provides additional explanatory\r\ninsights
as well as a natural representation of uncertainty. We evaluate our\r\nmodel in
terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST
data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic
Lorenz attractor system with two macro states, as well as on\r\na challenging
real world medical time series application on the eICU data set.\r\nOur learned
representations compare favorably with competitor methods and\r\nfacilitate downstream
tasks on the real world data."
article_processing_charge: No
author:
- first_name: Vincent
full_name: Fortuin, Vincent
last_name: Fortuin
- first_name: Matthias
full_name: Hüser, Matthias
last_name: Hüser
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Heiko
full_name: Strathmann, Heiko
last_name: Strathmann
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable
discrete representation learning on time series. In: International Conference
on Learning Representations. ; 2018.'
apa: 'Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018).
SOM-VAE: Interpretable discrete representation learning on time series. In International
Conference on Learning Representations. New Orleans, LA, United States.'
chicago: 'Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann,
and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on
Time Series.” In International Conference on Learning Representations,
2018.'
ieee: 'V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE:
Interpretable discrete representation learning on time series,” in International
Conference on Learning Representations, New Orleans, LA, United States, 2018.'
ista: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable
discrete representation learning on time series. International Conference on Learning
Representations. ICLR: International Conference on Learning Representations.'
mla: 'Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning
on Time Series.” International Conference on Learning Representations,
2018.'
short: V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International
Conference on Learning Representations, 2018.
conference:
end_date: 2019-05-09
location: New Orleans, LA, United States
name: 'ICLR: International Conference on Learning Representations'
start_date: 2019-05-06
date_created: 2023-08-22T14:12:48Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T06:35:12Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02199'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02199
month: '06'
oa: 1
oa_version: Preprint
publication: International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: 'SOM-VAE: Interpretable discrete representation learning on time series'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '14203'
abstract:
- lang: eng
text: We propose a conditional gradient framework for a composite convex minimization
template with broad applications. Our approach combines smoothing and homotopy
techniques under the CGM framework, and provably achieves the optimal O(1/k−−√)
convergence rate. We demonstrate that the same rate holds if the linear subproblems
are solved approximately with additive or multiplicative error. In contrast with
the relevant work, we are able to characterize the convergence when the non-smooth
term is an indicator function. Specific applications of our framework include
the non-smooth minimization, semidefinite programming, and minimization with linear
inclusion constraints over a compact domain. Numerical evidence demonstrates the
benefits of our framework.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
- first_name: Olivier
full_name: Fercoq, Olivier
last_name: Fercoq
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework
for composite convex minimization with applications to semidefinite programming.
In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:5727-5736.'
apa: 'Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional
gradient framework for composite convex minimization with applications to semidefinite
programming. In Proceedings of the 35th International Conference on Machine
Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.'
chicago: Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher.
“A Conditional Gradient Framework for Composite Convex Minimization with Applications
to Semidefinite Programming.” In Proceedings of the 35th International Conference
on Machine Learning, 80:5727–36. ML Research Press, 2018.
ieee: A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming,” in Proceedings of the 35th International Conference on Machine
Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.
ista: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming. Proceedings of the 35th International Conference on Machine Learning.
ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.'
mla: Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex
Minimization with Applications to Semidefinite Programming.” Proceedings of
the 35th International Conference on Machine Learning, vol. 80, ML Research
Press, 2018, pp. 5727–36.
short: A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the
35th International Conference on Machine Learning, ML Research Press, 2018, pp.
5727–5736.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2023-08-22T14:16:01Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-13T08:13:39Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1804.08544'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.08544
month: '07'
oa: 1
oa_version: Preprint
page: 5727-5736
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A conditional gradient framework for composite convex minimization with applications
to semidefinite programming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '282'
abstract:
- lang: eng
text: Adaptive introgression is common in nature and can be driven by selection
acting on multiple, linked genes. We explore the effects of polygenic selection
on introgression under the infinitesimal model with linkage. This model assumes
that the introgressing block has an effectively infinite number of genes, each
with an infinitesimal effect on the trait under selection. The block is assumed
to introgress under directional selection within a native population that is genetically
homogeneous. We use individual-based simulations and a branching process approximation
to compute various statistics of the introgressing block, and explore how these
depend on parameters such as the map length and initial trait value associated
with the introgressing block, the genetic variability along the block, and the
strength of selection. Our results show that the introgression dynamics of a block
under infinitesimal selection is qualitatively different from the dynamics of
neutral introgression. We also find that in the long run, surviving descendant
blocks are likely to have intermediate lengths, and clarify how the length is
shaped by the interplay between linkage and infinitesimal selection. Our results
suggest that it may be difficult to distinguish introgression of single loci from
that of genomic blocks with multiple, tightly linked and weakly selected loci.
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. Introgression of a block of genome under infinitesimal
selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018
apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome
under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018
chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301018.
ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal
selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp.
1279–1303, 2018.
ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal
selection. Genetics. 209(4), 1279–1303.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society
of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.
short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T08:22:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301018
external_id:
isi:
- '000440014100020'
intvolume: ' 209'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/11/30/227082
month: '08'
oa: 1
oa_version: Submitted Version
page: 1279 - 1303
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7617'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introgression of a block of genome under infinitesimal selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '14204'
abstract:
- lang: eng
text: Two popular examples of first-order optimization methods over linear spaces
are coordinate descent and matching pursuit algorithms, with their randomized
variants. While the former targets the optimization by moving along coordinates,
the latter considers a generalized notion of directions. Exploiting the connection
between the two algorithms, we present a unified analysis of both, providing affine
invariant sublinear O(1/t) rates on smooth objectives and linear convergence on
strongly convex objectives. As a byproduct of our affine invariant analysis of
matching pursuit, our rates for steepest coordinate descent are the tightest known.
Furthermore, we show the first accelerated convergence rate O(1/t2) for matching
pursuit and steepest coordinate descent on convex objectives.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Anant
full_name: Raj, Anant
last_name: Raj
- first_name: Sai Praneeth
full_name: Karimireddy, Sai Praneeth
last_name: Karimireddy
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Sebastian U.
full_name: Stich, Sebastian U.
last_name: Stich
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate
descent. In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:3198-3207.'
apa: Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich,
S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In
Proceedings of the 35th International Conference on Machine Learning (Vol.
80, pp. 3198–3207). ML Research Press.
chicago: Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch,
Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit
and Coordinate Descent.” In Proceedings of the 35th International Conference
on Machine Learning, 80:3198–3207. ML Research Press, 2018.
ieee: F. Locatello et al., “On matching pursuit and coordinate descent,”
in Proceedings of the 35th International Conference on Machine Learning,
2018, vol. 80, pp. 3198–3207.
ista: Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi
M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International
Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.
mla: Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.”
Proceedings of the 35th International Conference on Machine Learning, vol.
80, ML Research Press, 2018, pp. 3198–207.
short: F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich,
M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning,
ML Research Press, 2018, pp. 3198–3207.
date_created: 2023-08-22T14:16:25Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-13T08:19:05Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1803.09539'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.09539
month: '07'
oa: 1
oa_version: Preprint
page: 3198-3207
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On matching pursuit and coordinate descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '160'
abstract:
- lang: eng
text: We present layered concurrent programs, a compact and expressive notation
for specifying refinement proofs of concurrent programs. A layered concurrent
program specifies a sequence of connected concurrent programs, from most concrete
to most abstract, such that common parts of different programs are written exactly
once. These programs are expressed in the ordinary syntax of imperative concurrent
programs using gated atomic actions, sequencing, choice, and (recursive) procedure
calls. Each concurrent program is automatically extracted from the layered program.
We reduce refinement to the safety of a sequence of concurrent checker programs,
one each to justify the connection between every two consecutive concurrent programs.
These checker programs are also automatically extracted from the layered program.
Layered concurrent programs have been implemented in the CIVL verifier which has
been successfully used for the verification of several complex concurrent programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: 'Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102.
doi:10.1007/978-3-319-96145-3_5'
apa: 'Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981,
pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer.
https://doi.org/10.1007/978-3-319-96145-3_5'
chicago: Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102.
Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.
ieee: 'B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV:
Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.'
ista: 'Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided
Verification, LNCS, vol. 10981, 79–102.'
mla: Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol.
10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.
short: B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.
conference:
end_date: 2018-07-17
location: Oxford, UK
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-13T08:45:09Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_5
external_id:
isi:
- '000491481600005'
file:
- access_level: open_access
checksum: c64fff560fe5a7532ec10626ad1c215e
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:52:12Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5705'
file_name: 2018_LNCS_Kragl.pdf
file_size: 1603844
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 102
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '7761'
quality_controlled: '1'
related_material:
record:
- id: '8332'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Layered Concurrent Programs
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '82'
abstract:
- lang: eng
text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage,
bacterial cells resistant to the phage commonly emerge and become the dominant
population of bacteria. Following the ascent of resistant mutants, the densities
of bacteria in these simple communities become limited by resources rather than
the phage. Despite the evolution of resistant hosts, upon which the phage cannot
replicate, the lytic phage population is most commonly maintained in an apparently
stable state with the resistant bacteria. Several mechanisms have been put forward
to account for this result. Here we report the results of population dynamic/evolution
experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli
in serial transfer cultures. We show that, following the ascent of λVIR-resistant
bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal
media and in all cases in nutrient-rich broth. Using mathematical models and experiments,
we show that the dominant mechanism responsible for maintenance of λVIRin these
resource-limited populations dominated by resistant E. coli is a high rate of
either phenotypic or genetic transition from resistance to susceptibility—a hitherto
undemonstrated mechanism we term "leaky resistance." We discuss the
implications of leaky resistance to our understanding of the conditions for the
maintenance of phage in populations of bacteria—their “existence conditions.”.
article_number: '2005971'
article_processing_charge: Yes
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for
the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance
and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence
of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of
Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Leaky resistance and the conditions for the existence of lytic
bacteriophage. PLoS Biology. 16(8), 2005971.
mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence
of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public
Library of Science, 2018, doi:10.1371/journal.pbio.2005971.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:44:32Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971
external_id:
isi:
- '000443383300024'
file:
- access_level: open_access
checksum: 527076f78265cd4ea192cd1569851587
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:55:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5706'
file_name: 2018_Plos_Chaudhry.pdf
file_size: 4007095
relation: main_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7972'
quality_controlled: '1'
related_material:
record:
- id: '9810'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Leaky resistance and the conditions for the existence of lytic bacteriophage
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: 16
year: '2018'
...
