---
_id: '5555'
abstract:
- lang: eng
text: This FIJI script calculates the population average of the migration speed
as a function of time of all cells from wide field microscopy movies.
article_processing_charge: No
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. Fiji script to determine average speed and direction of migration
of cells. 2016. doi:10.15479/AT:ISTA:44
apa: Hauschild, R. (2016). Fiji script to determine average speed and direction
of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44
chicago: Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction
of Migration of Cells.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:44.
ieee: R. Hauschild, “Fiji script to determine average speed and direction of migration
of cells.” Institute of Science and Technology Austria, 2016.
ista: Hauschild R. 2016. Fiji script to determine average speed and direction of
migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.
mla: Hauschild, Robert. Fiji Script to Determine Average Speed and Direction
of Migration of Cells. Institute of Science and Technology Austria, 2016,
doi:10.15479/AT:ISTA:44.
short: R. Hauschild, (2016).
datarep_id: '44'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-07-08T00:00:00Z
date_updated: 2024-02-21T13:50:06Z
day: '08'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:44
file:
- access_level: open_access
checksum: 9f96cddbcd4ed689f48712ffe234d5e5
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:03Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5621'
file_name: IST-2016-44-v1+1_migrationAnalyzer.zip
file_size: 20692
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- cell migration
- wide field microscopy
- FIJI
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Fiji script to determine average speed and direction of migration of cells
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5556'
abstract:
- lang: eng
text: "MATLAB code and processed datasets available for reproducing the results
in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.\r\n*equal contributions"
article_processing_charge: No
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for
“Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional
Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:45
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code
for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both
Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and
Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.
ista: Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.
mla: Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.
short: M. Lukacisin, M. Landon, R. Jajoo, (2016).
datarep_id: '45'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-08-25T00:00:00Z
date_updated: 2024-02-21T13:51:53Z
day: '25'
ddc:
- '571'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:45
file:
- access_level: open_access
checksum: ee697f2b1ade4dc14d6ac0334dd832ab
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:58Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5616'
file_name: IST-2016-45-v1+1_PaperCode.zip
file_size: 296722548
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- transcription
- pausing
- backtracking
- polymerase
- RNA
- NET-seq
- nucleosome
- basepairing
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8431'
relation: used_in_publication
status: deleted
- id: '1029'
relation: research_paper
status: public
status: public
title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5557'
abstract:
- lang: eng
text: "Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and
256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."
article_processing_charge: No
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
citation:
ama: Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46
apa: Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:46
chicago: Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science
and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.
ieee: P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science
and Technology Austria, 2016.
ista: Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:46.
mla: Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of
Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46.
short: P. Swoboda, (2016).
contributor:
- contributor_type: data_collector
first_name: Jan
last_name: Kuske
datarep_id: '46'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-20T00:00:00Z
date_updated: 2024-02-21T13:50:21Z
day: '20'
ddc:
- '006'
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:46
file:
- access_level: open_access
checksum: aa5a16a0dc888da7186fb8fc45e88439
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:19Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5645'
file_name: IST-2016-46-v1+1_discrete_tomography_synthetic.zip
file_size: 36058401
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- discrete tomography
month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Synthetic discrete tomography problems
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5558'
abstract:
- lang: eng
text: PhD thesis LaTeX source code
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
citation:
ama: Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016.
doi:10.15479/AT:ISTA:48
apa: Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48
chicago: Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface
Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.
ieee: M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.”
Institute of Science and Technology Austria, 2016.
ista: Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.
mla: Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface
Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.
short: M. Bojsen-Hansen, (2016).
datarep_id: '48'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2024-02-21T13:50:48Z
day: '23'
ddc:
- '004'
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:48
file:
- access_level: open_access
checksum: 5b1b256ad796fbddb4b7729f5e45e444
content_type: application/x-bzip2
creator: system
date_created: 2018-12-12T13:02:18Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5589'
file_name: IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2
file_size: 55237885
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
month: '09'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '6238'
pubrep_id: '640'
related_material:
record:
- id: '1122'
relation: other
status: public
status: public
title: Tracking, Correcting and Absorbing Water Surface Waves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5749'
abstract:
- lang: eng
text: Parasitism creates selection for resistance mechanisms in host populations
and is hypothesized to promote increased host evolvability. However, the influence
of these traits on host evolution when parasites are no longer present is unclear.
We used experimental evolution and whole-genome sequencing of Escherichia coli
to determine the effects of past and present exposure to parasitic viruses (phages)
on the spread of mutator alleles, resistance, and bacterial competitive fitness.
