---
_id: '565'
abstract:
- lang: eng
text: 'We re-examine the model of Kirkpatrick and Barton for the spread of an inversion
into a local population. This model assumes that local selection maintains alleles
at two or more loci, despite immigration of alternative alleles at these loci
from another population. We show that an inversion is favored because it prevents
the breakdown of linkage disequilibrium generated by migration; the selective
advantage of an inversion is proportional to the amount of recombination between
the loci involved, as in other cases where inversions are selected for. We derive
expressions for the rate of spread of an inversion; when the loci covered by the
inversion are tightly linked, these conditions deviate substantially from those
proposed previously, and imply that an inversion can then have only a small advantage. '
article_processing_charge: No
article_type: original
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Charlesworth B, Barton NH. The spread of an inversion with migration and selection.
Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426
apa: Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with
migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426
chicago: Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion
with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.
ieee: B. Charlesworth and N. H. Barton, “The spread of an inversion with migration
and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.
ista: Charlesworth B, Barton NH. 2018. The spread of an inversion with migration
and selection. Genetics. 208(1), 377–382.
mla: Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with
Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp.
377–82, doi:10.1534/genetics.117.300426.
short: B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-19T10:12:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300426
external_id:
isi:
- '000419356300025'
pmid:
- '29158424'
intvolume: ' 208'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/
month: '01'
oa: 1
oa_version: Published Version
page: 377 - 382
pmid: 1
publication: Genetics
publication_status: published
publisher: 'Genetics '
publist_id: '7249'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The spread of an inversion with migration and selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '446'
abstract:
- lang: eng
text: We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge
Z > 0 can bind at most Z + C electrons, where C is a universal constant. This
result is obtained through a comparison with Thomas-Fermi theory which, as a by-product,
gives bounds on the screened nuclear potential and the radius of the minimizer.
A key ingredient of the proof is a novel technique to control the particles in
the exterior region, which also applies to the liquid drop model with a nuclear
background potential.
acknowledgement: "We thank the referee for helpful suggestions that improved the presentation
of the paper. We also acknowledge partial support by National Science Foundation
Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27
(P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa
Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática”
(H.V.D.B.).\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Nam
full_name: Phan Thanh, Nam
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Phan Thanh
- first_name: Hanne
full_name: Van Den Bosch, Hanne
last_name: Van Den Bosch
citation:
ama: Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von
Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614.
doi:10.1002/cpa.21717
apa: Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture
in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied
Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717
chicago: Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture
in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied
Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.
ieee: R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von
Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol.
71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.
ista: Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von
Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.
mla: Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von
Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol.
71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.
short: R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics
71 (2018) 577–614.
date_created: 2018-12-11T11:46:31Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-19T10:09:40Z
day: '01'
department:
- _id: RoSe
doi: 10.1002/cpa.21717
external_id:
arxiv:
- '1606.07355'
isi:
- '000422675800004'
intvolume: ' 71'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.07355
month: '03'
oa: 1
oa_version: Preprint
page: 577 - 614
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7377'
quality_controlled: '1'
status: public
title: The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2018'
...
---
_id: '430'
abstract:
- lang: eng
text: In this issue of GENETICS, a new method for detecting natural selection on
polygenic traits is developed and applied to sev- eral human examples ( Racimo
et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic
traits, and a challenge for evolutionary ge neticists has been that these traits
can evolve by small, nearly undetectable shifts in allele frequencies across each
of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide
associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated
jointly for c hanges in allele frequencies. By aggregating small signal s of change
across many such loci, directional natural selection is now in principle detect-
able using genetic data, even for highly polygenic traits. This is an exciting
arena of progress – with these methods, tests can be made for selection associated
with traits, and we can now study selection in what may be its most prevalent
mode. The continuing fast pace of GWAS publications suggest there will be many
more polygenic tests of selection in the near future, as every new GWAS is an
opportunity for an accom- panying test of polygenic selection. However, it is
important to be aware of complications th at arise in interpretation, especially
given that these studies may easily be misinter- preted both in and outside the
evolutionary genetics commu- nity. Here, we provide context for understanding
polygenic tests and urge caution regarding how these results are inter- preted
and reported upon more broadly.
article_processing_charge: No
author:
- first_name: John
full_name: Novembre, John
last_name: Novembre
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection.
Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786
apa: Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic
tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786
chicago: Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.
ieee: J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests
of selection,” Genetics, vol. 208, no. 4. Genetics Society of America,
pp. 1351–1355, 2018.
ista: Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of
selection. Genetics. 208(4), 1351–1355.
mla: Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America,
2018, pp. 1351–55, doi:10.1534/genetics.118.300786.
short: J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.
date_created: 2018-12-11T11:46:26Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-19T10:17:30Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.118.300786
external_id:
isi:
- '000429094400005'
file:
- access_level: open_access
checksum: 3d838dc285df394376555b794b6a5ad1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:40Z
date_updated: 2020-07-14T12:46:26Z
file_id: '4958'
file_name: IST-2018-1012-v1+1_2018_Barton_Tread.pdf
file_size: 500129
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1351 - 1355
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7393'
pubrep_id: '1012'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tread lightly interpreting polygenic tests of selection
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: 208
year: '2018'
...
---
_id: '199'
abstract:
- lang: eng
text: Sex-biased genes are central to the study of sexual selection, sexual antagonism,
and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome
in the common frog Rana temporaria based on five developmental stages and three
adult tissues from both sexes, obtained from a population with karyotypically
homomorphic but genetically differentiated sex chromosomes. This allows the study
of sex-biased gene expression throughout development, and its effect on the rate
of gene evolution while accounting for pleiotropic expression, which is known
to negatively correlate with the evolutionary rate. Overall, sex-biased genes
had little overlap among developmental stages and adult tissues. Late developmental
stages and gonad tissues had the highest numbers of stage-or tissue-specific genes.
We find that pleiotropic gene expression is a better predictor than sex bias for
the evolutionary rate of genes, though it often interacts with sex bias. Although
genetically differentiated, the sex chromosomes were not enriched in sex-biased
genes, possibly due to a very recent arrest of XY recombination. These results
extend our understanding of the developmental dynamics, tissue specificity, and
genomic localization of sex-biased genes.
article_number: '294'
article_processing_charge: No
author:
- first_name: Wen
full_name: Ma, Wen
last_name: Ma
- first_name: Paris
full_name: Veltsos, Paris
last_name: Veltsos
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Nicolas
full_name: Rodrigues, Nicolas
last_name: Rodrigues
- first_name: Roberto
full_name: Sermier, Roberto
last_name: Sermier
- first_name: Daniel
full_name: Jeffries, Daniel
last_name: Jeffries
- first_name: Nicolas
full_name: Perrin, Nicolas
last_name: Perrin
citation:
ama: Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased
gene expression in a common frog population with differentiated, yet homomorphic,
sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294
apa: Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D.,
& Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression
in a common frog population with differentiated, yet homomorphic, sex chromosomes.