---
_id: '4'
abstract:
- lang: eng
text: We present a data-driven technique to instantly predict how fluid flows around
various three-dimensional objects. Such simulation is useful for computational
fabrication and engineering, but is usually computationally expensive since it
requires solving the Navier-Stokes equation for many time steps. To accelerate
the process, we propose a machine learning framework which predicts aerodynamic
forces and velocity and pressure fields given a threedimensional shape input.
Handling detailed free-form three-dimensional shapes in a data-driven framework
is challenging because machine learning approaches usually require a consistent
parametrization of input and output. We present a novel PolyCube maps-based parametrization
that can be computed for three-dimensional shapes at interactive rates. This allows
us to efficiently learn the nonlinear response of the flow using a Gaussian process
regression. We demonstrate the effectiveness of our approach for the interactive
design and optimization of a car body.
article_number: '89'
article_processing_charge: No
author:
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic
design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325
apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325
chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for
Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.
ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive
aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.
ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. 37(4), 89.
mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive
Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018,
doi:10.1145/3197517.3201325.
short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:06Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:46:15Z
day: '04'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201325
ec_funded: 1
external_id:
isi:
- '000448185000050'
file:
- access_level: open_access
checksum: 7a2243668f215821bc6aecad0320079a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5216'
file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf
file_size: 22803163
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8053'
pubrep_id: '1049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/
scopus_import: '1'
status: public
title: Learning three-dimensional flow for interactive aerodynamic design
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '566'
abstract:
- lang: eng
text: "We consider large random matrices X with centered, independent entries which
have comparable but not necessarily identical variances. Girko's circular law
asserts that the spectrum is supported in a disk and in case of identical variances,
the limiting density is uniform. In this special case, the local circular law
by Bourgade et. al. [11,12] shows that the empirical density converges even locally
on scales slightly above the typical eigenvalue spacing. In the general case,
the limiting density is typically inhomogeneous and it is obtained via solving
a system of deterministic equations. Our main result is the local inhomogeneous
circular law in the bulk spectrum on the optimal scale for a general variance
profile of the entries of X. \r\n\r\n"
article_processing_charge: No
article_type: original
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 inhomogeneous circular law. Annals Applied
Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302
apa: Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular
law. Annals Applied Probability . Institute of Mathematical Statistics.
https://doi.org/10.1214/17-AAP1302
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous
Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics,
2018. https://doi.org/10.1214/17-AAP1302.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals
Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics,
pp. 148–203, 2018.
ista: Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals
Applied Probability . 28(1), 148–203.
mla: Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied
Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018,
pp. 148–203, doi:10.1214/17-AAP1302.
short: J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.
date_created: 2018-12-11T11:47:13Z
date_published: 2018-03-03T00:00:00Z
date_updated: 2023-09-13T08:47:52Z
day: '03'
department:
- _id: LaEr
doi: 10.1214/17-AAP1302
ec_funded: 1
external_id:
arxiv:
- '1612.07776 '
isi:
- '000431721800005'
intvolume: ' 28'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://arxiv.org/abs/1612.07776 '
month: '03'
oa: 1
oa_version: Preprint
page: 148-203
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annals Applied Probability '
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local inhomogeneous circular law
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '275'
abstract:
- lang: eng
text: Lymphatic endothelial cells (LECs) release extracellular chemokines to guide
the migration of dendritic cells. In this study, we report that LECs also release
basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater
numbers in the presence of inflammatory cytokines and accumulate in the perivascular
stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic
analyses of EEV fractions identified > 1,700 cargo proteins and revealed a
dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions
augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion
and enhanced the directional migratory response of human dendritic cells along
guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory
behavior and thus promote directional migration of CX3CR1-expressing cells in
complex tissue environments.
acknowledgement: M. Brown was supported by the Cell Communication in Health and Disease
Graduate Study Program of the Austrian Science Fund and Medizinische Universität
Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science
Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson
and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical
Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer
Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European
Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland
postdoctoral research grant (287853). This project has received funding from the
European Union’s Horizon 2020 research and innovation program under grant agreement
No. 668036 (RELENT).
article_processing_charge: No
author:
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Louise
full_name: Johnson, Louise
last_name: Johnson
- first_name: Dario
full_name: Leone, Dario
last_name: Leone
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Daniel
full_name: Senfter, Daniel
last_name: Senfter
- first_name: Nora
full_name: Bukosza, Nora
last_name: Bukosza
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Gabriele
full_name: Asfour, Gabriele
last_name: Asfour
- first_name: Brigitte
full_name: Langer, Brigitte
last_name: Langer
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Katja
full_name: Parapatics, Katja
last_name: Parapatics
- first_name: Young
full_name: Hong, Young
last_name: Hong
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Michael
full_name: Detmar, Michael
last_name: Detmar
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: David
full_name: Jackson, David
last_name: Jackson
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
citation:
ama: Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell
migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221.