We found that mutator alleles spread rapidly during adaptation to any of four
different phage species, and this pattern was even more pronounced with multiple
phages present simultaneously. However, hypermutability did not detectably accelerate
adaptation in the absence of phages and recovery of fitness costs associated with
resistance. Several lineages evolved phage resistance through elevated mucoidy,
and during subsequent evolution in phage-free conditions they rapidly reverted
to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this
phenotypic reversion was achieved by additional genetic changes rather than by
genotypic reversion of the initial resistance mutations. Insertion sequence (IS)
elements played a key role in both the acquisition of resistance and adaptation
in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions
were not more frequent in mutator lineages. Our results provide a genetic explanation
for rapid reversion of mucoidy, a phenotype observed in other bacterial species
including human pathogens. Moreover, this demonstrates that the types of genetic
change underlying adaptation to fitness costs, and consequently the impact of
evolvability mechanisms such as increased point-mutation rates, depend critically
on the mechanism of resistance.
acknowledgement: The authors thank three anonymous reviewers and the editor for helpful
comments on the manuscript, as well as Dominique Schneider for feedback on an earlier
draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was
supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an
EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824
to S.W.).
article_processing_charge: No
author:
- first_name: Sébastien
full_name: Wielgoss, Sébastien
last_name: Wielgoss
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M.
full_name: Bischofberger, Anna M.
last_name: Bischofberger
- first_name: Alex R.
full_name: Hall, Alex R.
last_name: Hall
citation:
ama: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 2016;33(3):770-782. doi:10.1093/molbev/msv270
apa: Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2016).
Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv270
chicago: Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex
R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator
and Nonmutator Bacteria.” Molecular Biology and Evolution. Oxford University
Press, 2016. https://doi.org/10.1093/molbev/msv270.
ieee: S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation
to parasites and costs of parasite resistance in mutator and nonmutator bacteria,”
Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press,
pp. 770–782, 2016.
ista: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 33(3), 770–782.
mla: Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite
Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution,
vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:10.1093/molbev/msv270.
short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology
and Evolution 33 (2016) 770–782.
date_created: 2018-12-18T13:18:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-05T13:46:05Z
day: '01'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/molbev/msv270
external_id:
pmid:
- '26609077'
file:
- access_level: open_access
checksum: 47d9010690b6c5c17f2ac830cc63ac5c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:21:45Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5750'
file_name: 2016_MolBiolEvol_Wielgoss.pdf
file_size: 634037
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 770-782
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
pubrep_id: '587'
quality_controlled: '1'
related_material:
record:
- id: '9719'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria
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: 33
year: '2016'
...
---
_id: '5771'
abstract:
- lang: eng
text: Retroviruses such as HIV-1 assemble and bud from infected cells in an immature,
non-infectious form. Subsequently, a series of proteolytic cleavages catalysed
by the viral protease leads to a spectacular structural rearrangement of the viral
particle into a mature form that is competent to fuse with and infect a new cell.
Maturation involves changes in the structures of protein domains, in the interactions
between protein domains, and in the architecture of the viral components that
are assembled by the proteins. Tight control of proteolytic cleavages at different
sites is required for successful maturation, and the process is a major target
of antiretroviral drugs. Here we will describe what is known about the structures
of immature and mature retrovirus particles, and about the maturation process
by which one transitions into the other. Despite a wealth of available data, fundamental
questions about retroviral maturation remain unanswered.
author:
- first_name: Simone
full_name: Mattei, Simone
last_name: Mattei
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John AG
full_name: Briggs, John AG
last_name: Briggs
citation:
ama: Mattei S, Schur FK, Briggs JA. Retrovirus maturation—an extraordinary structural
transformation. Current Opinion in Virology. 2016;18(6):27-35. doi:10.1016/j.coviro.2016.02.008
apa: Mattei, S., Schur, F. K., & Briggs, J. A. (2016). Retrovirus maturation—an
extraordinary structural transformation. Current Opinion in Virology. Elsevier.
https://doi.org/10.1016/j.coviro.2016.02.008
chicago: Mattei, Simone, Florian KM Schur, and John AG Briggs. “Retrovirus Maturation—an
Extraordinary Structural Transformation.” Current Opinion in Virology.
Elsevier, 2016. https://doi.org/10.1016/j.coviro.2016.02.008.
ieee: S. Mattei, F. K. Schur, and J. A. Briggs, “Retrovirus maturation—an extraordinary
structural transformation,” Current Opinion in Virology, vol. 18, no. 6.
Elsevier, pp. 27–35, 2016.
ista: Mattei S, Schur FK, Briggs JA. 2016. Retrovirus maturation—an extraordinary
structural transformation. Current Opinion in Virology. 18(6), 27–35.
mla: Mattei, Simone, et al. “Retrovirus Maturation—an Extraordinary Structural Transformation.”
Current Opinion in Virology, vol. 18, no. 6, Elsevier, 2016, pp. 27–35,
doi:10.1016/j.coviro.2016.02.008.
short: S. Mattei, F.K. Schur, J.A. Briggs, Current Opinion in Virology 18 (2016)
27–35.
date_created: 2018-12-20T21:13:59Z
date_published: 2016-03-22T00:00:00Z
date_updated: 2021-01-12T08:03:22Z
day: '22'
ddc:
- '570'
doi: 10.1016/j.coviro.2016.02.008
extern: '1'
file:
- access_level: open_access
checksum: 320939d28ebd1adfb122338019892508
content_type: application/pdf
creator: dernst
date_created: 2019-01-09T13:05:44Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5812'
file_name: 2016_CurrentOpinion_Mattei.pdf
file_size: 1773842
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 27-35
publication: Current Opinion in Virology
publication_identifier:
issn:
- 1879-6257
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Retrovirus maturation—an extraordinary structural transformation
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: 18
year: '2016'
...