Genes. MDPI AG. https://doi.org/10.3390/genes9060294
chicago: Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier,
Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased
Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic,
Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.
ieee: W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression
in a common frog population with differentiated, yet homomorphic, sex chromosomes,”
Genes, vol. 9, no. 6. MDPI AG, 2018.
ista: Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018.
Tissue specificity and dynamics of sex biased gene expression in a common frog
population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6),
294.
mla: Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression
in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.”
Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.
short: W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N.
Perrin, Genes 9 (2018).
date_created: 2018-12-11T11:45:09Z
date_published: 2018-06-12T00:00:00Z
date_updated: 2023-09-19T10:15:31Z
day: '12'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes9060294
external_id:
isi:
- '000436494200026'
file:
- access_level: open_access
checksum: 423069beb1cd3cdd25bf3f464b38f1d7
content_type: application/pdf
creator: dernst
date_created: 2019-02-01T07:52:28Z
date_updated: 2020-07-14T12:45:22Z
file_id: '5905'
file_name: 2018_Genes_Ma.pdf
file_size: 3985796
relation: main_file
file_date_updated: 2020-07-14T12:45:22Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Genes
publication_status: published
publisher: MDPI AG
publist_id: '7714'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tissue specificity and dynamics of sex biased gene expression in a common frog
population with differentiated, yet homomorphic, sex chromosomes
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: 9
year: '2018'
...
---
_id: '543'
abstract:
- lang: eng
text: A central goal in theoretical neuroscience is to predict the response properties
of sensory neurons from first principles. To this end, “efficient coding” posits
that sensory neurons encode maximal information about their inputs given internal
constraints. There exist, however, many variants of efficient coding (e.g., redundancy
reduction, different formulations of predictive coding, robust coding, sparse
coding, etc.), differing in their regimes of applicability, in the relevance of
signals to be encoded, and in the choice of constraints. It is unclear how these
types of efficient coding relate or what is expected when different coding objectives
are combined. Here we present a unified framework that encompasses previously
proposed efficient coding models and extends to unique regimes. We show that optimizing
neural responses to encode predictive information can lead them to either correlate
or decorrelate their inputs, depending on the stimulus statistics; in contrast,
at low noise, efficiently encoding the past always predicts decorrelation. Later,
we investigate coding of naturalistic movies and show that qualitatively different
types of visual motion tuning and levels of response sparsity are predicted, depending
on whether the objective is to recover the past or predict the future. Our approach
promises a way to explain the observed diversity of sensory neural responses,
as due to multiple functional goals and constraints fulfilled by different cell
types and/or circuits.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115
apa: Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of
efficient, predictive, and sparse coding. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1711114115
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory
of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of
Sciences, 2018. https://doi.org/10.1073/pnas.1711114115.
ieee: M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient,
predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy
of Sciences, pp. 186–191, 2018.
ista: Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive,
and sparse coding. PNAS. 115(1), 186–191.
mla: Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive,
and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences,
2018, pp. 186–91, doi:10.1073/pnas.1711114115.
short: M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-02T00:00:00Z
date_updated: 2023-09-19T10:16:35Z
day: '02'
department:
- _id: GaTk
doi: 10.1073/pnas.1711114115
external_id:
isi:
- '000419128700049'
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/152660 '
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 191
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7273'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unified theory of efficient, predictive, and sparse coding
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '421'
abstract:
- lang: eng
text: Cell shape is determined by a balance of intrinsic properties of the cell
as well as its mechanochemical environment. Inhomogeneous shape changes underlie
many morphogenetic events and involve spatial gradients in active cellular forces
induced by complex chemical signaling. Here, we introduce a mechanochemical model
based on the notion that cell shape changes may be induced by external diffusible
biomolecules that influence cellular contractility (or equivalently, adhesions)
in a concentration-dependent manner—and whose spatial profile in turn is affected
by cell shape. We map out theoretically the possible interplay between chemical
concentration and cellular structure. Besides providing a direct route to spatial
gradients in cell shape profiles in tissues, we show that the dependence on cell
shape helps create robust mechanochemical gradients.
article_processing_charge: No
author:
- first_name: Kinjal
full_name: Dasbiswas, Kinjal
last_name: Dasbiswas
- first_name: Claude-Edouard B
full_name: Hannezo, Claude-Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977.
doi:10.1016/j.bpj.2017.12.022
apa: Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial
cell shape transitions induced by mechanoactive chemical gradients. Biophysical
Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022
chicago: Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial
Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical
Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.
ieee: K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape
transitions induced by mechanoactive chemical gradients,” Biophysical Journal,
vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.
ista: Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.
mla: Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced
by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no.
4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.
short: K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.
date_created: 2018-12-11T11:46:23Z
date_published: 2018-02-27T00:00:00Z
date_updated: 2023-09-19T10:13:55Z
day: '27'
department:
- _id: EdHa
doi: 10.1016/j.bpj.2017.12.022
external_id:
arxiv:
- '1709.01486'
isi:
- '000428016700021'
intvolume: ' 114'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.01486
month: '02'
oa: 1
oa_version: Submitted Version
page: 968 - 977
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '7403'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theory of eppithelial cell shape transitions induced by mechanoactive chemical
gradients
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
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 AG. https://doi.org/10.3390/genes9100480
chicago: Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes
in African Cichlid Fishes.” Genes. MDPI AG, 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 AG, 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 AG, 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: 2023-09-19T10:37:03Z
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 AG
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '296'
abstract:
- lang: eng
text: The thermodynamic description of many-particle systems rests on the assumption
of ergodicity, the ability of a system to explore all allowed configurations in
the phase space. Recent studies on many-body localization have revealed the existence
of systems that strongly violate ergodicity in the presence of quenched disorder.
Here, we demonstrate that ergodicity can be weakly broken by a different mechanism,
arising from the presence of special eigenstates in the many-body spectrum that
are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle
case, quantum scars correspond to wavefunctions that concentrate in the vicinity
of unstable periodic classical trajectories. We show that many-body scars appear
in the Fibonacci chain, a model with a constrained local Hilbert space that has
recently been experimentally realized in a Rydberg-atom quantum simulator. The
quantum scarred eigenstates are embedded throughout the otherwise thermalizing
many-body spectrum but lead to direct experimental signatures, as we show for
periodic recurrences that reproduce those observed in the experiment. Our results
suggest that scarred many-body bands give rise to a new universality class of
quantum dynamics, opening up opportunities for the creation of novel states with
long-lived coherence in systems that are now experimentally realizable.
acknowledgement: C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1
and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support
from the Swiss National Science Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Turner, Christopher
last_name: Turner
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking
from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5
apa: Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018).
Weak ergodicity breaking from quantum many-body scars. Nature Physics.
Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5
chicago: Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn,
and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature
Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5.
ieee: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity
breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature
Publishing Group, pp. 745–749, 2018.
ista: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity
breaking from quantum many-body scars. Nature Physics. 14, 745–749.
mla: Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body
Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49,
doi:10.1038/s41567-018-0137-5.
short: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics
14 (2018) 745–749.
date_created: 2018-12-11T11:45:40Z
date_published: 2018-05-14T00:00:00Z
date_updated: 2023-09-19T10:37:55Z
day: '14'
department:
- _id: MaSe
doi: 10.1038/s41567-018-0137-5
external_id:
isi:
- '000438253600028'
intvolume: ' 14'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprints.whiterose.ac.uk/130860/
month: '05'
oa: 1
oa_version: Submitted Version
page: 745 - 749
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7585'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weak ergodicity breaking from quantum many-body scars
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '607'
abstract:
- lang: eng
text: We study the Fokker-Planck equation derived in the large system limit of the
Markovian process describing the dynamics of quantitative traits. The Fokker-Planck
equation is posed on a bounded domain and its transport and diffusion coefficients
vanish on the domain's boundary. We first argue that, despite this degeneracy,
the standard no-flux boundary condition is valid. We derive the weak formulation
of the problem and prove the existence and uniqueness of its solutions by constructing
the corresponding contraction semigroup on a suitable function space. Then, we
prove that for the parameter regime with high enough mutation rate the problem
exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next,
we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt)
method for approximation of observables (moments) of the Fokker-Planck solution,
which can be interpreted as a nonlinear Galerkin approximation. The limited applicability
of the DynMaxEnt method inspires us to introduce its modified version that is
valid for the whole range of admissible parameters. Finally, we present several
numerical experiments to demonstrate the performance of both the original and
modified DynMaxEnt methods. We observe that in the parameter regimes where both
methods are valid, the modified one exhibits slightly better approximation properties
compared to the original one.
acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193
.\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions.
\r\n\r\n"
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Jan
full_name: Haskovec, Jan
last_name: Haskovec
- first_name: Peter
full_name: Markowich, Peter
last_name: Markowich
citation:
ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation
for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015'
apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum
entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear
Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015'
chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and
Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica
D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.'
ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy
approximation for the dynamics of quantitative traits,” Physica D: Nonlinear
Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.'
ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy
approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
376–377, 108–120.'
mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation
for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena,
vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.'
short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377
(2018) 108–120.'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:38:34Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1016/j.physd.2017.10.015
external_id:
arxiv:
- '1704.08757'
isi:
- '000437962900012'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.08757
month: '08'
oa: 1
oa_version: Submitted Version
page: 108-120
publication: 'Physica D: Nonlinear Phenomena'
publication_status: published
publisher: Elsevier
publist_id: '7198'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well posedness and maximum entropy approximation for the dynamics of quantitative
traits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 376-377
year: '2018'
...
---
_id: '294'
abstract:
- lang: eng
text: We developed a method to calculate two-photon processes in quantum mechanics
that replaces the infinite summation over the intermediate states by a perturbation
expansion. This latter consists of a series of commutators that involve position,
momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle
cases for which a closed-form solution to the perturbation expansion exists, as
well as more complicated cases for which a solution is found by convergence. Throughout
the article, Rayleigh and Raman scattering are taken as examples of two-photon
processes. The present method provides a clear distinction between the Thomson
scattering, regarded as classical scattering, and quantum contributions. Such
a distinction lets us derive general results concerning light scattering. Finally,
possible extensions to the developed formalism are discussed.
article_processing_charge: No
author:
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum
commutators. Physical Review A - Atomic, Molecular, and Optical Physics.
2018;97(4). doi:10.1103/PhysRevA.97.043842
apa: Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes
based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842
chicago: Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon
Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.
ieee: F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based
on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 4. American Physical Society, 2018.
ista: Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on
quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics.
97(4).
mla: Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no.
4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.
short: F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular,
and Optical Physics 97 (2018).
date_created: 2018-12-11T11:45:40Z
date_published: 2018-04-18T00:00:00Z
date_updated: 2023-09-19T10:17:56Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.97.043842
ec_funded: 1
external_id:
arxiv:
- '1801.06892'
isi:
- '000430296800008'
intvolume: ' 97'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1801.06892
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '7587'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Two-photon processes based on quantum commutators
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '606'
abstract:
- lang: eng
text: We establish the existence of a global solution for a new family of fluid-like
equations, which are obtained in certain regimes in as the mean-field evolution
of the supercurrent density in a (2D section of a) type-II superconductor with
pinning and with imposed electric current. We also consider general vortex-sheet
initial data, and investigate the uniqueness and regularity properties of the
solution. For some choice of parameters, the equation under investigation coincides
with the so-called lake equation from 2D shallow water fluid dynamics, and our
analysis then leads to a new existence result for rough initial data.
acknowledgement: "The work of the author is supported by F.R.S.-FNRS ( Fonds de la
Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n"
article_processing_charge: No
author:
- first_name: Mitia
full_name: Duerinckx, Mitia
last_name: Duerinckx
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in
superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004
apa: Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions
arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non
Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004
chicago: Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field
Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare
(C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.
ieee: M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions
arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.
ista: Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising
in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis.
35(5), 1267–1319.
mla: Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions
Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non
Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.
short: M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non
Linear Analysis 35 (2018) 1267–1319.
date_created: 2018-12-11T11:47:27Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:39:09Z
day: '01'
department:
- _id: JuFi
doi: 10.1016/j.anihpc.2017.11.004
external_id:
arxiv:
- '1607.00268'
isi:
- '000437975500005'
intvolume: ' 35'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00268
month: '08'
oa: 1
oa_version: Submitted Version
page: 1267-1319
publication: Annales de l'Institut Henri Poincare (C) Non Linear Analysis
publication_status: published
publisher: Elsevier
publist_id: '7199'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well-posedness for mean-field evolutions arising in superconductivity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 35
year: '2018'
...
---
_id: '5959'
abstract:
- lang: eng
text: Formalizing properties of systems with continuous dynamics is a challenging
task. In this paper, we propose a formal framework for specifying and monitoring
rich temporal properties of real-valued signals. We introduce signal first-order
logic (SFO) as a specification language that combines first-order logic with linear-real
arithmetic and unary function symbols interpreted as piecewise-linear signals.
We first show that while the satisfiability problem for SFO is undecidable, its
membership and monitoring problems are decidable. We develop an offline monitoring
procedure for SFO that has polynomial complexity in the size of the input trace
and the specification, for a fixed number of quantifiers and function symbols.
We show that the algorithm has computation time linear in the size of the input
trace for the important fragment of bounded-response specifications interpreted
over input traces with finite variability. We can use our results to extend signal
temporal logic with first-order quantifiers over time and value parameters, while
preserving its efficient monitoring. We finally demonstrate the practical appeal
of our logic through a case study in the micro-electronics domain.
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Deian
full_name: Nickovicl, Deian
last_name: Nickovicl
citation:
ama: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order
logic of signals. In: 2018 International Conference on Embedded Software.
IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203'
apa: 'Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018).
