---
_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: '6195'
abstract:
- lang: eng
text: In the context of robotic manipulation and grasping, the shift from a view
that is static (force closure of a single posture) and contact-deprived (only
contact for force closure is allowed, everything else is obstacle) towards a view
that is dynamic and contact-rich (soft manipulation) has led to an increased interest
in soft hands. These hands can easily exploit environmental constraints and object
surfaces without risk, and safely interact with humans, but present also some
challenges. Designing them is difficult, as well as predicting, modelling, and
“programming” their interactions with the objects and the environment. This paper
tackles the problem of simulating them in a fast and effective way, leveraging
on novel and existing simulation technologies. We present a triple-layered simulation
framework where dynamic properties such as stiffness are determined from slow
but accurate FEM simulation data once, and then condensed into a lumped parameter
model that can be used to fast simulate soft fingers and soft hands. We apply
our approach to the simulation of soft pneumatic fingers.
article_number: '8461106'
article_processing_charge: No
author:
- first_name: Maria
full_name: Pozzi, Maria
last_name: Pozzi
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
orcid: 0000-0001-5665-0430
- first_name: Raphael
full_name: Deimel, Raphael
last_name: Deimel
- first_name: Monica
full_name: Malvezzi, Monica
last_name: Malvezzi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Oliver
full_name: Brock, Oliver
last_name: Brock
- first_name: Domenico
full_name: Prattichizzo, Domenico
last_name: Prattichizzo
citation:
ama: 'Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation
of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106'
apa: 'Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock,
O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots
modeled as kinematic chains. Presented at the ICRA: International Conference on
Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106'
chicago: Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd
Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation
of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.
ieee: 'M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled
as kinematic chains,” presented at the ICRA: International Conference on Robotics
and Automation, Brisbane, Australia, 2018.'
ista: 'Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo
D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains.
ICRA: International Conference on Robotics and Automation, 8461106.'
mla: Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled
as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.
short: M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock,
D. Prattichizzo, in:, IEEE, 2018.
conference:
end_date: 2018-05-25
location: Brisbane, Australia
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2018-05-21
date_created: 2019-04-04T09:50:38Z
date_published: 2018-09-10T00:00:00Z
date_updated: 2023-09-19T14:49:03Z
day: '10'
department:
- _id: BeBi
doi: 10.1109/icra.2018.8461106
external_id:
isi:
- '000446394503031'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
publication_identifier:
isbn:
- '9781538630815'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient FEM-based simulation of soft robots modeled as kinematic chains
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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: '620'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis requires the coordinated assembly of various
endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates
a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis,
but specific roles for PtdIns(4)P other than as the biosynthetic precursor of
PtdIns(4,5)P2 have not been clarified. In this study we investigated the role
of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction
of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and
the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that
both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic
internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts)
and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment
of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2
is required for membrane internalization. We also found that the localization
to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p
and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant,
but not in the mss4(ts) mutant. These results suggest distinct roles in successive
steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.
article_number: jcs207696
article_processing_charge: No
author:
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- first_name: Suguru
full_name: Wada, Suguru
last_name: Wada
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns
4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of
Cell Science. 2018;131(1). doi:10.1242/jcs.207696
apa: Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima,
J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and
PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.207696
chicago: Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus,
Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4
P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.
ieee: W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P
and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell
Science, vol. 131, no. 1. Company of Biologists, 2018.
ista: Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J.
2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.
mla: Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and
PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell
Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.
short: W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J.
Toshima, Journal of Cell Science 131 (2018).
date_created: 2018-12-11T11:47:32Z
date_published: 2018-01-04T00:00:00Z
date_updated: 2023-09-11T12:57:13Z
day: '04'
department:
- _id: DaSi
doi: 10.1242/jcs.207696
external_id:
isi:
- '000424786900012'
pmid:
- '29192062'
intvolume: ' 131'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29192062
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '7184'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast
receptor mediated endocytosis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 131
year: '2018'
...
---
_id: '63'
abstract:
- lang: eng
text: African cichlids display a remarkable assortment of jaw morphologies, pigmentation
patterns, and mating behaviors. In addition to this previously documented diversity,
recent studies have documented a rich diversity of sex chromosomes within these
fishes. Here we review the known sex-determination network within vertebrates,
and the extraordinary number of sex chromosomes systems segregating in African
cichlids. We also propose a model for understanding the unusual number of sex
chromosome systems within this clade.
acknowledgement: NSF DEB-1830753 and ISTPlus Fellowship
article_number: '480'
article_processing_charge: No
author:
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Thomas
full_name: Kocher, Thomas
last_name: Kocher
citation:
ama: Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480
apa: Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes
in African cichlid fishes. Genes. MDPI. https://doi.org/10.3390/genes9100480
chicago: Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9100480.
ieee: W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in
African cichlid fishes,” Genes, vol. 9, no. 10. MDPI, 2018.