---
_id: '587'
abstract:
- lang: eng
text: Quantum metrology exploits entangled states of particles to improve sensing
precision beyond the limit achievable with uncorrelated particles. All previous
methods required detection noise levels below this standard quantum limit to realize
the benefits of the intrinsic sensitivity provided by these states.We experimentally
demonstrate a widely applicable method for entanglement-enhanced measurements
without low-noise detection. The method involves an intermediate quantum phase
magnification step that eases implementation complexity. We used it to perform
squeezed-state metrology 8 decibels below the standard quantum limit with a detection
system that has a noise floor 10 decibels above the standard quantum limit.
author:
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Nils
full_name: Engelsen, Nils J
last_name: Engelsen
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Hosten O, Krishnakumar R, Engelsen N, Kasevich M. Quantum phase magnification.
Science. 2016;352(6293):1552-1555. doi:10.1126/science.aaf3397
apa: Hosten, O., Krishnakumar, R., Engelsen, N., & Kasevich, M. (2016). Quantum
phase magnification. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aaf3397
chicago: Hosten, Onur, Rajiv Krishnakumar, Nils Engelsen, and Mark Kasevich. “Quantum
Phase Magnification.” Science. American Association for the Advancement
of Science, 2016. https://doi.org/10.1126/science.aaf3397.
ieee: O. Hosten, R. Krishnakumar, N. Engelsen, and M. Kasevich, “Quantum phase magnification,”
Science, vol. 352, no. 6293. American Association for the Advancement of
Science, pp. 1552–1555, 2016.
ista: Hosten O, Krishnakumar R, Engelsen N, Kasevich M. 2016. Quantum phase magnification.
Science. 352(6293), 1552–1555.
mla: Hosten, Onur, et al. “Quantum Phase Magnification.” Science, vol. 352,
no. 6293, American Association for the Advancement of Science, 2016, pp. 1552–55,
doi:10.1126/science.aaf3397.
short: O. Hosten, R. Krishnakumar, N. Engelsen, M. Kasevich, Science 352 (2016)
1552–1555.
date_created: 2018-12-11T11:47:21Z
date_published: 2016-06-24T00:00:00Z
date_updated: 2021-01-12T08:05:06Z
day: '24'
doi: 10.1126/science.aaf3397
extern: 1
intvolume: ' 352'
issue: '6293'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.07683
month: '06'
oa: 1
page: 1552 - 1555
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7214'
quality_controlled: 0
status: public
title: Quantum phase magnification
type: journal_article
volume: 352
year: '2016'
...
---
_id: '1431'
abstract:
- lang: eng
text: The rare socially parasitic butterfly Maculinea alcon occurs in two forms,
which are characteristic of hygric or xeric habitats and which exploit different
host plants and host ants. The status of these two forms has been the subject
of considerable controversy. Populations of the two forms are usually spatially
distinct, but at Răscruci in Romania both forms occur on the same site (syntopically).
We examined the genetic differentiation between the two forms using eight microsatellite
markers, and compared with a nearby hygric site, Şardu. Our results showed that
while the two forms are strongly differentiated at Răscruci, it is the xeric form
there that is most similar to the hygric form at Şardu, and Bayesian clustering
algorithms suggest that these two populations have exchanged genes relatively
recently. We found strong evidence for population substructuring, caused by high
within host ant nest relatedness, indicating very limited dispersal of most ovipositing
females, but not association with particular host ant species. Our results are
consistent with the results of larger scale phylogeographic studies that suggest
that the two forms represent local ecotypes specialising on different host plants,
each with a distinct flowering phenology, providing a temporal rather than spatial
barrier to gene flow.
article_number: '1865'
author:
- first_name: András
full_name: Tartally, András
last_name: Tartally
- first_name: Andreas
full_name: Kelager, Andreas
last_name: Kelager
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: David
full_name: Nash, David
last_name: Nash
citation:
ama: Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation
in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865
apa: Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use
drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ.
PeerJ. https://doi.org/10.7717/peerj.1865
chicago: Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host
Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea
Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.
ieee: A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic
differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol.
2016, no. 3. PeerJ, 2016.
ista: Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic
differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.
mla: Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in
Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865,
PeerJ, 2016, doi:10.7717/peerj.1865.
short: A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).
date_created: 2018-12-11T11:51:59Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.7717/peerj.1865
file:
- access_level: open_access
checksum: c27d898598a1e3d7f629607a309254e1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:19Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5272'
file_name: IST-2016-584-v1+1_peerj-1865.pdf
file_size: 1216360
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 2016'
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '5767'
pubrep_id: '584'
quality_controlled: '1'
scopus_import: 1
status: public
title: Host plant use drives genetic differentiation in syntopic populations of Maculinea
alcon
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1432'
abstract:
- lang: eng
text: CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory
storage and pattern completion. Whether the plasticity properties of these synapses
are consistent with their proposed network functions remains unclear. Here, we
examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3
synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs)
and action potentials (APs) induces long-term potentiation (LTP), independent
of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms).
Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear
summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs)
following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and
EPSPs summate with dendritic ADPs. In autoassociative network models, storage
and recall are more robust with symmetric than with asymmetric STDP rules. Thus,
a specialized STDP induction rule allows reliable storage and recall of information
in the hippocampal CA3 network.
acknowledgement: 'We thank Jozsef Csicsvari and Nelson Spruston for critically reading
the manuscript. We also thank A. Schlögl for programming, F. Marr for technical
assistance and E. Kramberger for manuscript editing. '
article_number: '11552'
author:
- first_name: Rajiv Kumar
full_name: Mishra, Rajiv Kumar
id: 46CB58F2-F248-11E8-B48F-1D18A9856A87
last_name: Mishra
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity
at CA3–CA3 synapses optimizes storage and recall in autoassociative networks.
Nature Communications. 2016;7. doi:10.1038/ncomms11552
apa: Mishra, R. K., Kim, S., Guzmán, J., & Jonas, P. M. (2016). Symmetric spike
timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in
autoassociative networks. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms11552
chicago: Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric
Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall
in Autoassociative Networks.” Nature Communications. Nature Publishing
Group, 2016. https://doi.org/10.1038/ncomms11552.
ieee: R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks,” Nature Communications, vol. 7. Nature Publishing Group, 2016.
ista: Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent
plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative
networks. Nature Communications. 7, 11552.
mla: Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at
CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature
Communications, vol. 7, 11552, Nature Publishing Group, 2016, doi:10.1038/ncomms11552.
short: R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:59Z
date_published: 2016-05-13T00:00:00Z
date_updated: 2023-09-07T11:55:25Z
day: '13'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/ncomms11552
ec_funded: 1
file:
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checksum: 7e84d0392348c874d473b62f1042de22
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:33Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5355'
file_name: IST-2016-582-v1+1_ncomms11552.pdf
file_size: 4510512
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5766'
pubrep_id: '582'
quality_controlled: '1'
related_material:
record:
- id: '1396'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage
and recall in autoassociative networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1434'
abstract:
- lang: eng
text: We prove that the system of subordination equations, defining the free additive
convolution of two probability measures, is stable away from the edges of the
support and blow-up singularities by showing that the recent smoothness condition
of Kargin is always satisfied. As an application, we consider the local spectral
statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed
random unitary or orthogonal matrix, and A and B are deterministic matrices.
In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎
concentrates around the free additive convolution of the spectral distributions
of A and B on scales down to N−2/3N−2/3.
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution.
Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006
apa: Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free
additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the
Free Additive Convolution.” Journal of Functional Analysis. Academic Press,
2016. https://doi.org/10.1016/j.jfa.2016.04.006.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,”
Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719,
2016.
ista: Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution.
Journal of Functional Analysis. 271(3), 672–719.
mla: Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal
of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719,
doi:10.1016/j.jfa.2016.04.006.
short: Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016)
672–719.
date_created: 2018-12-11T11:52:00Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:50:42Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.jfa.2016.04.006
ec_funded: 1
intvolume: ' 271'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.05905
month: '08'
oa: 1
oa_version: Preprint
page: 672 - 719
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5764'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local stability of the free additive convolution
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 271
year: '2016'
...
---
_id: '1435'
abstract:
- lang: eng
text: ATP released from neurons and astrocytes during neuronal activity or under
pathophysiological circumstances is able to influence information flow in neuronal
circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent
modulation of cellular excitability, synaptic strength, and plasticity. In the
present paper we review cellular and network effects of P2Y receptors in the brain.
We show that P2Y receptors inhibit the release of neurotransmitters, modulate
voltage- and ligand-gated ion channels, and differentially influence the induction
of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum.
The findings discussed here may explain how P2Y1 receptor activation during brain
injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to
an impairment of cognitive processes. Hence, it is suggested that the blockade
of P2Y1 receptors may have therapeutic potential against cognitive disturbances
in these states.
article_number: '1207393'
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Zoltan
full_name: Gerevich, Zoltan
last_name: Gerevich
citation:
ama: 'Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016.
doi:10.1155/2016/1207393'
apa: 'Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission
and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity.
Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393'
chicago: 'Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission
and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity.
Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393.'
ieee: 'J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol.
2016. Hindawi Publishing Corporation, 2016.'
ista: 'Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.'
mla: 'Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission
and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity,
vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.'
short: J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).
date_created: 2018-12-11T11:52:00Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:43Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1155/2016/1207393
file:
- access_level: open_access
checksum: 8dc5c2f3d44d4775a6e7e3edb0d7a0da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:17Z
date_updated: 2020-07-14T12:44:54Z
file_id: '4740'
file_name: IST-2016-580-v1+1_1207393.pdf
file_size: 1395180
relation: main_file
file_date_updated: 2020-07-14T12:44:54Z
has_accepted_license: '1'
intvolume: ' 2016'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Neural Plasticity
publication_status: published
publisher: Hindawi Publishing Corporation
publist_id: '5762'
pubrep_id: '580'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'P2Y receptors in synaptic transmission and plasticity: Therapeutic potential
in cognitive dysfunction'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1436'
abstract:
- lang: eng
text: We study the time evolution of a system of N spinless fermions in R3 which
interact through a pair potential, e.g., the Coulomb potential. We compare the
dynamics given by the solution to Schrödinger's equation with the time-dependent
Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation
in terms of the kinetic energy of the system. This leads, in turn, to bounds in
terms of the initial total energy of the system.
author:
- first_name: Volker
full_name: Bach, Volker
last_name: Bach
- first_name: Sébastien
full_name: Breteaux, Sébastien
last_name: Breteaux
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Tim
full_name: Tzaneteas, Tim
last_name: Tzaneteas
citation:
ama: Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates
for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb
interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30.
doi:10.1016/j.matpur.2015.09.003
apa: Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016).
Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation
with Coulomb interaction. Journal de Mathématiques Pures et Appliquées.
Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003
chicago: Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim
Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock
Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et
Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003.
ieee: V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy
estimates for the accuracy of the time-dependent Hartree-Fock approximation with
Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol.
105, no. 1. Elsevier, pp. 1–30, 2016.
ista: Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy
estimates for the accuracy of the time-dependent Hartree-Fock approximation with
Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.
mla: Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent
Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques
Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.
short: V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques
Pures et Appliquées 105 (2016) 1–30.
date_created: 2018-12-11T11:52:00Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:43Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1016/j.matpur.2015.09.003
ec_funded: 1
file:
- access_level: open_access
checksum: c5afe1f6935bc7f2b546adbde1d31a35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:36Z
date_updated: 2020-07-14T12:44:54Z
file_id: '4825'
file_name: IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf
file_size: 658491
relation: main_file
file_date_updated: 2020-07-14T12:44:54Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1 - 30
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal de Mathématiques Pures et Appliquées
publication_status: published
publisher: Elsevier
publist_id: '5763'
pubrep_id: '581'
quality_controlled: '1'
scopus_import: 1
status: public
title: Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock
approximation with Coulomb interaction
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2016'
...
---
_id: '1437'
abstract:
- lang: eng
text: We study algorithmic questions for concurrent systems where the transitions
are labeled from a complete, closed semiring, and path properties are algebraic
with semiring operations. The algebraic path properties can model dataflow analysis
problems, the shortest path problem, and many other natural problems that arise
in program analysis. We consider that each component of the concurrent system
is a graph with constant treewidth, a property satisfied by the controlflow graphs
of most programs. We allow for multiple possible queries, which arise naturally
in demand driven dataflow analysis. The study of multiple queries allows us to
consider the tradeoff between the resource usage of the one-time preprocessing
and for each individual query. The traditional approach constructs the product
graph of all components and applies the best-known graph algorithm on the product.
In this approach, even the answer to a single query requires the transitive closure
(i.e., the results of all possible queries), which provides no room for tradeoff
between preprocessing and query time. Our main contributions are algorithms that
significantly improve the worst-case running time of the traditional approach,
and provide various tradeoffs depending on the number of queries. For example,
in a concurrent system of two components, the traditional approach requires hexic
time in the worst case for answering one query as well as computing the transitive
closure, whereas we show that with one-time preprocessing in almost cubic time,
each subsequent query can be answered in at most linear time, and even the transitive
closure can be computed in almost quartic time. Furthermore, we establish conditional
optimality results showing that the worst-case running time of our algorithms
cannot be improved without achieving major breakthroughs in graph algorithms (i.e.,
improving the worst-case bound for the shortest path problem in general graphs).
Preliminary experimental results show that our algorithms perform favorably on
several benchmarks.
alternative_title:
- POPL
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for
algebraic path properties in concurrent systems of constant treewidth components.
In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624'
apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A.
(2016). Algorithms for algebraic path properties in concurrent systems of constant
treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles
of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen,
and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624.
ieee: 'K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms
for algebraic path properties in concurrent systems of constant treewidth components,”
presented at the POPL: Principles of Programming Languages, St. Petersburg, FL,
USA, 2016, vol. 20–22, pp. 733–747.'
ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties
in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016,
pp. 733–47, doi:10.1145/2837614.2837624.
short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM,
2016, pp. 733–747.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2024-03-25T23:30:18Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/2837614.2837624
ec_funded: 1
external_id:
arxiv:
- '1510.07565'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.07565
month: '01'
oa: 1
oa_version: Preprint
page: 733 - 747
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'
publication_status: published
publisher: ACM
publist_id: '5761'
quality_controlled: '1'
related_material:
record:
- id: '5441'
relation: earlier_version
status: public
- id: '5442'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
- id: '6009'
relation: later_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '1438'
abstract:
- lang: eng
text: 'In this paper, we consider termination of probabilistic programs with real-valued
variables. The questions concerned are: (a) qualitative ones that ask (i) whether
the program terminates with probability 1 (almost-sure termination) and (ii) whether
the expected termination time is finite (finite termination); (b) quantitative
ones that ask (i) to approximate the expected termination time (expectation problem)
and (ii) to compute a bound B such that the probability to terminate after B steps
decreases exponentially (concentration problem). To solve these questions, we
utilize the notion of ranking supermartingales which is a powerful approach for
proving termination of probabilistic programs. In detail, we focus on algorithmic
synthesis of linear ranking-supermartingales over affine probabilistic programs
(APP''s) with both angelic and demonic non-determinism. An important subclass
of APP''s is LRAPP which is defined as the class of all APP''s over which a linear
ranking-supermartingale exists. Our main contributions are as follows. Firstly,
we show that the membership problem of LRAPP (i) can be decided in polynomial
time for APP''s with at most demonic non-determinism, and (ii) is NP-hard and
in PSPACE for APP''s with angelic non-determinism; moreover, the NP-hardness result
holds already for APP''s without probability and demonic non-determinism. Secondly,
we show that the concentration problem over LRAPP can be solved in the same complexity
as for the membership problem of LRAPP. Finally, we show that the expectation
problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP''s
without probability and non-determinism (i.e., deterministic programs). Our experimental
results demonstrate the effectiveness of our approach to answer the qualitative
and quantitative questions over APP''s with at most demonic non-determinism.'