Keynote: The first-order logic of signals. In 2018 International Conference
on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203'
chicago: 'Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl.
“Keynote: The First-Order Logic of Signals.” In 2018 International Conference
on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.'
ieee: 'A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The
first-order logic of signals,” in 2018 International Conference on Embedded
Software, Turin, Italy, 2018, pp. 1–10.'
ista: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order
logic of signals. 2018 International Conference on Embedded Software. EMSOFT:
International Conference on Embedded Software, 1–10.'
mla: 'Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018
International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.'
short: A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International
Conference on Embedded Software, IEEE, 2018, pp. 1–10.
conference:
end_date: 2018-10-05
location: Turin, Italy
name: 'EMSOFT: International Conference on Embedded Software'
start_date: 2018-09-30
date_created: 2019-02-13T09:19:28Z
date_published: 2018-09-30T00:00:00Z
date_updated: 2023-09-19T10:41:29Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/emsoft.2018.8537203
external_id:
isi:
- '000492828500005'
file:
- access_level: open_access
checksum: 234a33ad9055b3458fcdda6af251b33a
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:01:29Z
date_updated: 2020-07-14T12:47:13Z
file_id: '7839'
file_name: 2018_EMSOFT_Bakhirkin.pdf
file_size: 338006
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1-10
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 2018 International Conference on Embedded Software
publication_identifier:
isbn:
- '9781538655603'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Keynote: The first-order logic of signals'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5962'
abstract:
- lang: eng
text: Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning,
representing the optimization backbone for training several classic models, from
regression to neural networks. Given the recent practical focus on distributed
machine learning, significant work has been dedicated to the convergence properties
of this algorithm under the inconsistent and noisy updates arising from execution
in a distributed environment. However, surprisingly, the convergence properties
of this classic algorithm in the standard shared-memory model are still not well-understood.
In this work, we address this gap, and provide new convergence bounds for lock-free
concurrent stochastic gradient descent, executing in the classic asynchronous
shared memory model, against a strong adaptive adversary. Our results give improved
upper and lower bounds on the "price of asynchrony'' when executing the fundamental
SGD algorithm in a concurrent setting. They show that this classic optimization
tool can converge faster and with a wider range of parameters than previously
known under asynchronous iterations. At the same time, we exhibit a fundamental
trade-off between the maximum delay in the system and the rate at which SGD can
converge, which governs the set of parameters under which this algorithm can still
work efficiently.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Christopher
full_name: De Sa, Christopher
last_name: De Sa
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
citation:
ama: 'Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient
descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178.
doi:10.1145/3212734.3212763'
apa: 'Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence
of stochastic gradient descent in asynchronous shared memory. In Proceedings
of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18
(pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763'
chicago: Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The
Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In
Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing
- PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.
ieee: D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic
gradient descent in asynchronous shared memory,” in Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United
Kingdom, 2018, pp. 169–178.
ista: 'Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic
gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed
Computing, 169–178.'
mla: Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent
in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles
of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.
short: D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018,
pp. 169–178.
conference:
end_date: 2018-07-27
location: Egham, United Kingdom
name: 'PODC: Principles of Distributed Computing'
start_date: 2018-07-23
date_created: 2019-02-13T09:58:58Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2023-09-19T10:42:53Z
day: '23'
department:
- _id: DaAl
doi: 10.1145/3212734.3212763
external_id:
arxiv:
- '1803.08841'
isi:
- '000458186900022'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08841
month: '07'
oa: 1
oa_version: Preprint
page: 169-178
publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing -
PODC '18
publication_identifier:
isbn:
- '9781450357951'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The convergence of stochastic gradient descent in asynchronous shared memory
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5860'
abstract:
- lang: eng
text: 'A major problem for evolutionary theory is understanding the so-called open-ended
nature of evolutionary change, from its definition to its origins. Open-ended
evolution (OEE) refers to the unbounded increase in complexity that seems to characterize
evolution on multiple scales. This property seems to be a characteristic feature
of biological and technological evolution and is strongly tied to the generative
potential associated with combinatorics, which allows the system to grow and expand
their available state spaces. Interestingly, many complex systems presumably displaying
OEE, from language to proteins, share a common statistical property: the presence
of Zipf''s Law. Given an inventory of basic items (such as words or protein domains)
required to build more complex structures (sentences or proteins) Zipf''s Law
tells us that most of these elements are rare whereas a few of them are extremely
common. Using algorithmic information theory, in this paper we provide a fundamental
definition for open-endedness, which can be understood as postulates. Its statistical
counterpart, based on standard Shannon information theory, has the structure of
a variational problem which is shown to lead to Zipf''s Law as the expected consequence
of an evolutionary process displaying OEE. We further explore the problem of information
conservation through an OEE process and we conclude that statistical information
(standard Shannon information) is not conserved, resulting in the paradoxical
situation in which the increase of information content has the effect of erasing
itself. We prove that this paradox is solved if we consider non-statistical forms
of information. This last result implies that standard information theory may
not be a suitable theoretical framework to explore the persistence and increase
of the information content in OEE systems.'
article_number: '20180395'
article_processing_charge: No
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Luís F.
full_name: Seoane, Luís F.
last_name: Seoane
- first_name: Ricard
full_name: Solé, Ricard
last_name: Solé
citation:
ama: Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and
open-ended evolution. Journal of the Royal Society Interface. 2018;15(149).
doi:10.1098/rsif.2018.0395
apa: Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded
complexity and open-ended evolution. Journal of the Royal Society Interface.
Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395
chicago: Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law,
Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society
Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.
ieee: B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity
and open-ended evolution,” Journal of the Royal Society Interface, vol.
15, no. 149. Royal Society Publishing, 2018.
ista: Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity
and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.
mla: Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended
Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395,
Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.
short: B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface
15 (2018).
date_created: 2019-01-20T22:59:19Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-19T10:40:38Z
day: '12'
department:
- _id: EdHa
doi: 10.1098/rsif.2018.0395
external_id:
arxiv:
- '1612.01605'
isi:
- '000456783800002'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.01605
month: '12'
oa: 1
oa_version: Preprint
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Zipf's Law, unbounded complexity and open-ended evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '5961'
abstract:
- lang: eng
text: "The area of machine learning has made considerable progress over the past
decade, enabled by the widespread availability of large datasets, as well as by
improved algorithms and models. Given the large computational demands of machine
learning workloads, parallelism, implemented either through single-node concurrency
or through multi-node distribution, has been a third key ingredient to advances
in machine learning.\r\nThe goal of this tutorial is to provide the audience with
an overview of standard distribution techniques in machine learning, with an eye
towards the intriguing trade-offs between synchronization and communication costs
of distributed machine learning algorithms, on the one hand, and their convergence,
on the other.The tutorial will focus on parallelization strategies for the fundamental
stochastic gradient descent (SGD) algorithm, which is a key tool when training
machine learning models, from classical instances such as linear regression, to
state-of-the-art neural network architectures.\r\nThe tutorial will describe the
guarantees provided by this algorithm in the sequential case, and then move on
to cover both shared-memory and message-passing parallelization strategies, together
with the guarantees they provide, and corresponding trade-offs. The presentation
will conclude with a broad overview of ongoing research in distributed and concurrent
machine learning. The tutorial will assume no prior knowledge beyond familiarity
with basic concepts in algebra and analysis.\r\n"
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Alistarh D-A. A brief tutorial on distributed and concurrent machine learning.