ista: Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African
cichlid fishes. Genes. 9(10), 480.
mla: Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI, 2018, doi:10.3390/genes9100480.
short: W.J. Gammerdinger, T. Kocher, Genes 9 (2018).
date_created: 2018-12-11T11:44:26Z
date_published: 2018-10-04T00:00:00Z
date_updated: 2025-04-15T06:50:01Z
day: '04'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes9100480
ec_funded: 1
external_id:
isi:
- '000448656700018'
file:
- access_level: open_access
checksum: bec527692e2c9b56919c0429634ff337
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:54:46Z
date_updated: 2020-07-14T12:47:27Z
file_id: '5743'
file_name: 2018_Genes_Gammerdinger.pdf
file_size: 1415791
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genes
publication_status: published
publisher: MDPI
publist_id: '7991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unusual diversity of sex chromosomes in African cichlid fishes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '6339'
abstract:
- lang: eng
text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties
of quantum many-particle systems possessing a macroscopic number of degrees of
freedom. The treatment is based on a diagrammatic expansion that merges the usual
Feynman diagrams with the angular momentum diagrams known from atomic and nuclear
structure theory, thereby incorporating the non-Abelian algebra inherent to quantum
rotations. Our approach is applicable at arbitrary coupling, is free of systematic
errors and of finite-size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model; however, the method is quite general and can be applied
to a broad variety of systems in which particles exchange quantum angular momentum
with their many-body environment.
article_number: '165301'
article_processing_charge: No
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular
momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16).
doi:10.1103/physrevlett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to angular momentum in quantum many-particle systems. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo
Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review
Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems,” Physical Review Letters,
vol. 121, no. 16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems. Physical Review Letters.
121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum
in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no.
16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-04-17T10:53:38Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2025-04-15T07:59:29Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/physrevlett.121.165301
external_id:
arxiv:
- '1803.07990'
isi:
- '000447468400008'
intvolume: ' 121'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle
systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '6354'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis, but also play
diverse roles during immune responses. We have recently reported that platelets
migrate at sites of infection in vitro and in vivo. Importantly, platelets use
their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing
efficient intravascular bacterial trapping. Here, we describe a method that allows
analyzing platelet migration in vitro, focusing on their ability to collect bacteria
and trap bacteria under flow.
acknowledgement: This protocol was adapted from a previously published study (Gaertner
et al., 2017). We thank Michael Lorenz for his excellent assistance in bacteria
culture. This work was funded by the DFG SFB 914 (S.M. [B02 and Z01]), the DFG SFB
1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Centre for Cardiovascular
Research (DZHK) (MHA 1.4VD [S.M.]), FP7 program (project 260309, PRESTIGE [S.M.]),
FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.), Marie
Sklodowska Curie Individual Fellowship (EU project 747687, LamelliaActin [F.G.]).
article_number: e3018
article_processing_charge: Yes
article_type: original
author:
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
citation:
ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping
assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018
apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration
and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018
chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet
Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol,
2018. https://doi.org/10.21769/bioprotoc.3018.
ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and
bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol,
2018.
ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial
trapping assay under flow. Bio-Protocol. 8(18), e3018.
mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under
Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.
short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).
corr_author: '1'
date_created: 2019-04-29T09:40:33Z
date_published: 2018-09-20T00:00:00Z
date_updated: 2025-05-20T07:43:06Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.21769/bioprotoc.3018
ec_funded: 1
external_id:
pmid:
- '34395806'
file:
- access_level: open_access
checksum: d4588377e789da7f360b553ae02c5119
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T08:04:33Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6360'
file_name: 2018_BioProtocol_Fan.pdf
file_size: 2928337
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '18'
keyword:
- Platelets
- Cell migration
- Bacteria
- Shear flow
- Fibrinogen
- E. coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Bio-Protocol
publication_identifier:
issn:
- 2331-8325
publication_status: published
publisher: Bio-Protocol
quality_controlled: '1'
status: public
title: Platelet migration and bacterial trapping assay under flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2018'
...
---
_id: '64'
abstract:
- lang: eng
text: Tropical geometry, an established field in pure mathematics, is a place where
string theory, mirror symmetry, computational algebra, auction theory, and so
forth meet and influence one another. In this paper, we report on our discovery
of a tropical model with self-organized criticality (SOC) behavior. Our model
is continuous, in contrast to all known models of SOC, and is a certain scaling
limit of the sandpile model, the first and archetypical model of SOC. We describe
how our model is related to pattern formation and proportional growth phenomena
and discuss the dichotomy between continuous and discrete models in several contexts.