acknowledgement: 'Supported by the Natural Science Foundation of China (NSFC) under
Grant No. 61532019 '
alternative_title:
- POPL
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Rouzbeh
full_name: Hasheminezhad, Rouzbeh
last_name: Hasheminezhad
citation:
ama: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative
and quantitative termination problems for affine probabilistic programs. In: Vol
20-22. ACM; 2016:327-342. doi:10.1145/2837614.2837639'
apa: 'Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2016). Algorithmic
analysis of qualitative and quantitative termination problems for affine probabilistic
programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming
Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837639'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad.
“Algorithmic Analysis of Qualitative and Quantitative Termination Problems for
Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. https://doi.org/10.1145/2837614.2837639.
ieee: 'K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg,
FL, USA, 2016, vol. 20–22, pp. 327–342.'
ista: 'Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.'
mla: Chatterjee, Krishnendu, et al. Algorithmic Analysis of Qualitative and Quantitative
Termination Problems for Affine Probabilistic Programs. Vol. 20–22, ACM, 2016,
pp. 327–42, doi:10.1145/2837614.2837639.
short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2023-09-19T14:38:41Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/2837614.2837639
ec_funded: 1
external_id:
arxiv:
- '1510.08517'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.08517
month: '01'
oa: 1
oa_version: Preprint
page: 327 - 342
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: ACM
publist_id: '5760'
quality_controlled: '1'
related_material:
record:
- id: '5993'
relation: later_version
status: public
scopus_import: 1
status: public
title: Algorithmic analysis of qualitative and quantitative termination problems for
affine probabilistic programs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '1439'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. We introduce PSYNC, a domain specific
language based on the Heard-Of model, which views asynchronous faulty systems
as synchronous ones with an adversarial environment that simulates asynchrony
and faults by dropping messages. We define a runtime system for PSYNC that efficiently
executes on asynchronous networks. We formalize the relation between the runtime
system and PSYNC in terms of observational refinement. The high-level lockstep
abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant
distributed algorithms and enables automated formal verification. We have implemented
an embedding of PSYNC in the SCALA programming language with a runtime system
for asynchronous networks. We show the applicability of PSYNC by implementing
several important fault-tolerant distributed algorithms and we compare the implementation
of consensus algorithms in PSYNC against implementations in other languages in
terms of code size, runtime efficiency, and verification.
acknowledgement: 'Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192
and FA8650-15-C-7564) and NSF (Grant CCF-1138967). '
alternative_title:
- ACM SIGPLAN Notices
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- 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: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language
for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650'
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially
synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp.
400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg,
FL, USA: ACM. https://doi.org/10.1145/2837614.2837650'
chicago: 'Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially
Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415.
ACM, 2016. https://doi.org/10.1145/2837614.2837650.'
ieee: 'C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous
language for fault-tolerant distributed algorithms,” presented at the POPL: Principles
of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.'
ista: 'Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous
language for fault-tolerant distributed algorithms. POPL: Principles of Programming
Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.'
mla: 'Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant
Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.'
short: C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2021-01-12T06:50:45Z
day: '11'
department:
- _id: ToHe
doi: 10.1145/2837614.2837650
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-01251199/
month: '01'
oa: 1
oa_version: Preprint
page: 400 - 415
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: ACM
publist_id: '5759'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'PSYNC: A partially synchronous language for fault-tolerant distributed algorithms'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '1441'
abstract:
- lang: eng
text: 'Optogenetics and photopharmacology enable the spatio-temporal control of
cell and animal behavior by light. Although red light offers deep-tissue penetration
and minimal phototoxicity, very few red-light-sensitive optogenetic methods are
currently available. We have now developed a red-light-induced homodimerization
domain. We first showed that an optimized sensory domain of the cyanobacterial
phytochrome 1 can be expressed robustly and without cytotoxicity in human cells.
We then applied this domain to induce the dimerization of two receptor tyrosine
kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor
trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway
non-invasively in mammalian tissue and in multicolor cell-signaling experiments.
The light-controlled dimerizer and red-light-activated receptor tyrosine kinases
will prove useful to regulate a variety of cellular processes with light. Go deep
with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was
repurposed to induce the homodimerization of proteins in living cells by red light.
By using this domain, light-activated protein kinases were engineered that can
be activated orthogonally from many fluorescent proteins and through mammalian
tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.'
acknowledgement: 'A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by
the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and
a FemTech fellowship (Austrian Research Promotion Agency: 3580812).'
author:
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736
apa: Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &
Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation
by red light. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.201601736
chicago: Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy,
Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits
Receptor Activation by Red Light.” Angewandte Chemie - International Edition.
Wiley, 2016. https://doi.org/10.1002/anie.201601736.
ieee: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H.
L. Janovjak, “A phytochrome sensory domain permits receptor activation by red
light,” Angewandte Chemie - International Edition, vol. 55, no. 21. Wiley,
pp. 6339–6342, 2016.
ista: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL.