In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing
- PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798'
apa: 'Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine
learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed
Computing - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798'
chicago: Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine
Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed
Computing - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798.
ieee: D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,”
in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing
- PODC ’18, Egham, United Kingdom, 2018, pp. 487–488.
ista: 'Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine
learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing
- PODC ’18. PODC: Principles of Distributed Computing, 487–488.'
mla: Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine
Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed
Computing - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798.
short: D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles
of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–488.
conference:
end_date: 2018-07-27
location: Egham, United Kingdom
name: 'PODC: Principles of Distributed Computing'
start_date: 2018-07-23
date_created: 2019-02-13T09:48:55Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2023-09-19T10:42:28Z
day: '27'
department:
- _id: DaAl
doi: 10.1145/3212734.3212798
external_id:
isi:
- '000458186900063'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 487-488
publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing -
PODC '18
publication_identifier:
isbn:
- '9781450357951'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A brief tutorial on distributed and concurrent machine learning
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5960'
abstract:
- lang: eng
text: In this paper we present a reliable method to verify the existence of loops
along the uncertain trajectory of a robot, based on proprioceptive measurements
only, within a bounded-error context. The loop closure detection is one of the
key points in simultaneous localization and mapping (SLAM) methods, especially
in homogeneous environments with difficult scenes recognitions. The proposed approach
is generic and could be coupled with conventional SLAM algorithms to reliably
reduce their computing burden, thus improving the localization and mapping processes
in the most challenging environments such as unexplored underwater extents. To
prove that a robot performed a loop whatever the uncertainties in its evolution,
we employ the notion of topological degree that originates in the field of differential
topology. We show that a verification tool based on the topological degree is
an optimal method for proving robot loops. This is demonstrated both on datasets
from real missions involving autonomous underwater vehicles and by a mathematical
discussion.
article_processing_charge: No
author:
- first_name: Simon
full_name: Rohou, Simon
last_name: Rohou
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
orcid: 0000-0001-8878-8397
- first_name: Clément
full_name: Aubry, Clément
last_name: Aubry
- first_name: Luc
full_name: Jaulin, Luc
last_name: Jaulin
citation:
ama: Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot
trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516.
doi:10.1177/0278364918808367
apa: Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence
of loops in robot trajectories. The International Journal of Robotics Research.
SAGE Publications. https://doi.org/10.1177/0278364918808367
chicago: Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the
Existence of Loops in Robot Trajectories.” The International Journal of Robotics
Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.
ieee: S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops
in robot trajectories,” The International Journal of Robotics Research,
vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.
ista: Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops
in robot trajectories. The International Journal of Robotics Research. 37(12),
1500–1516.
mla: Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.”
The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications,
2018, pp. 1500–16, doi:10.1177/0278364918808367.
short: S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics
Research 37 (2018) 1500–1516.
date_created: 2019-02-13T09:36:20Z
date_published: 2018-10-24T00:00:00Z
date_updated: 2023-09-19T10:41:59Z
day: '24'
department:
- _id: UlWa
doi: 10.1177/0278364918808367
external_id:
arxiv:
- '1712.01341'
isi:
- '000456881100004'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.01341
month: '10'
oa: 1
oa_version: Preprint
page: 1500-1516
publication: The International Journal of Robotics Research
publication_identifier:
eissn:
- 1741-3176
issn:
- 0278-3649
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proving the existence of loops in robot trajectories
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '5963'
abstract:
- lang: eng
text: 'There has been significant progress in understanding the parallelism inherent
to iterative sequential algorithms: for many classic algorithms, the depth of
the dependence structure is now well understood, and scheduling techniques have
been developed to exploit this shallow dependence structure for efficient parallel
implementations. A related, applied research strand has studied methods by which
certain iterative task-based algorithms can be efficiently parallelized via relaxed
concurrent priority schedulers. These allow for high concurrency when inserting
and removing tasks, at the cost of executing superfluous work due to the relaxed
semantics of the scheduler. In this work, we take a step towards unifying these
two research directions, by showing that there exists a family of relaxed priority
schedulers that can efficiently and deterministically execute classic iterative
algorithms such as greedy maximal independent set (MIS) and matching. Our primary
result shows that, given a randomized scheduler with an expected relaxation factor
of k in terms of the maximum allowed priority inversions on a task, and any graph
on n vertices, the scheduler is able to execute greedy MIS with only an additive
factor of \poly(k) expected additional iterations compared to an exact (but not
scalable) scheduler. This counter-intuitive result demonstrates that the overhead
of relaxation when computing MIS is not dependent on the input size or structure
of the input graph. Experimental results show that this overhead can be clearly
offset by the gain in performance due to the highly scalable scheduler. In sum,
we present an efficient method to deterministically parallelize iterative sequential
algorithms, with provable runtime guarantees in terms of the number of executed
tasks to completion.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Giorgi
full_name: Nadiradze, Giorgi
last_name: Nadiradze
citation:
ama: 'Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently
parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386.
doi:10.1145/3212734.3212756'
apa: 'Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed
schedulers can efficiently parallelize iterative algorithms. In Proceedings
of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18
(pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756'
chicago: Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze.
“Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings
of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18,
377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756.
ieee: D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers
can efficiently parallelize iterative algorithms,” in Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United
Kingdom, 2018, pp. 377–386.
ista: 'Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers
can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM
Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles
of Distributed Computing, 377–386.'
mla: Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize
Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles
of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.
short: D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of
the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM
Press, 2018, pp. 377–386.
conference:
end_date: 2018-07-27
location: Egham, United Kingdom
name: 'PODC: Principles of Distributed Computing'
start_date: 2018-07-23
date_created: 2019-02-13T10:03:25Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2023-09-19T10:43:21Z
day: '23'
department:
- _id: DaAl
doi: 10.1145/3212734.3212756
external_id:
arxiv:
- '1808.04155'
isi:
- '000458186900048'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.04155
month: '07'
oa: 1
oa_version: Preprint
page: 377-386
publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing -
PODC '18
publication_identifier:
isbn:
- '9781450357951'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relaxed schedulers can efficiently parallelize iterative algorithms
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5965'
abstract:
- lang: eng
text: Relaxed concurrent data structures have become increasingly popular, due to
their scalability in graph processing and machine learning applications (\citeNguyen13,
gonzalez2012powergraph ). Despite considerable interest, there exist families
of natural, high performing randomized relaxed concurrent data structures, such
as the popular MultiQueue~\citeMQ pattern for implementing relaxed priority queue
data structures, for which no guarantees are known in the concurrent setting~\citeAKLN17.