doi:10.1083/jcb.201612051
apa: Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D.,
… Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along
guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051
chicago: Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri,
Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell
Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University
Press, 2018. https://doi.org/10.1083/jcb.201612051.
ieee: M. Brown et al., “Lymphatic exosomes promote dendritic cell migration
along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller
University Press, pp. 2205–2221, 2018.
ista: Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N,
Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K,
Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote
dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6),
2205–2221.
mla: Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration
along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller
University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.
short: M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza,
H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett,
R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology
217 (2018) 2205–2221.
date_created: 2018-12-11T11:45:33Z
date_published: 2018-04-12T00:00:00Z
date_updated: 2023-09-13T08:51:29Z
day: '12'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1083/jcb.201612051
ec_funded: 1
external_id:
isi:
- '000438077800026'
pmid:
- '29650776'
file:
- access_level: open_access
checksum: 9c7eba51a35c62da8c13f98120b64df4
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:50:07Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5704'
file_name: 2018_JournalCellBiology_Brown.pdf
file_size: 2252043
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 217'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2205 - 2221
pmid: 1
project:
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '7627'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lymphatic exosomes promote dendritic cell migration along guidance cues
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: 217
year: '2018'
...
---
_id: '158'
abstract:
- lang: eng
text: 'The angiosperm seed is composed of three genetically distinct tissues: the
diploid embryo that originates from the fertilized egg cell, the triploid endosperm
that is produced from the fertilized central cell, and the maternal sporophytic
integuments that develop into the seed coat1. At the onset of embryo development
in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small
apical embryonic cell and a larger basal cell that connects the embryo to the
maternal tissue2. The coordinated and synchronous development of the embryo and
the surrounding integuments, and the alignment of their growth axes, suggest communication
between maternal tissues and the embryo. In contrast to animals, however, where
a network of maternal factors that direct embryo patterning have been identified3,4,
only a few maternal mutations have been described to affect embryo development
in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of
the phytohormone auxin in the apical cell by directed transport from the suspensor8–10.
However, the origin of this auxin has remained obscure. Here we investigate the
source of auxin for early embryogenesis and provide evidence that the mother plant
coordinates seed development by supplying auxin to the early embryo from the integuments
of the ovule. We show that auxin response increases in ovules after fertilization,
due to upregulated auxin biosynthesis in the integuments, and this maternally
produced auxin is required for correct embryo development.'
acknowledgement: This work was further supported by the Czech Science Foundation GACR
(GA13-40637S) to J.F.;
article_processing_charge: No
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Chulmin
full_name: Park, Chulmin
last_name: Park
- first_name: Carla
full_name: Gutièrrez, Carla
last_name: Gutièrrez
- first_name: Barbara
full_name: Wójcikowska, Barbara
last_name: Wójcikowska
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Junyi
full_name: Chen, Junyi
last_name: Chen
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Thomas
full_name: Dresselhaus, Thomas
last_name: Dresselhaus
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Thomas
full_name: Laux, Thomas
last_name: Laux
citation:
ama: Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to
early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553.
doi:10.1038/s41477-018-0204-z
apa: Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O.,
… Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z
chicago: Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš
Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to
Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.
ieee: H. Robert et al., “Maternal auxin supply contributes to early embryo
patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing
Group, pp. 548–553, 2018.
ista: Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald
W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to
early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.
mla: Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning
in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group,
2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.
short: H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J.
Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018)
548–553.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T08:53:28Z
day: '16'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0204-z
ec_funded: 1
external_id:
isi:
- '000443861300011'
pmid:
- '30013211'
intvolume: ' 4'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30013211
month: '07'
oa: 1
oa_version: Submitted Version
page: 548 - 553
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7763'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/
scopus_import: '1'
status: public
title: Maternal auxin supply contributes to early embryo patterning in Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '152'
abstract:
- lang: eng
text: Complex I has an essential role in ATP production by coupling electron transfer
from NADH to quinone with translocation of protons across the inner mitochondrial
membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited
diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative
conditions. Until recently, the understanding of complex I deficiency on the molecular
level was limited due to the lack of high-resolution structures of the enzyme.
However, due to developments in single particle cryo-electron microscopy (cryo-EM),
recent studies have reported nearly atomic resolution maps and models of mitochondrial
complex I. These structures significantly add to our understanding of complex
I mechanism and assembly. The disease-causing mutations are discussed here in
their structural context.
article_processing_charge: No
article_type: original
author:
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease
causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006
apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex
I structure and disease causing mutations. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2018.06.006
chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier,
2018. https://doi.org/10.1016/j.tcb.2018.06.006.
ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure
and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10.
Elsevier, pp. 835–867, 2018.
ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure
and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.
mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol.
28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.
short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-13T08:51:56Z
day: '26'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1016/j.tcb.2018.06.006
external_id:
isi:
- '000445118200007'
file:
- access_level: open_access
checksum: ef6d2b4e1fd63948539639242610bfa6
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:55:20Z
date_updated: 2020-07-14T12:45:00Z
file_id: '6994'
file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf
file_size: 2185385
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '10'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 835 - 867
publication: Trends in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '7769'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mammalian mitochondrial complex I structure and disease causing mutations
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: 28
year: '2018'
...