Our aim in this context is to present an idealized tropical toy model (cf. Turing
reaction-diffusion model), requiring further investigation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Aldo
full_name: Guzmán Sáenz, Aldo
last_name: Guzmán Sáenz
- first_name: Y
full_name: Prieto, Y
last_name: Prieto
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: V
full_name: Kalinina, V
last_name: Kalinina
- first_name: Ernesto
full_name: Lupercio, Ernesto
last_name: Lupercio
citation:
ama: Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
Self-organized criticality and pattern emergence through the lens of tropical
geometry. Proceedings of the National Academy of Sciences of the United States
of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115
apa: Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &
Lupercio, E. (2018). Self-organized criticality and pattern emergence through
the lens of tropical geometry. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115
chicago: Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina,
and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through
the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.
ieee: N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E.
Lupercio, “Self-organized criticality and pattern emergence through the lens of
tropical geometry,” Proceedings of the National Academy of Sciences of the
United States of America, vol. 115, no. 35. National Academy of Sciences,
pp. E8135–E8142, 2018.
ista: Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
2018. Self-organized criticality and pattern emergence through the lens of tropical
geometry. Proceedings of the National Academy of Sciences of the United States
of America. 115(35), E8135–E8142.
mla: Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through
the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 115, no. 35, National Academy of Sciences,
2018, pp. E8135–42, doi:10.1073/pnas.1805847115.
short: N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio,
Proceedings of the National Academy of Sciences of the United States of America
115 (2018) E8135–E8142.
date_created: 2018-12-11T11:44:26Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2025-06-03T11:21:16Z
day: '28'
department:
- _id: TaHa
doi: 10.1073/pnas.1805847115
ec_funded: 1
external_id:
arxiv:
- '1806.09153'
isi:
- '000442861600009'
intvolume: ' 115'
isi: 1
issue: '35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.09153
month: '08'
oa: 1
oa_version: Preprint
page: E8135 - E8142
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '7990'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized criticality and pattern emergence through the lens of tropical
geometry
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '6497'
abstract:
- lang: eng
text: T cells are actively scanning pMHC-presenting cells in lymphoid organs and
nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the
T cell actomyosin cytoskeleton facilitates this task in distinct environments
is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative
regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface
stiffness in primary T cells. Nonetheless, intravital imaging revealed robust
motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and
differentiation during immune responses. In contrast, accumulation of Myo9b−/−
CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for
T cell crossing of basement membranes, such as those which are present between
dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control
of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell
adaptation from lymphoid to NLT surveillance and the establishment of protective
tissue–resident T cell populations.
article_processing_charge: No
author:
- first_name: Federica
full_name: Moalli, Federica
last_name: Moalli
- first_name: Xenia
full_name: Ficht, Xenia
last_name: Ficht
- first_name: Philipp
full_name: Germann, Philipp
last_name: Germann
- first_name: Mykhailo
full_name: Vladymyrov, Mykhailo
last_name: Vladymyrov
- first_name: Bettina
full_name: Stolp, Bettina
last_name: Stolp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Ruth
full_name: Lyck, Ruth
last_name: Lyck
- first_name: Jasmin
full_name: Balmer, Jasmin
last_name: Balmer
- first_name: Amleto
full_name: Fiocchi, Amleto
last_name: Fiocchi
- first_name: Mario
full_name: Kreutzfeldt, Mario
last_name: Kreutzfeldt
- first_name: Doron
full_name: Merkler, Doron
last_name: Merkler
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Akitaka
full_name: Ariga, Akitaka
last_name: Ariga
- first_name: Michael H.
full_name: Stoffel, Michael H.
last_name: Stoffel
- first_name: James
full_name: Sharpe, James
last_name: Sharpe
- first_name: Martin
full_name: Bähler, Martin
last_name: Bähler
- 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: Alba
full_name: Diz-Muñoz, Alba
last_name: Diz-Muñoz
- first_name: Jens V.
full_name: Stein, Jens V.
last_name: Stein
citation:
ama: Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine.
2018;2015(7):1869–1890. doi:10.1084/jem.20170896
apa: Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I.,
… Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue
seeding of protective CD8+T cells. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20170896
chicago: Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina
Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables
Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.
ieee: F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine,
vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.
ista: Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer
J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe
J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb
enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental
Medicine. 2015(7), 1869–1890.
mla: Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid
Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine,
vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896.
short: F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R.
Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga,
M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal
of Experimental Medicine 2015 (2018) 1869–1890.
date_created: 2019-05-28T12:36:47Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-19T14:52:08Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20170896
external_id:
isi:
- '000440822900011'
file:
- access_level: open_access
checksum: 86ae5331f9bfced9a6358a790a04bef4
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T12:40:05Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6498'
file_name: 2018_rupress_Moalli.pdf
file_size: 3841660
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 2015'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 1869–1890
publication: The Journal of Experimental Medicine
publication_identifier:
eissn:
- 1540-9538
issn:
- 0022-1007
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective
CD8+T cells
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: 2015
year: '2018'
...