Our main contribution is in showing for the first time that, under a set of analytic
assumptions, a family of relaxed concurrent data structures, including variants
of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter,
provides strong probabilistic guarantees on the degree of relaxation with respect
to the sequential specification, in arbitrary concurrent executions. We formalize
these guarantees via a new correctness condition called distributional linearizability,
tailored to concurrent implementations with randomized relaxations. Our result
is based on a new analysis of an asynchronous variant of the classic power-of-two-choices
load balancing algorithm, in which placement choices can be based on inconsistent,
outdated information (this result may be of independent interest). We validate
our results empirically, showing that the MultiCounter algorithm can implement
scalable relaxed timestamps.
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Jerry Z.
full_name: Li, Jerry Z.
last_name: Li
- first_name: Giorgi
full_name: Nadiradze, Giorgi
last_name: Nadiradze
citation:
ama: 'Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. Distributionally linearizable
data structures. In: Proceedings of the 30th on Symposium on Parallelism in
Algorithms and Architectures - SPAA ’18. ACM Press; 2018:133-142. doi:10.1145/3210377.3210411'
apa: 'Alistarh, D.-A., Brown, T. A., Kopinsky, J., Li, J. Z., & Nadiradze, G.
(2018). Distributionally linearizable data structures. In Proceedings of the
30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18
(pp. 133–142). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210411'
chicago: Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, Jerry Z. Li, and
Giorgi Nadiradze. “Distributionally Linearizable Data Structures.” In Proceedings
of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA
’18, 133–42. ACM Press, 2018. https://doi.org/10.1145/3210377.3210411.
ieee: D.-A. Alistarh, T. A. Brown, J. Kopinsky, J. Z. Li, and G. Nadiradze, “Distributionally
linearizable data structures,” in Proceedings of the 30th on Symposium on Parallelism
in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 133–142.
ista: 'Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. 2018. Distributionally
linearizable data structures. Proceedings of the 30th on Symposium on Parallelism
in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in
Algorithms and Architectures, 133–142.'
mla: Alistarh, Dan-Adrian, et al. “Distributionally Linearizable Data Structures.”
Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures
- SPAA ’18, ACM Press, 2018, pp. 133–42, doi:10.1145/3210377.3210411.
short: D.-A. Alistarh, T.A. Brown, J. Kopinsky, J.Z. Li, G. Nadiradze, in:, Proceedings
of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA
’18, ACM Press, 2018, pp. 133–142.
conference:
end_date: 2018-07-18
location: Vienna, Austria
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2018-07-16
date_created: 2019-02-13T10:17:19Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-19T10:44:13Z
day: '16'
department:
- _id: DaAl
doi: 10.1145/3210377.3210411
external_id:
arxiv:
- '1804.01018'
isi:
- '000545269600016'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.01018
month: '07'
oa: 1
oa_version: Preprint
page: 133-142
publication: Proceedings of the 30th on Symposium on Parallelism in Algorithms and
Architectures - SPAA '18
publication_identifier:
isbn:
- '9781450357999'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Distributionally linearizable data structures
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5967'
abstract:
- lang: eng
text: "The Big Match is a multi-stage two-player game. In each stage Player 1 hides
one or two pebbles in his hand, and his opponent has to guess that number; Player
1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon
as Player 1 hides one pebble, the players cannot change their choices in any future
stage.\r\nBlackwell and Ferguson (1968) give an ε-optimal strategy for Player
1 that hides, in each stage, one pebble with a probability that depends on the
entire past history. Any strategy that depends just on the clock or on a finite
memory is worthless. The long-standing natural open problem has been whether every
strategy that depends just on the clock and a finite memory is worthless. We prove
that there is such a strategy that is ε-optimal. In fact, we show that just two
states of memory are sufficient.\r\n"
article_processing_charge: No
author:
- first_name: Kristoffer Arnsfelt
full_name: Hansen, Kristoffer Arnsfelt
last_name: Hansen
- 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: Abraham
full_name: Neyman, Abraham
last_name: Neyman
citation:
ama: 'Hansen KA, Ibsen-Jensen R, Neyman A. The Big Match with a clock and a bit
of memory. In: Proceedings of the 2018 ACM Conference on Economics and Computation
- EC ’18. ACM Press; 2018:149-150. doi:10.1145/3219166.3219198'
apa: 'Hansen, K. A., Ibsen-Jensen, R., & Neyman, A. (2018). The Big Match with
a clock and a bit of memory. In Proceedings of the 2018 ACM Conference on Economics
and Computation - EC ’18 (pp. 149–150). Ithaca, NY, United States: ACM Press.
https://doi.org/10.1145/3219166.3219198'
chicago: Hansen, Kristoffer Arnsfelt, Rasmus Ibsen-Jensen, and Abraham Neyman. “The
Big Match with a Clock and a Bit of Memory.” In Proceedings of the 2018 ACM
Conference on Economics and Computation - EC ’18, 149–50. ACM Press, 2018.
https://doi.org/10.1145/3219166.3219198.
ieee: K. A. Hansen, R. Ibsen-Jensen, and A. Neyman, “The Big Match with a clock
and a bit of memory,” in Proceedings of the 2018 ACM Conference on Economics
and Computation - EC ’18, Ithaca, NY, United States, 2018, pp. 149–150.
ista: 'Hansen KA, Ibsen-Jensen R, Neyman A. 2018. The Big Match with a clock and
a bit of memory. Proceedings of the 2018 ACM Conference on Economics and Computation
- EC ’18. EC: Conference on Economics and Computation, 149–150.'
mla: Hansen, Kristoffer Arnsfelt, et al. “The Big Match with a Clock and a Bit of
Memory.” Proceedings of the 2018 ACM Conference on Economics and Computation
- EC ’18, ACM Press, 2018, pp. 149–50, doi:10.1145/3219166.3219198.
short: K.A. Hansen, R. Ibsen-Jensen, A. Neyman, in:, Proceedings of the 2018 ACM
Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–150.
conference:
end_date: 2018-06-22
location: Ithaca, NY, United States
name: 'EC: Conference on Economics and Computation'
start_date: 2018-06-18
date_created: 2019-02-13T10:31:41Z
date_published: 2018-06-18T00:00:00Z
date_updated: 2023-09-19T10:45:15Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3219166.3219198
external_id:
isi:
- '000492755100020'
file:
- access_level: open_access
checksum: bb52683e349cfd864f4769a8f38f2798
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:24:24Z
date_updated: 2020-07-14T12:47:14Z
file_id: '7054'
file_name: 2018_EC18_Hansen.pdf
file_size: 302539
relation: main_file
file_date_updated: 2020-07-14T12:47:14Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 149-150
publication: Proceedings of the 2018 ACM Conference on Economics and Computation -
EC '18
publication_identifier:
isbn:
- '9781450358293'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Big Match with a clock and a bit of memory
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5966'
abstract:
- lang: eng
text: 'The transactional conflict problem arises in transactional systems whenever
two or more concurrent transactions clash on a data item. While the standard solution
to such conflicts is to immediately abort one of the transactions, some practical
systems consider the alternative of delaying conflict resolution for a short interval,
which may allow one of the transactions to commit. The challenge in the transactional
conflict problem is to choose the optimal length of this delay interval so as
to minimize the overall running time penalty for the conflicting transactions.