2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte
Chemie - International Edition. 55(21), 6339–6342.
mla: Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor
Activation by Red Light.” Angewandte Chemie - International Edition, vol.
55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736.
short: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L.
Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.
date_created: 2018-12-11T11:52:02Z
date_published: 2016-05-17T00:00:00Z
date_updated: 2023-09-07T12:49:08Z
day: '17'
ddc:
- '571'
- '576'
department:
- _id: HaJa
doi: 10.1002/anie.201601736
ec_funded: 1
file:
- access_level: open_access
checksum: 26da07960e57ac4750b54179197ce57f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:03Z
date_updated: 2020-07-14T12:44:55Z
file_id: '5255'
file_name: IST-2017-840-v1+1_reichhart.pdf
file_size: 1268662
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 6339 - 6342
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley
publist_id: '5755'
pubrep_id: '840'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: A phytochrome sensory domain permits receptor activation by red light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1446'
abstract:
- lang: eng
text: The accuracy of interdisciplinarity measurements is directly related to the
quality of the underlying bibliographic data. Existing indicators of interdisciplinarity
are not capable of reflecting the inaccuracies introduced by incorrect and incomplete
records because correct and complete bibliographic data can rarely be obtained.
This is the case for the Rao–Stirling index, which cannot handle references that
are not categorized into disciplinary fields. We introduce a method that addresses
this problem. It extends the Rao–Stirling index to acknowledge missing data by
calculating its interval of uncertainty using computational optimization. The
evaluation of our method indicates that the uncertainty interval is not only useful
for estimating the inaccuracy of interdisciplinarity measurements, but it also
delivers slightly more accurate aggregated interdisciplinarity measurements than
the Rao–Stirling index.
article_processing_charge: No
author:
- first_name: Maria
full_name: Calatrava Moreno, Maria
last_name: Calatrava Moreno
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Hannes
full_name: Werthner, Hannes
last_name: Werthner
citation:
ama: Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232.
doi:10.1007/s11192-016-1842-4
apa: Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty
of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics.
Springer. https://doi.org/10.1007/s11192-016-1842-4
chicago: Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the
Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic
Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.
ieee: M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of
interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics,
vol. 107, no. 1. Springer, pp. 213–232, 2016.
ista: Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.
mla: Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity
Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol.
107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.
short: M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016)
213–232.
date_created: 2018-12-11T11:52:04Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-11-16T08:29:11Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1007/s11192-016-1842-4
file:
- access_level: open_access
checksum: 32d46268588b87d9b686492018e6a2b2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:56Z
date_updated: 2020-07-14T12:44:55Z
file_id: '4848'
file_name: IST-2016-530-v1+1_s11192-016-1842-4.pdf
file_size: 806035
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 107'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 213 - 232
publication: Scientometrics
publication_status: published
publisher: Springer
publist_id: '5750'
pubrep_id: '530'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11192-016-1902-9
scopus_import: '1'
status: public
title: On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2016'
...
---
_id: '1448'
abstract:
- lang: eng
text: We develop a new and systematic method for proving entropic Ricci curvature
lower bounds for Markov chains on discrete sets. Using different methods, such
bounds have recently been obtained in several examples (e.g., 1-dimensional birth
and death chains, product chains, Bernoulli–Laplace models, and random transposition
models). However, a general method to obtain discrete Ricci bounds had been lacking.
Our method covers all of the examples above. In addition we obtain new Ricci curvature
bounds for zero-range processes on the complete graph. The method is inspired
by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.
acknowledgement: "Supported by the German Research Foundation through the Collaborative
Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center
for Mathematics. Part of this work has been done while M. Fathi visited J. Maas
at the University of Bonn in July 2014.We would like to thank the referees for their
careful reading of the manuscript. "
author:
- first_name: Max
full_name: Fathi, Max
last_name: Fathi
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems.
The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133
apa: Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete
interacting systems. The Annals of Applied Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/15-AAP1133
chicago: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete
Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical
Statistics, 2016. https://doi.org/10.1214/15-AAP1133.
ieee: M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting
systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute
of Mathematical Statistics, pp. 1774–1806, 2016.
ista: Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting
systems. The Annals of Applied Probability. 26(3), 1774–1806.
mla: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting
Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute
of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.
short: M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.
date_created: 2018-12-11T11:52:05Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:49Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/15-AAP1133
intvolume: ' 26'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00562
month: '06'
oa: 1
oa_version: Preprint
page: 1774 - 1806
publication: The Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5748'
quality_controlled: '1'
scopus_import: 1
status: public
title: Entropic Ricci curvature bounds for discrete interacting systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1475'
abstract:
- lang: eng
text: The actin cytoskeleton plays important roles in the formation and internalization
of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes
along actin cables, however, the molecular machinery regulating interaction between
endocytic vesicles and actin cables is poorly understood. The Eps15-like protein
Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated
by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation
at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as
ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several
endocytic compartments. Early endosomes were highly localized in the actin concentrations
and displayed movement along actin cables. The dephosphorylated form of Pan1p
also caused stable associations between endocytic vesicles and actin cables, and
between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of
a novel mechanism that regulates endocytic compartment interactions with each
other and with actin cables.