---
_id: '310'
abstract:
- lang: eng
text: A model of computation that is widely used in the formal analysis of reactive
systems is symbolic algorithms. In this model the access to the input graph is
restricted to consist of symbolic operations, which are expensive in comparison
to the standard RAM operations. We give lower bounds on the number of symbolic
operations for basic graph problems such as the computation of the strongly connected
components and of the approximate diameter as well as for fundamental problems
in model checking such as safety, liveness, and coliveness. Our lower bounds are
linear in the number of vertices of the graph, even for constant-diameter graphs.
For none of these problems lower bounds on the number of symbolic operations were
known before. The lower bounds show an interesting separation of these problems
from the reachability problem, which can be solved with O(D) symbolic operations,
where D is the diameter of the graph. Additionally we present an approximation
algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve
a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic
steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation.
Finally we also give a refined analysis of the strongly connected components algorithms
of [15], showing that it uses an optimal number of symbolic steps that is proportional
to the sum of the diameters of the strongly connected components.
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: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic
computation on graphs: Strongly connected components, liveness, safety, and diameter.
In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018).
Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium
on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151'
chicago: 'Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika
Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected
Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.'
ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans,
Louisiana, United States, 2018, pp. 2341–2356.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.'
mla: 'Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on
Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM,
2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.'
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018,
pp. 2341–2356.
conference:
end_date: 2018-01-10
location: New Orleans, Louisiana, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:45Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-13T08:50:16Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611975031.151
ec_funded: 1
external_id:
arxiv:
- '1711.09148'
isi:
- '000483921200152'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.09148
month: '01'
oa: 1
oa_version: Preprint
page: 2341 - 2356
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: ACM
publist_id: '7555'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '436'
abstract:
- lang: eng
text: There has been significant interest recently in using complex quantum systems
to create effective nonreciprocal dynamics. Proposals have been put forward for
the realization of artificial magnetic fields for photons and phonons; experimental
progress is fast making these proposals a reality. Much work has concentrated
on the use of such systems for controlling the flow of signals, e.g., to create
isolators or directional amplifiers for optical signals. In this Letter, we build
on this work but move in a different direction. We develop the theory of and discuss
a potential realization for the controllable flow of thermal noise in quantum
systems. We demonstrate theoretically that the unidirectional flow of thermal
noise is possible within quantum cascaded systems. Viewing an optomechanical platform
as a cascaded system we show here that one can ultimately control the direction
of the flow of thermal noise. By appropriately engineering the mechanical resonator,
which acts as an artificial reservoir, the flow of thermal noise can be constrained
to a desired direction, yielding a thermal rectifier. The proposed quantum thermal
noise rectifier could potentially be used to develop devices such as a thermal
modulator, a thermal router, and a thermal amplifier for nanoelectronic devices
and superconducting circuits.
article_number: '060601 '
article_processing_charge: No
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
citation:
ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in
quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601
apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow
of thermal noise in quantum devices. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601
chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the
Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American
Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.
ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal
noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American
Physical Society, 2018.
ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal
noise in quantum devices. Physical Review Letters. 120(6), 060601.
mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum
Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical
Society, 2018, doi:10.1103/PhysRevLett.120.060601.
short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2023-09-13T08:52:27Z
day: '07'
department:
- _id: JoFi
doi: 10.1103/PhysRevLett.120.060601
ec_funded: 1
external_id:
arxiv:
- '1706.09051'
isi:
- '000424382100004'
intvolume: ' 120'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09051
month: '02'
oa: 1
oa_version: Preprint
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 SUPEREOM'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7387'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/
scopus_import: '1'
status: public
title: Manipulating the flow of thermal noise in quantum devices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 120
year: '2018'
...
---
_id: '5858'
abstract:
- lang: eng
text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level,
and can be studied using imaging techniques such as light and fluorescence microscopy.
Imaging data provide quantitative information about biological systems; however,
mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal
mathematical modelling has helped to overcome this problem. Yet, outliers and
structured noise limit modelling of whole imaging data, and models often consider
spatial summary statistics. Here, we introduce an integrated data-driven modelling
approach that can cope with measurement artefacts and whole imaging data. Our
approach combines mechanistic models of the biological processes with robust statistical
models of the measurement process. The parameters of the integrated model are
calibrated using a maximum-likelihood approach. We used this integrated modelling
approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21).
CCL21 gradients guide dendritic cells and are important in the adaptive immune
response. Using artificial data, we verified that the integrated modelling approach
provides reliable parameter estimates in the presence of measurement noise and
that bias and variance of these estimates are reduced compared to conventional
approaches. The application to experimental data allowed the parametrization and
subsequent refinement of the model using additional mechanisms. Among other results,
model-based hypothesis testing predicted lymphatic vessel-dependent concentration
of heparan sulfate, the binding partner of CCL21. The selected model provided
an accurate description of the experimental data and was partially validated using
published data. Our findings demonstrate that integrated statistical modelling
of whole imaging data is computationally feasible and can provide novel biological
insights.
article_number: '20180600'
article_processing_charge: No
author:
- first_name: Sabrina
full_name: Hross, Sabrina
last_name: Hross
- first_name: Fabian J.
full_name: Theis, Fabian J.
last_name: Theis
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jan
full_name: Hasenauer, Jan
last_name: Hasenauer
citation:
ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial
processes using integrative modelling of noise-corrupted imaging data. Journal
of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600
apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic
description of spatial processes using integrative modelling of noise-corrupted
imaging data. Journal of the Royal Society Interface. Royal Society Publishing.
https://doi.org/10.1098/rsif.2018.0600
chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic
Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted
Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing,
2018. https://doi.org/10.1098/rsif.2018.0600.
ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description
of spatial processes using integrative modelling of noise-corrupted imaging data,”
Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society
Publishing, 2018.
ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of
spatial processes using integrative modelling of noise-corrupted imaging data.
Journal of the Royal Society Interface. 15(149), 20180600.
mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using
Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal
Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018,
doi:10.1098/rsif.2018.0600.
short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society
Interface 15 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-05T00:00:00Z
date_updated: 2023-09-13T08:55:05Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1098/rsif.2018.0600
external_id:
isi:
- '000456783800011'
file:
- access_level: open_access
checksum: 56eb4308a15b7190bff938fab1f780e8
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:46:44Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5925'
file_name: 2018_Interface_Hross.pdf
file_size: 1464288
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic description of spatial processes using integrative modelling of
noise-corrupted imaging data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '16'
abstract:
- lang: eng
text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic
fluid flow between two widely spaced obstacles hindering a channel flow at Re
1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed
in the region between the obstacles. The mixing-layer instability arises in the
vicinity of an inflection point on the shear velocity profile with a steep variation
in the elastic stress. The instability results in an intermittent appearance of
small vortices in the mixing layers and an amplification of spatiotemporal averaged
vorticity in the elastic turbulence regime. The latter is characterized through
scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore,
the observations reported provide improved understanding of the stability of the
mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1
and oppose the current view of suppression of vorticity solely by polymer additives.
acknowledgement: This work was partially supported by the Israel Science Foundation
(ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No.
2016145).
article_number: '103303'
article_processing_charge: No
article_type: original
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303
apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity
amplification in a creeping viscoelastic flow. Physical Review Fluids.
American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303
chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.
ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10.
American Physical Society, 2018.
ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.
mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids,
vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:10Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2023-09-13T08:57:05Z
day: '16'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103303
ec_funded: 1
external_id:
isi:
- '000447469200001'
file:
- access_level: open_access
checksum: 7fc0a2322214d1c04debef36d5bf2e8a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5043'
file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf
file_size: 1838431
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8039'
pubrep_id: '1062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixing layer instability and vorticity amplification in a creeping viscoelastic
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '43'
abstract:
- lang: eng
text: 'The initial amount of pathogens required to start an infection within a susceptible
host is called the infective dose and is known to vary to a large extent between
different pathogen species. We investigate the hypothesis that the differences
in infective doses are explained by the mode of action in the underlying mechanism
of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller
infective doses than pathogens with distantly acting mechanisms. While empirical
evidence tends to support the hypothesis, a formal theoretical explanation has
been lacking. We give simple analytical models to gain insight into this phenomenon
and also investigate a stochastic, spatially explicit, mechanistic within-host
model for toxin-dependent bacterial infections. The model shows that pathogens
secreting locally acting toxins have smaller infective doses than pathogens secreting
diffusive toxins, as hypothesized. While local pathogenetic mechanisms require
smaller infective doses, pathogens with distantly acting toxins tend to spread
faster and may cause more damage to the host. The proposed model can serve as
a basis for the spatially explicit analysis of various virulence factors also
in the context of other problems in infection dynamics.'
acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants
1273253 and 267541.
article_processing_charge: No
author:
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Eva
full_name: Kisdi, Eva
last_name: Kisdi
- first_name: Jani
full_name: Anttila, Jani
last_name: Anttila
citation:
ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115
apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent
pathogenesis explains infective dose. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1721061115
chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent
Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1721061115.
ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent
pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National
Academy of Sciences, pp. 10690–10695, 2018.
ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 115(42), 10690–10695.
mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains
Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences,
2018, pp. 10690–95, doi:10.1073/pnas.1721061115.
short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-02T00:00:00Z
date_updated: 2023-09-13T08:57:38Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: DaAl
doi: 10.1073/pnas.1721061115
ec_funded: 1
external_id:
isi:
- '000447491300057'
file:
- access_level: open_access
checksum: df7ac544a587c06b75692653b9fabd18
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T08:02:50Z
date_updated: 2020-07-14T12:46:26Z
file_id: '6258'
file_name: 2018_PNAS_Rybicki.pdf
file_size: 4070777
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '42'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 10690 - 10695
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '8011'
pubrep_id: '1063'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model of bacterial toxin-dependent pathogenesis explains infective dose
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '13'
abstract:
- lang: eng
text: We propose a new method for fabricating digital objects through reusable silicone
molds. Molds are generated by casting liquid silicone into custom 3D printed containers
called metamolds. Metamolds automatically define the cuts that are needed to extract
the cast object from the silicone mold. The shape of metamolds is designed through
a novel segmentation technique, which takes into account both geometric and topological
constraints involved in the process of mold casting. Our technique is simple,
does not require changing the shape or topology of the input objects, and only
requires off-the- shelf materials and technologies. We successfully tested our
method on a set of challenging examples with complex shapes and rich geometric
detail. © 2018 Association for Computing Machinery.
article_number: '136'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Daniela
full_name: Giorgi, Daniela
last_name: Giorgi
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds:
Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381'
apa: 'Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni,
P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph.