In this paper, we propose a family of optimal online algorithms for the transactional
conflict problem. Specifically, we consider variants of this problem which arise
in different implementations of transactional systems, namely "requestor wins''''
and "requestor aborts'''' implementations: in the former, the recipient of a coherence
request is aborted, whereas in the latter, it is the requestor which has to abort.
Both strategies are implemented by real systems. We show that the requestor aborts
case can be reduced to a classic instance of the ski rental problem, while the
requestor wins case leads to a new version of this classical problem, for which
we derive optimal deterministic and randomized algorithms. Moreover, we prove
that, under a simplified adversarial model, our algorithms are constant-competitive
with the offline optimum in terms of throughput. We validate our algorithmic results
empirically through a hardware simulation of hardware transactional memory (HTM),
showing that our algorithms can lead to non-trivial performance improvements for
classic concurrent data structures.'
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Syed Kamran
full_name: Haider, Syed Kamran
last_name: Haider
- first_name: Raphael
full_name: Kübler, Raphael
last_name: Kübler
- first_name: Giorgi
full_name: Nadiradze, Giorgi
last_name: Nadiradze
citation:
ama: 'Alistarh D-A, Haider SK, Kübler R, Nadiradze G. The transactional conflict
problem. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms
and Architectures - SPAA ’18. ACM Press; 2018:383-392. doi:10.1145/3210377.3210406'
apa: 'Alistarh, D.-A., Haider, S. K., Kübler, R., & Nadiradze, G. (2018). The
transactional conflict problem. In Proceedings of the 30th on Symposium on
Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 383–392). Vienna,
Austria: ACM Press. https://doi.org/10.1145/3210377.3210406'
chicago: Alistarh, Dan-Adrian, Syed Kamran Haider, Raphael Kübler, and Giorgi Nadiradze.
“The Transactional Conflict Problem.” In Proceedings of the 30th on Symposium
on Parallelism in Algorithms and Architectures - SPAA ’18, 383–92. ACM Press,
2018. https://doi.org/10.1145/3210377.3210406.
ieee: D.-A. Alistarh, S. K. Haider, R. Kübler, and G. Nadiradze, “The transactional
conflict problem,” in Proceedings of the 30th on Symposium on Parallelism in
Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 383–392.
ista: 'Alistarh D-A, Haider SK, Kübler R, Nadiradze G. 2018. The transactional conflict
problem. Proceedings of the 30th on Symposium on Parallelism in Algorithms and
Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures,
383–392.'
mla: Alistarh, Dan-Adrian, et al. “The Transactional Conflict Problem.” Proceedings
of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA
’18, ACM Press, 2018, pp. 383–92, doi:10.1145/3210377.3210406.
short: D.-A. Alistarh, S.K. Haider, R. Kübler, G. Nadiradze, in:, Proceedings of
the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18,
ACM Press, 2018, pp. 383–392.
conference:
end_date: 2018-07-18
location: Vienna, Austria
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2018-07-16
date_created: 2019-02-13T10:26:07Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-19T10:44:49Z
day: '16'
department:
- _id: DaAl
doi: 10.1145/3210377.3210406
external_id:
arxiv:
- '1804.00947'
isi:
- '000545269600046'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.00947
month: '07'
oa: 1
oa_version: Preprint
page: 383-392
publication: Proceedings of the 30th on Symposium on Parallelism in Algorithms and
Architectures - SPAA '18
publication_identifier:
isbn:
- '9781450357999'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The transactional conflict problem
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5975'
abstract:
- lang: eng
text: We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N.
Har-vey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas
and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F.
Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms,
arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG.
Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the
method picks aflaw present in the current state and goes to a new state according
to some prespecified probabilitydistribution (which depends on the current state
and the selected flaw). However, the recent formu-lation is less flexible than
the Moser–Tardos method since it requires a specific flaw selection rule,whereas
the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially
beimplemented more efficiently). We formulate a new “commutativity” condition
and prove that it issufficient for an arbitrary rule to work. It also enables
an efficient parallelization under an additionalassumption. We then show that
existing resampling oracles for perfect matchings and permutationsdo satisfy this
condition.
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Commutativity in the algorithmic Lovász local lemma. SIAM
Journal on Computing. 2018;47(6):2029-2056. doi:10.1137/16m1093306
apa: Kolmogorov, V. (2018). Commutativity in the algorithmic Lovász local lemma.
SIAM Journal on Computing. Society for Industrial & Applied Mathematics
(SIAM). https://doi.org/10.1137/16m1093306
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.”
SIAM Journal on Computing. Society for Industrial & Applied Mathematics
(SIAM), 2018. https://doi.org/10.1137/16m1093306.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovász local lemma,” SIAM
Journal on Computing, vol. 47, no. 6. Society for Industrial & Applied
Mathematics (SIAM), pp. 2029–2056, 2018.
ista: Kolmogorov V. 2018. Commutativity in the algorithmic Lovász local lemma. SIAM
Journal on Computing. 47(6), 2029–2056.
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.”
SIAM Journal on Computing, vol. 47, no. 6, Society for Industrial &
Applied Mathematics (SIAM), 2018, pp. 2029–56, doi:10.1137/16m1093306.
short: V. Kolmogorov, SIAM Journal on Computing 47 (2018) 2029–2056.
date_created: 2019-02-13T12:59:33Z
date_published: 2018-11-08T00:00:00Z
date_updated: 2023-09-19T14:24:58Z
day: '08'
department:
- _id: VlKo
doi: 10.1137/16m1093306
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
isi:
- '000453785100001'
intvolume: ' 47'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547
month: '11'
oa: 1
oa_version: Preprint
page: 2029-2056
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: SIAM Journal on Computing
publication_identifier:
eissn:
- 1095-7111
issn:
- 0097-5397
publication_status: published
publisher: Society for Industrial & Applied Mathematics (SIAM)
quality_controlled: '1'
related_material:
record:
- id: '1193'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Commutativity in the algorithmic Lovász local lemma
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 47
year: '2018'
...
---
_id: '5964'
abstract:
- lang: eng
text: A standard design pattern found in many concurrent data structures, such as
hash tables or ordered containers, is an alternation of parallelizable sections
that incur no data conflicts and critical sections that must run sequentially
and are protected with locks. A lock can be viewed as a queue that arbitrates
the order in which the critical sections are executed, and a natural question
is whether we can use stochastic analysis to predict the resulting throughput.
As a preliminary evidence to the affirmative, we describe a simple model that
can be used to predict the throughput of coarse-grained lock-based algorithms.