article_number: e10276
author:
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Eri
full_name: Furuya, Eri
last_name: Furuya
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Chisa
full_name: Kanno, Chisa
last_name: Kanno
- first_name: Yuta
full_name: Sakamoto, Yuta
last_name: Sakamoto
- first_name: Masashi
full_name: Ebihara, Masashi
last_name: Ebihara
- 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: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p
regulates the interaction between endocytic vesicles, endosomes and the actin
cytoskeleton. eLife. 2016;5(February 2016). doi:10.7554/eLife.10276
apa: Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M.,
… Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction
between endocytic vesicles, endosomes and the actin cytoskeleton. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.10276
chicago: Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto,
Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic
Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes
and the Actin Cytoskeleton.” ELife. eLife Sciences Publications, 2016.
https://doi.org/10.7554/eLife.10276.
ieee: J. Toshima et al., “Yeast Eps15-like endocytic protein Pan1p regulates
the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,”
eLife, vol. 5, no. February 2016. eLife Sciences Publications, 2016.
ista: Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE,
Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction
between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February
2016), e10276.
mla: Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates
the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.”
ELife, vol. 5, no. February 2016, e10276, eLife Sciences Publications,
2016, doi:10.7554/eLife.10276.
short: J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E.
Siekhaus, J. Toshima, ELife 5 (2016).
date_created: 2018-12-11T11:52:14Z
date_published: 2016-02-25T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '25'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.10276
ec_funded: 1
file:
- access_level: open_access
checksum: d1cc44870580756ba8badd8e41adfdb5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:08Z
date_updated: 2020-07-14T12:44:56Z
file_id: '4793'
file_name: IST-2016-529-v1+1_elife-10276-v1.pdf
file_size: 5198001
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 5'
issue: February 2016
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5721'
pubrep_id: '529'
quality_controlled: '1'
scopus_import: 1
status: public
title: Yeast Eps15-like endocytic protein Pan1p regulates the interaction between
endocytic vesicles, endosomes and the actin cytoskeleton
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '1476'
abstract:
- lang: eng
text: The dynamic assembly and disassembly of actin filaments is essential for the
formation and transport of vesicles during endocytosis. In yeast, two types of
actin structures, namely cortical patches and cytoplasmic cables, play a direct
role in endocytosis, but how their interaction is regulated remains unclear. Here,
we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required
for efficient endocytosis owing to its role in the formation of the actin patches
that aid initial vesicle invagination and of the actin cables that these move
along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented
actin cables that frequently moved past actin patches, the sites of endocytosis.
We find that the C-terminal CARP domain of Srv2p is vitally important for the
proper assembly of actin patches and cables; we also demonstrate that the N-terminal
helical folded domain of Srv2 is required for its localization to actin patches,
specifically to the ADP-actin rich region through an interaction with cofilin.
These results demonstrate the in vivo roles of Srv2p in the regulation of the
actin cytoskeleton during clathrin-mediated endocytosis
acknowledgement: We are grateful to Anthony Bretscher (Cornell University, NY) for
providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society
for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda
Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a
JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the
Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported
by the European Union [grant number PCIG12-GA-2012-334077].
author:
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Chika
full_name: Horikomi, Chika
last_name: Horikomi
- first_name: Asuka
full_name: Okada, Asuka
last_name: Okada
- first_name: Makiko
full_name: Hatori, Makiko
last_name: Hatori
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Atsushi
full_name: Masuda, Atsushi
last_name: Masuda
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- 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: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin
cable assembly and patch internalization during clathrin-mediated endocytosis.
Journal of Cell Science. 2016;129(2):367-379. doi:10.1242/jcs.176651
apa: Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., …
Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and
patch internalization during clathrin-mediated endocytosis. Journal of Cell
Science. Company of Biologists. https://doi.org/10.1242/jcs.176651
chicago: Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano,
Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP
Is Required for Polarized Actin Cable Assembly and Patch Internalization during
Clathrin-Mediated Endocytosis.” Journal of Cell Science. Company of Biologists,
2016. https://doi.org/10.1242/jcs.176651.
ieee: J. Toshima et al., “Srv2/CAP is required for polarized actin cable
assembly and patch internalization during clathrin-mediated endocytosis,” Journal
of Cell Science, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.
ista: Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W,
Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly
and patch internalization during clathrin-mediated endocytosis. Journal of Cell
Science. 129(2), 367–379.
mla: Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly
and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of
Cell Science, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:10.1242/jcs.176651.
short: J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto,
D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.
date_created: 2018-12-11T11:52:14Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T06:51:00Z
day: '15'
ddc:
- '570'
- '576'
department:
- _id: DaSi
doi: 10.1242/jcs.176651
ec_funded: 1
file:
- access_level: open_access
checksum: 2da0a09149a9ed956cdf79a95c17f08a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:08Z
date_updated: 2020-07-14T12:44:56Z
file_id: '4861'
file_name: IST-2017-767-v1+1_367.full.pdf
file_size: 7176912
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 129'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 367 - 379
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '5720'
pubrep_id: '767'
quality_controlled: '1'
scopus_import: 1
status: public
title: Srv2/CAP is required for polarized actin cable assembly and patch internalization
during clathrin-mediated endocytosis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2016'
...