---
_id: '6499'
abstract:
- lang: eng
text: Expansion microscopy is a recently introduced imaging technique that achieves
super‐resolution through physically expanding the specimen by ~4×, after embedding
into a swellable gel. The resolution attained is, correspondingly, approximately
fourfold better than the diffraction limit, or ~70 nm. This is a major improvement
over conventional microscopy, but still lags behind modern STED or STORM setups,
whose resolution can reach 20–30 nm. We addressed this issue here by introducing
an improved gel recipe that enables an expansion factor of ~10× in each dimension,
which corresponds to an expansion of the sample volume by more than 1,000‐fold.
Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm
on conventional epifluorescence microscopes. X10 provides multi‐color images similar
or even superior to those produced with more challenging methods, such as STED,
STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest
and easiest option for high‐quality super‐resolution imaging currently available.
X10 should be usable in any laboratory, irrespective of the machinery owned or
of the technical knowledge.
article_number: e45836
article_processing_charge: No
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Manuel
full_name: Maidorn, Manuel
last_name: Maidorn
- first_name: Dagmar
full_name: Crzan, Dagmar
last_name: Crzan
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Selda
full_name: Kabatas, Selda
last_name: Kabatas
- first_name: Silvio O
full_name: Rizzoli, Silvio O
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10
expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO
reports. 2018;19(9). doi:10.15252/embr.201845836
apa: Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &
Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.201845836
chicago: Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda
Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports. Embo Press, 2018. https://doi.org/10.15252/embr.201845836.
ieee: S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S.
O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes,” EMBO reports, vol. 19, no. 9. Embo Press, 2018.
ista: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018.
X10 expansion microscopy enables 25‐nm resolution on conventional microscopes.
EMBO reports. 19(9), e45836.
mla: Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, Embo
Press, 2018, doi:10.15252/embr.201845836.
short: S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli,
EMBO Reports 19 (2018).
date_created: 2019-05-28T13:16:08Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-12-11T11:48:40Z
day: '01'
ddc:
- '580'
department:
- _id: JoDa
doi: 10.15252/embr.201845836
external_id:
isi:
- '000443682200009'
file:
- access_level: open_access
checksum: 6ec90abc637f09cca3a7b6424d7e7a26
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T13:17:19Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6500'
file_name: 2018_embo_Truckenbrodt.pdf
file_size: 2005572
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: X10 expansion microscopy enables 25‐nm resolution on conventional microscopes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
_id: '6558'
abstract:
- lang: eng
text: This paper studies the problem of distributed stochastic optimization in an
adversarial setting where, out of m machines which allegedly compute stochastic
gradients every iteration, an α-fraction are Byzantine, and may behave adversarially.
Our main result is a variant of stochastic gradient descent (SGD) which finds
ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations.
In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot
tolerate Byzantine failures. Further, we provide a lower bound showing that, up
to logarithmic factors, our algorithm is information-theoretically optimal both
in terms of sample complexity and time complexity.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Zeyuan
full_name: Allen-Zhu, Zeyuan
last_name: Allen-Zhu
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
citation:
ama: 'Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In:
Advances in Neural Information Processing Systems. Vol 2018. Neural Information
Processing Systems Foundation; 2018:4613-4623.'
apa: 'Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic
gradient descent. In Advances in Neural Information Processing Systems
(Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems
Foundation.'
chicago: Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic
Gradient Descent.” In Advances in Neural Information Processing Systems,
2018:4613–23. Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,”
in Advances in Neural Information Processing Systems, Montreal, Canada,
2018, vol. 2018, pp. 4613–4623.
ista: 'Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent.
Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural
Information Processing Systems vol. 2018, 4613–4623.'
mla: Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances
in Neural Information Processing Systems, vol. 2018, Neural Information Processing
Systems Foundation, 2018, pp. 4613–23.
short: D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2018, pp.
4613–4623.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-13T08:22:37Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-19T15:12:45Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1803.08917'
isi:
- '000461823304061'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08917
month: '12'
oa: 1
oa_version: Published Version
page: 4613-4623
publication: Advances in Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Byzantine stochastic gradient descent
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '6589'
abstract:
- lang: eng
text: Distributed training of massive machine learning models, in particular deep
neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace.
Several families of communication-reduction methods, such as quantization, large-batch
methods, and gradient sparsification, have been proposed. To date, gradient sparsification
methods--where each node sorts gradients by magnitude, and only communicates a
subset of the components, accumulating the rest locally--are known to yield some
of the largest practical gains. Such methods can reduce the amount of communication
per step by up to \emph{three orders of magnitude}, while preserving model accuracy.