ACM. https://doi.org/10.1145/3197517.3201381'
chicago: 'Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd
Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.'
ieee: 'T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni,
“Metamolds: Computational design of silicone molds,” ACM Trans. Graph.,
vol. 37, no. 4. ACM, 2018.'
ista: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds:
Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.'
mla: 'Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.'
short: T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM
Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:56:07Z
day: '04'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201381
ec_funded: 1
external_id:
isi:
- '000448185000097'
file:
- access_level: open_access
checksum: 61d46273dca4de626accef1d17a0aaad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:52Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5374'
file_name: IST-2018-1038-v1+1_metamolds_authorversion.pdf
file_size: 91939066
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8043'
pubrep_id: '1038'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/metamolds-molding-a-mold/
scopus_import: '1'
status: public
title: 'Metamolds: Computational design of silicone molds'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '137'
abstract:
- lang: eng
text: Fluorescent sensors are an essential part of the experimental toolbox of the
life sciences, where they are used ubiquitously to visualize intra- and extracellular
signaling. In the brain, optical neurotransmitter sensors can shed light on temporal
and spatial aspects of signal transmission by directly observing, for instance,
neurotransmitter release and spread. Here we report the development and application
of the first optical sensor for the amino acid glycine, which is both an inhibitory
neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs)
involved in synaptic plasticity. Computational design of a glycine-specific binding
protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can
be used with single and two-photon excitation fluorescence microscopy. We took
advantage of this newly developed sensor to test predictions about the uneven
spatial distribution of glycine in extracellular space and to demonstrate that
extracellular glycine levels are controlled by plasticity-inducing stimuli.
article_processing_charge: No
article_type: original
author:
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Andreas
full_name: Wulff, Andreas
last_name: Wulff
- first_name: Vanessa
full_name: Vongsouthi, Vanessa
last_name: Vongsouthi
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Polina
full_name: Gulakova, Polina
last_name: Gulakova
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Björn
full_name: Breithausen, Björn
last_name: Breithausen
- first_name: Susanne
full_name: Schoch, Susanne
last_name: Schoch
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
citation:
ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the
computationally designed optical sensor GlyFS. Nature Chemical Biology.
2018;14(9):861-869. doi:10.1038/s41589-018-0108-2
apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V.,
… Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing
Group. https://doi.org/10.1038/s41589-018-0108-2
chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas
Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal
Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical
Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.
ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9.
Nature Publishing Group, pp. 861–869, 2018.
ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero
I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger
C. 2018. Monitoring hippocampal glycine with the computationally designed optical
sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.
mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally
Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9,
Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.
short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I.
Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak,
C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-13T08:58:05Z
day: '30'
department:
- _id: HaJa
doi: 10.1038/s41589-018-0108-2
external_id:
isi:
- '000442174500013'
pmid:
- '30061718 '
intvolume: ' 14'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30061718
month: '07'
oa: 1
oa_version: Submitted Version
page: 861 - 869
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring hippocampal glycine with the computationally designed optical sensor
GlyFS
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '276'
abstract:
- lang: eng
text: Directed migration of cells relies on their ability to sense directional guidance
cues and to interact with pericellular structures in order to transduce contractile
cytoskeletal- into mechanical forces. These biomechanical processes depend highly
on microenvironmental factors such as exposure to 2D surfaces or 3D matrices.
In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell
migration are mostly derived from intravital microscopy or collagen-based in vitro
assays. Both approaches offer only limited controlla-bility of experimental conditions.
Here, we developed an automated microfluidic system that allows positioning of
cells in 3D microenvironments containing highly controlled diffusion-based chemokine
gradients. Tracking migration in such gradients was feasible in real time at the
single cell level. Moreover, the setup allowed on-chip immunocytochemistry and
thus linking of functional with phenotypical properties in individual cells. Spatially
defined retrieval of cells from the device allows down-stream off-chip analysis.
Using dendritic cells as a model, our setup specifically allowed us for the first
time to quantitate key migration characteristics of cells exposed to identical
gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration
properties between 2D and 3D migration were distinct. Morphological features of
cells migrating in an in vitro 3D environment were similar to those of cells migrating
in animal tissues, but different from cells migrating on a surface. Our system
thus offers a highly controllable in vitro-mimic of a 3D environment that cells
traffic in vivo.
acknowledgement: This work was supported by the Swiss National Science Foundation
(MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863
to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.),
a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship
(ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409)
to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.
article_number: e0198330
article_processing_charge: No
article_type: original
author:
- first_name: Corina
full_name: Frick, Corina
last_name: Frick
- first_name: Philip
full_name: Dettinger, Philip
last_name: Dettinger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Annaïse
full_name: Jauch, Annaïse
last_name: Jauch
- first_name: Christoph
full_name: Berger, Christoph
last_name: Berger
- first_name: Mike
full_name: Recher, Mike
last_name: Recher
- first_name: Timm
full_name: Schroeder, Timm
last_name: Schroeder
- first_name: Matthias
full_name: Mehling, Matthias
last_name: Mehling
citation:
ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study
3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330
apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M.,
… Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330
chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph
Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics
to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library
of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.
ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at
the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science,
2018.
ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder
T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. 13(6), e0198330.
mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the
Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library
of Science, 2018, doi:10.1371/journal.pone.0198330.
short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T.
Schroeder, M. Mehling, PLoS One 13 (2018).
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2023-09-13T09:00:15Z
day: '07'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0198330
external_id:
isi:
- '000434384900031'
file:
- access_level: open_access
checksum: 95fc5dc3938b3ad3b7697d10c83cc143
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:10:32Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5709'
file_name: 2018_Plos_Frick.pdf
file_size: 7682167
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level
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: 13
year: '2018'
...
---
_id: '283'
abstract:
- lang: eng
text: Light represents the principal signal driving circadian clock entrainment.
However, how light influences the evolution of the clock remains poorly understood.
The cavefish Phreatichthys andruzzii represents a fascinating model to explore
how evolution under extreme aphotic conditions shapes the circadian clock, since
in this species the clock is unresponsive to light. We have previously demonstrated
that loss-of-function mutations targeting non-visual opsins contribute in part
to this blind clock phenotype. Here, we have compared orthologs of two core clock
genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish
and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii
per2 transcript. The most abundant transcript encodes a truncated protein lacking
the C-terminal Cry binding domain and incorporating an intronic, transposon-derived
coding sequence. We demonstrate that the transposon insertion leads to a predominantly
cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish
ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems
that during evolution in complete darkness, the photic entrainment pathway of
the circadian clock has been subject to mutation at multiple levels, extending
from opsin photoreceptors to nuclear effectors.
article_number: '8754'
article_processing_charge: No
author:
- first_name: Rosa Maria
full_name: Ceinos, Rosa Maria
last_name: Ceinos
- first_name: Elena
full_name: Frigato, Elena
last_name: Frigato
- first_name: Cristina
full_name: Pagano, Cristina
last_name: Pagano
- first_name: Nadine
full_name: Frohlich, Nadine
last_name: Frohlich
- first_name: Pietro
full_name: Negrini, Pietro
last_name: Negrini
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Daniela
full_name: Vallone, Daniela
last_name: Vallone
- first_name: Silvia
full_name: Fuselli, Silvia
last_name: Fuselli
- first_name: Cristiano
full_name: Bertolucci, Cristiano
last_name: Bertolucci
- first_name: Nicholas S
full_name: Foulkes, Nicholas S
last_name: Foulkes
citation:
ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the
light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1).
doi:10.1038/s41598-018-27080-2
apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari,
N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated
circadian clock gene period 2. Scientific Reports. Nature Publishing Group.
https://doi.org/10.1038/s41598-018-27080-2
chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro
Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci,
and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group,
2018. https://doi.org/10.1038/s41598-018-27080-2.
ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light
regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no.
1. Nature Publishing Group, 2018.
ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone
D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target
the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.
mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754,
Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.
short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari,
D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-08T00:00:00Z
date_updated: 2023-09-13T08:59:27Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1038/s41598-018-27080-2
external_id:
isi:
- '000434640800008'
file:
- access_level: open_access
checksum: 9c3942d772f84f3df032ffde0ed9a8ea
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T13:04:46Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5707'
file_name: 2018_ScientificReports_Ceinos.pdf
file_size: 1855324
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7616'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations in blind cavefish target the light regulated circadian clock gene
period 2
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: '2018'
...
---
_id: '81'
abstract:
- lang: eng
text: We solve the offline monitoring problem for timed propositional temporal logic
(TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider
extends linear temporal logic (LTL) with clock variables and reset quantifiers,
providing a mechanism to specify real-time constraints. We first describe a general
monitoring algorithm based on an exhaustive computation of the set of satisfying
clock assignments as a finite union of zones. We then propose a specialized monitoring
algorithm for the one-variable case using a partition of the time domain based
on the notion of region equivalence, whose complexity is linear in the length
of the signal, thereby generalizing a known result regarding the monitoring of
metric temporal logic (MTL). The region and zone representations of time constraints
are known from timed automata verification and can also be used in the discrete-time
case. Our prototype implementation appears to outperform previous discrete-time
implementations of TPTL monitoring,
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables.
In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4'
apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal
logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4'
chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal
Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.
ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with
clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.'
ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with
clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 11022, 53–70.'
mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables.
Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.
short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.
conference:
end_date: 2018-09-06
location: Beijing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2023-09-13T08:58:34Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_4
external_id:
isi:
- '000884993200004'
file:
- access_level: open_access
checksum: e5d81c9b50a6bd9d8a2c16953aad7e23
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T06:24:21Z
date_updated: 2020-10-09T06:24:21Z
file_id: '8638'
file_name: 2018_LNCS_Elgyuett.pdf
file_size: 537219
relation: main_file
success: 1
file_date_updated: 2020-10-09T06:24:21Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 53 - 70
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_status: published
publisher: Springer
publist_id: '7973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring temporal logic with clock variables
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...