Yet, this family of methods currently has no theoretical justification. This is
the question we address in this paper. We prove that, under analytic assumptions,
sparsifying gradients by magnitude with local error correction provides convergence
guarantees, for both convex and non-convex smooth objectives, for data-parallel
SGD. The main insight is that sparsification methods implicitly maintain bounds
on the maximum impact of stale updates, thanks to selection by magnitude. Our
analysis and empirical validation also reveal that these methods do require analytical
conditions to converge well, justifying existing heuristics.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
- first_name: Mikael
full_name: Johansson, Mikael
last_name: Johansson
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
- first_name: Sarit
full_name: Khirirat, Sarit
last_name: Khirirat
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
citation:
ama: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. The convergence of sparsified gradient methods. In: Advances in Neural Information
Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems
Foundation; 2018:5973-5983.'
apa: 'Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat,
S., & Renggli, C. (2018). The convergence of sparsified gradient methods.
In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018,
pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.'
chicago: Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov,
Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.”
In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83.
Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat,
and C. Renggli, “The convergence of sparsified gradient methods,” in Advances
in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol.
Volume 2018, pp. 5973–5983.
ista: 'Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli
C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information
Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems
vol. Volume 2018, 5973–5983.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.”
Advances in Neural Information Processing Systems 31, vol. Volume 2018,
Neural Information Processing Systems Foundation, 2018, pp. 5973–83.
short: D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat,
C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural
Information Processing Systems Foundation, 2018, pp. 5973–5983.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
corr_author: '1'
date_created: 2019-06-27T09:32:55Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2025-06-26T12:23:06Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '1809.10505'
isi:
- '000461852000047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.10505
month: '12'
oa: 1
oa_version: Preprint
page: 5973-5983
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Neural Information Processing Systems 31
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of sparsified gradient methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: Volume 2018
year: '2018'
...
---
_id: '690'
abstract:
- lang: eng
text: We consider spectral properties and the edge universality of sparse random
matrices, the class of random matrices that includes the adjacency matrices of
the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density
up to the spectral edges. Under a suitable condition on the sparsity, we also
prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations
if a deterministic shift of the spectral edge due to the sparsity is included.
For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom
fluctuations of the second largest eigenvalue when p is much larger than N−2/3
with a deterministic shift of order (Np)−1.
article_number: 543-616
article_processing_charge: No
arxiv: 1
author:
- first_name: Jii
full_name: Lee, Jii
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices.
Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8
apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse
random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8
chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse
Random Matrices.” Probability Theory and Related Fields. Springer, 2018.
https://doi.org/10.1007/s00440-017-0787-8.
ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random
matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer,
2018.
ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random
matrices. Probability Theory and Related Fields. 171(1–2), 543–616.
mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random
Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616,
Springer, 2018, doi:10.1007/s00440-017-0787-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).
date_created: 2018-12-11T11:47:56Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2025-09-10T14:00:58Z
day: '14'
department:
- _id: LaEr
doi: 10.1007/s00440-017-0787-8
ec_funded: 1
external_id:
arxiv:
- '1605.08767'
isi:
- '000432129600012'
intvolume: ' 171'
isi: 1
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.08767
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '7017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law and Tracy–Widom limit for sparse random matrices
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 171
year: '2018'
...
---
_id: '691'
abstract:
- lang: eng
text: "Background: Transport protein particle (TRAPP) is a multisubunit complex
that regulates membrane trafficking through the Golgi apparatus. The clinical
phenotype associated with mutations in various TRAPP subunits has allowed elucidation
of their functions in specific tissues. The role of some subunits in human disease,
however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective:
We aimed to expand the range of neurodevelopmental disorders associated with mutations
in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods:
Linkage and homozygosity mapping and candidate gene analysis were used to identify
homozygous mutations in families. Patient fibroblasts were used to study splicing
defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals
from three unrelated families with a founder homozygous splice mutation in TRAPPC6B,
encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental
disorder characterised by microcephaly, epilepsy and autistic features, and showed
splicing defect. Zebrafish trappc6b morphants replicated the human phenotype,
displaying decreased head size and neuronal hyperexcitability, leading to a lower
seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional
evidence of the role of TRAPPC6B in brain development and function."
article_processing_charge: No
article_type: original
author:
- first_name: Isaac
full_name: Marin Valencia, Isaac
last_name: Marin Valencia
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Damir
full_name: Musaev, Damir
last_name: Musaev
- first_name: Gifty
full_name: Bhat, Gifty
last_name: Bhat
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Valentina
full_name: Stanley, Valentina
last_name: Stanley
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Jeremy
full_name: Gleeson, Jeremy
last_name: Gleeson
- first_name: Farhad
full_name: Imam, Farhad
last_name: Imam
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation
in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly
epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54.
doi:10.1136/jmedgenet-2017-104627
apa: Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev,
D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates
with a neurodevelopmental disorder characterised by microcephaly epilepsy and
autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627
chicago: Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud
Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B
Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy
and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group,
2018. https://doi.org/10.1136/jmedgenet-2017-104627.
ieee: I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B
associates with a neurodevelopmental disorder characterised by microcephaly epilepsy
and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ
Publishing Group, pp. 48–54, 2018.
ista: Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat
G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson
J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features. Journal
of Medical Genetics. 55(1), 48–54.
mla: Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates
with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and
Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing
Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.
short: I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev,
G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki,
J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.
date_created: 2018-12-11T11:47:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-04-15T07:50:28Z
day: '01'
department:
- _id: GaNo
doi: 10.1136/jmedgenet-2017-104627
external_id:
isi:
- '000418199800007'
pmid:
- '28626029'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/
month: '01'
oa: 1
oa_version: Submitted Version
page: 48 - 54
pmid: 1
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Journal of Medical Genetics
publication_identifier:
issn:
- 0022-2593
publication_status: published
publisher: BMJ Publishing Group
publist_id: '7016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental
disorder characterised by microcephaly epilepsy and autistic features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2018'
...
---
_id: '692'
abstract:
- lang: eng
text: We consider families of confocal conics and two pencils of Apollonian circles
having the same foci. We will show that these families of curves generate trivial
3-webs and find the exact formulas describing them.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
citation:
ama: Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata.
2018;194(1):55-64. doi:10.1007/s10711-017-0265-6
apa: Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6
chicago: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.
ieee: A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae
Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.
ista: Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae
Dedicata. 194(1), 55–64.
mla: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae
Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.
short: A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.
corr_author: '1'
date_created: 2018-12-11T11:47:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2025-04-15T06:50:29Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s10711-017-0265-6
ec_funded: 1
external_id:
isi:
- '000431418800004'
file:
- access_level: open_access
checksum: 1febcfc1266486053a069e3425ea3713
content_type: application/pdf
creator: kschuh
date_created: 2020-01-03T11:35:08Z
date_updated: 2020-07-14T12:47:44Z
file_id: '7222'
file_name: 2018_Springer_Akopyan.pdf
file_size: 1140860
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 194'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 55 - 64
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Geometriae Dedicata
publication_status: published
publisher: Springer
publist_id: '7014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3-Webs generated by confocal conics and circles
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: 194
year: '2018'
...
---
_id: '7'
abstract:
- lang: eng
text: Animal social networks are shaped by multiple selection pressures, including
the need to ensure efficient communication and functioning while simultaneously
limiting disease transmission. Social animals could potentially further reduce
epidemic risk by altering their social networks in the presence of pathogens,
yet there is currently no evidence for such pathogen-triggered responses. We tested
this hypothesis experimentally in the ant Lasius niger using a combination of
automated tracking, controlled pathogen exposure, transmission quantification,
and temporally explicit simulations. Pathogen exposure induced behavioral changes
in both exposed ants and their nestmates, which helped contain the disease by
reinforcing key transmission-inhibitory properties of the colony's contact network.
This suggests that social network plasticity in response to pathogens is an effective
strategy for mitigating the effects of disease in social groups.
acknowledgement: This project was funded by two European Research Council Advanced
Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science
Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research
Council Starting Grant (SocialVaccines, 243071) to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Alessandro
full_name: Crespi, Alessandro
last_name: Crespi
- first_name: Danielle
full_name: Mersch, Danielle
last_name: Mersch
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Laurent
full_name: Keller, Laurent
last_name: Keller
citation:
ama: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network
plasticity decreases disease transmission in a eusocial insect. Science.
2018;362(6417):941-945. doi:10.1126/science.aat4793
apa: Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller,
L. (2018). Social network plasticity decreases disease transmission in a eusocial
insect. Science. AAAS. https://doi.org/10.1126/science.aat4793
chicago: Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch,
Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease
Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.
ieee: N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller,
“Social network plasticity decreases disease transmission in a eusocial insect,”
Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.
ista: Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social
network plasticity decreases disease transmission in a eusocial insect. Science.
362(6417), 941–945.
mla: Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission
in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45,
doi:10.1126/science.aat4793.
short: N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science
362 (2018) 941–945.
date_created: 2018-12-11T11:44:07Z
date_published: 2018-11-23T00:00:00Z
date_updated: 2025-04-15T08:20:52Z
day: '23'
department:
- _id: SyCr
doi: 10.1126/science.aat4793
ec_funded: 1
external_id:
isi:
- '000451124500041'
intvolume: ' 362'
isi: 1
issue: '6417'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 941 - 945
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Science
publication_identifier:
issn:
- 1095-9203
publication_status: published
publisher: AAAS
publist_id: '8049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/
record:
- id: '13055'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Social network plasticity decreases disease transmission in a eusocial insect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 362
year: '2018'
...
---
_id: '70'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process in a critical
scaling parametrized by a≥0, which creates a shock in the particle density of
order aT−1/3, T the observation time. When starting from step initial data, we
provide bounds on the limiting law which in particular imply that in the double
limit lima→∞limT→∞ one recovers the product limit law and the degeneration of
the correlation length observed at shocks of order 1. This result is shown to
apply to a general last-passage percolation model. We also obtain bounds on the
two-point functions of several airy processes.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Nejjar P. Transition to shocks in TASEP and decoupling of last passage times.
Latin American Journal of Probability and Mathematical Statistics. 2018;15(2):1311-1334.
doi:10.30757/ALEA.v15-49
apa: Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v15-49
chicago: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics.
Instituto Nacional de Matematica Pura e Aplicada, 2018. https://doi.org/10.30757/ALEA.v15-49.
ieee: P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,”
Latin American Journal of Probability and Mathematical Statistics, vol.
15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.
ista: Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage
times. Latin American Journal of Probability and Mathematical Statistics. 15(2),
1311–1334.
mla: Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage
Times.” Latin American Journal of Probability and Mathematical Statistics,
vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34,
doi:10.30757/ALEA.v15-49.
short: P. Nejjar, Latin American Journal of Probability and Mathematical Statistics
15 (2018) 1311–1334.
date_created: 2018-12-11T11:44:28Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2025-04-14T07:27:49Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
- _id: JaMa
doi: 10.30757/ALEA.v15-49
ec_funded: 1
external_id:
arxiv:
- '1705.08836'
isi:
- '000460475800022'
file:
- access_level: open_access
checksum: 2ded46aa284a836a8cbb34133a64f1cb
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T09:44:10Z
date_updated: 2020-07-14T12:47:46Z
file_id: '5981'
file_name: 2018_ALEA_Nejjar.pdf
file_size: 394851
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1311-1334
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Latin American Journal of Probability and Mathematical Statistics
publication_identifier:
issn:
- 1980-0436
publication_status: published
publisher: Instituto Nacional de Matematica Pura e Aplicada
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to shocks in TASEP and decoupling of last passage times
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2018'
...
---
_id: '705'
abstract:
- lang: eng
text: Although dopamine receptors D1 and D2 play key roles in hippocampal function,
their synaptic localization within the hippocampus has not been fully elucidated.
In order to understand precise functions of pre- or postsynaptic dopamine receptors
(DRs), the development of protocols to differentiate pre- and postsynaptic DRs
is essential. So far, most studies on determination and quantification of DRs
did not discriminate between subsynaptic localization. Therefore, the aim of the
study was to generate a robust workflow for the localization of DRs. This work
provides the basis for future work on hippocampal DRs, in light that DRs may have
different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi
isolated by a sucrose gradient protocol were prepared for super-resolution direct
stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic
zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated
antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594
enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites.
D1R immunoreactivity clusters were observed within the presynaptic active zone
as well as at perisynaptic sites at the edge of the presynaptic active zone. The
results may be useful for the interpretation of previous studies and the design
of future work on DRs in the hippocampus. Moreover, the reduction of the complexity
of brain tissue by the use of synaptosomal preparations and dSTORM technology
may represent a useful tool for synaptic localization of brain proteins.
article_processing_charge: No
author:
- first_name: Andras
full_name: Miklosi, Andras
last_name: Miklosi
- first_name: Giorgia
full_name: Del Favero, Giorgia
last_name: Del Favero
- first_name: Tanja
full_name: Bulat, Tanja
last_name: Bulat
- first_name: Harald
full_name: Höger, Harald
last_name: Höger
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Doris
full_name: Marko, Doris
last_name: Marko
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
citation:
ama: Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization
of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology.
2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y
apa: Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D.,
& Lubec, G. (2018). Super resolution microscopical localization of dopamine
receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology.
Springer. https://doi.org/10.1007/s12035-017-0688-y
chicago: Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi
Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization
of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology.
Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y.
ieee: A. Miklosi et al., “Super resolution microscopical localization of
dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology,
vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.
ista: Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G.
2018. Super resolution microscopical localization of dopamine receptors 1 and
2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.
mla: Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine
Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology,
vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.
short: A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G.
Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.
date_created: 2018-12-11T11:48:02Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T09:58:11Z
day: '01'
department:
- _id: RySh
doi: 10.1007/s12035-017-0688-y
external_id:
isi:
- '000431991500025'
intvolume: ' 55'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 4857 – 4869
publication: Molecular Neurobiology
publication_status: published
publisher: Springer
publist_id: '6991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Super resolution microscopical localization of dopamine receptors 1 and 2 in
rat hippocampal synaptosomes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2018'
...
---
_id: '7116'
abstract:
- lang: eng
text: 'Training deep learning models has received tremendous research interest recently.
In particular, there has been intensive research on reducing the communication
cost of training when using multiple computational devices, through reducing the
precision of the underlying data representation. Naturally, such methods induce
system trade-offs—lowering communication precision could de-crease communication
overheads and improve scalability; but, on the other hand, it can also reduce
the accuracy of training. In this paper, we study this trade-off space, and ask:Can
low-precision communication consistently improve the end-to-end performance of
training modern neural networks, with no accuracy loss?From the performance point
of view, the answer to this question may appear deceptively easy: compressing
communication through low precision should help when the ratio between communication
and computation is high. However, this answer is less straightforward when we
try to generalize this principle across various neural network architectures (e.g.,
AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g.,
EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL),
and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is
not clear how a realistic realization of all these factors maps to the speed up
provided by low-precision communication. In this paper, we conduct an empirical
study to answer this question and report the insights.'
article_processing_charge: No
author:
- first_name: Demjan
full_name: Grubic, Demjan
last_name: Grubic
- first_name: Leo
full_name: Tam, Leo
last_name: Tam
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for
deep learning with low-precision communications: An empirical study. In: Proceedings
of the 21st International Conference on Extending Database Technology. OpenProceedings;
2018:145-156. doi:10.5441/002/EDBT.2018.14'
apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous
multi-GPU training for deep learning with low-precision communications: An empirical
study. In Proceedings of the 21st International Conference on Extending Database
Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14'
chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous
Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical
Study.” In Proceedings of the 21st International Conference on Extending Database
Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.'
ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study,” in Proceedings
of the 21st International Conference on Extending Database Technology, Vienna,
Austria, 2018, pp. 145–156.'
ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training
for deep learning with low-precision communications: An empirical study. Proceedings
of the 21st International Conference on Extending Database Technology. EDBT: Conference
on Extending Database Technology, 145–156.'
mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with
Low-Precision Communications: An Empirical Study.” Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings,
2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.'
short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st
International Conference on Extending Database Technology, OpenProceedings, 2018,
pp. 145–156.
conference:
end_date: 2018-03-29
location: Vienna, Austria
name: 'EDBT: Conference on Extending Database Technology'
start_date: 2018-03-26
corr_author: '1'
date_created: 2019-11-26T14:19:11Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2024-10-09T20:59:05Z
day: '26'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.5441/002/EDBT.2018.14
file:
- access_level: open_access
checksum: ec979b56abc71016d6e6adfdadbb4afe
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T14:23:04Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7118'
file_name: 2018_OpenProceedings_Grubic.pdf
file_size: 1603204
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 145-156
publication: Proceedings of the 21st International Conference on Extending Database
Technology
publication_identifier:
isbn:
- '9783893180783'
issn:
- 2367-2005
publication_status: published
publisher: OpenProceedings
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Synchronous multi-GPU training for deep learning with low-precision communications:
An empirical study'
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7123'
abstract:
- lang: eng
text: "Population protocols are a popular model of distributed computing, in which
n agents with limited local state interact randomly, and cooperate to collectively
compute global predicates. Inspired by recent developments in DNA programming,
an extensive series of papers, across different communities, has examined the
computability and complexity characteristics of this model. Majority, or consensus,
is a central task in this model, in which agents need to collectively reach a
decision as to which one of two states A or B had a higher initial count. Two
metrics are important: the time that a protocol requires to stabilize to an output
decision, and the state space size that each agent requires to do so. It is known
that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic
time) stabilization, and that O(log2 n) states are sufficient. Thus, there is
an exponential gap between the space upper and lower bounds for this problem.
This paper addresses this question.\r\n\r\nOn the negative side, we provide a
new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c)
expected time, for any constant c > 0. This result is conditional on monotonicity
and output assumptions, satisfied by all known protocols. Technically, it represents
a departure from previous lower bounds, in that it does not rely on the existence
of dense configurations. Instead, we introduce a new generalized surgery technique
to prove the existence of incorrect executions for any algorithm which would contradict
the lower bound. Subsequently, our lower bound also applies to general initial
configurations, including ones with a leader. On the positive side, we give a
new algorithm for majority which uses O(log n) states, and stabilizes in O(log2
n) expected time. Central to the algorithm is a new leaderless phase clock technique,
which allows agents to synchronize in phases of Θ(n log n) consecutive interactions
using O(log n) states per agent, exploiting a new connection between population
protocols and power-of-two-choices load balancing mechanisms. We also employ our
phase clock to build a leader election algorithm with a state space of size O(log
n), which stabilizes in O(log2 n) expected time."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population
protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144'
apa: 'Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority
in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium
on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM.
https://doi.org/10.1137/1.9781611975031.144'
chicago: Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal
Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM
Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144.
ieee: D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population
protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.
ista: 'Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population
protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms, 2221–2239.'
mla: Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.”
Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms,
ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144.
short: D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual
ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.
conference:
end_date: 2018-01-10
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2019-11-26T15:10:55Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2024-10-21T06:02:41Z
day: '30'
department:
- _id: DaAl
doi: 10.1137/1.9781611975031.144
external_id:
arxiv:
- '1704.04947'
isi:
- '000483921200145'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.04947
month: '01'
oa: 1
oa_version: Preprint
page: 2221-2239
publication: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611975031'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Space-optimal majority in population protocols
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...