We show that our model works well for CLH lock, and we expect it to work for other
popular lock designs such as TTAS, MCS, etc.
article_processing_charge: No
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- 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: Petr
full_name: Kuznetsov, Petr
last_name: Kuznetsov
citation:
ama: 'Aksenov V, Alistarh D-A, Kuznetsov P. Brief Announcement: Performance prediction
for coarse-grained locking. In: Proceedings of the 2018 ACM Symposium on Principles
of Distributed Computing - PODC ’18. ACM Press; 2018:411-413. doi:10.1145/3212734.3212785'
apa: 'Aksenov, V., Alistarh, D.-A., & Kuznetsov, P. (2018). Brief Announcement:
Performance prediction for coarse-grained locking. In Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 411–413).
Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212785'
chicago: 'Aksenov, Vitaly, Dan-Adrian Alistarh, and Petr Kuznetsov. “Brief Announcement:
Performance Prediction for Coarse-Grained Locking.” In Proceedings of the 2018
ACM Symposium on Principles of Distributed Computing - PODC ’18, 411–13.
ACM Press, 2018. https://doi.org/10.1145/3212734.3212785.'
ieee: 'V. Aksenov, D.-A. Alistarh, and P. Kuznetsov, “Brief Announcement: Performance
prediction for coarse-grained locking,” in Proceedings of the 2018 ACM Symposium
on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom,
2018, pp. 411–413.'
ista: 'Aksenov V, Alistarh D-A, Kuznetsov P. 2018. Brief Announcement: Performance
prediction for coarse-grained locking. Proceedings of the 2018 ACM Symposium on
Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed
Computing, 411–413.'
mla: 'Aksenov, Vitaly, et al. “Brief Announcement: Performance Prediction for Coarse-Grained
Locking.” Proceedings of the 2018 ACM Symposium on Principles of Distributed
Computing - PODC ’18, ACM Press, 2018, pp. 411–13, doi:10.1145/3212734.3212785.'
short: V. Aksenov, D.-A. Alistarh, P. Kuznetsov, in:, Proceedings of the 2018 ACM
Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018,
pp. 411–413.
conference:
end_date: 2018-07-27
location: Egham, United Kingdom
name: 'PODC: Principles of Distributed Computing'
start_date: 2018-07-23
date_created: 2019-02-13T10:08:19Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2023-09-19T10:43:45Z
day: '23'
department:
- _id: DaAl
doi: 10.1145/3212734.3212785
external_id:
isi:
- '000458186900052'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal-univ-lyon3.archives-ouvertes.fr/INRIA/hal-01887733v1
month: '07'
oa: 1
oa_version: Submitted Version
page: 411-413
publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing -
PODC '18
publication_identifier:
isbn:
- '9781450357951'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief Announcement: Performance prediction for coarse-grained locking'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5971'
abstract:
- lang: eng
text: "We consider a Wigner-type ensemble, i.e. large hermitian N×N random matrices
H=H∗ with centered independent entries and with a general matrix of variances
Sxy=\U0001D53C∣∣Hxy∣∣2. The norm of H is asymptotically given by the maximum of
the support of the self-consistent density of states. We establish a bound on
this maximum in terms of norms of powers of S that substantially improves the
earlier bound 2∥S∥1/2∞ given in [O. Ajanki, L. Erdős and T. Krüger, Universality
for general Wigner-type matrices, Prob. Theor. Rel. Fields169 (2017) 667–727].
The key element of the proof is an effective Markov chain approximation for the
contributions of the weighted Dyck paths appearing in the iterative solution of
the corresponding Dyson equation."
article_number: '1950009'
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Peter
full_name: Mühlbacher, Peter
last_name: Mühlbacher
citation:
ama: 'Erdös L, Mühlbacher P. Bounds on the norm of Wigner-type random matrices.
Random matrices: Theory and applications. 2018. doi:10.1142/s2010326319500096'
apa: 'Erdös, L., & Mühlbacher, P. (2018). Bounds on the norm of Wigner-type
random matrices. Random Matrices: Theory and Applications. World Scientific
Publishing. https://doi.org/10.1142/s2010326319500096'
chicago: 'Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type
Random Matrices.” Random Matrices: Theory and Applications. World Scientific
Publishing, 2018. https://doi.org/10.1142/s2010326319500096.'
ieee: 'L. Erdös and P. Mühlbacher, “Bounds on the norm of Wigner-type random matrices,”
Random matrices: Theory and applications. World Scientific Publishing,
2018.'
ista: 'Erdös L, Mühlbacher P. 2018. Bounds on the norm of Wigner-type random matrices.
Random matrices: Theory and applications., 1950009.'
mla: 'Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random
Matrices.” Random Matrices: Theory and Applications, 1950009, World Scientific
Publishing, 2018, doi:10.1142/s2010326319500096.'
short: 'L. Erdös, P. Mühlbacher, Random Matrices: Theory and Applications (2018).'
date_created: 2019-02-13T10:40:54Z
date_published: 2018-09-26T00:00:00Z
date_updated: 2023-09-19T14:24:05Z
day: '26'
department:
- _id: LaEr
doi: 10.1142/s2010326319500096
ec_funded: 1
external_id:
arxiv:
- '1802.05175'
isi:
- '000477677200002'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.05175
month: '09'
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: 'Random matrices: Theory and applications'
publication_identifier:
eissn:
- 2010-3271
issn:
- 2010-3263
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bounds on the norm of Wigner-type random matrices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5984'
abstract:
- lang: eng
text: G-protein-coupled receptors (GPCRs) form the largest receptor family, relay
environmental stimuli to changes in cell behavior and represent prime drug targets.
Many GPCRs are classified as orphan receptors because of the limited knowledge
on their ligands and coupling to cellular signaling machineries. Here, we engineer
a library of 63 chimeric receptors that contain the signaling domains of human
orphan and understudied GPCRs functionally linked to the light-sensing domain
of rhodopsin. Upon stimulation with visible light, we identify activation of canonical
cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent
pathways, downstream of the engineered receptors. For the human pseudogene GPR33,
we resurrect a signaling function that supports its hypothesized role as a pathogen
entry site. These results demonstrate that substituting unknown chemical activators
with a light switch can reveal information about protein function and provide
an optically controlled protein library for exploring the physiology and therapeutic
potential of understudied GPCRs.
article_number: '1950'
article_processing_charge: No
author:
- first_name: Maurizio
full_name: Morri, Maurizio
id: 4863116E-F248-11E8-B48F-1D18A9856A87
last_name: Morri
- first_name: Inmaculada
full_name: Sanchez-Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez-Romero
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Elliot J.
full_name: Gerrard, Elliot J.
last_name: Gerrard
- first_name: Priscila
full_name: Hirschfeld, Priscila
id: 435ACB3A-F248-11E8-B48F-1D18A9856A87
last_name: Hirschfeld
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- 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: Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human
class A orphan G-protein-coupled receptors. Nature Communications. 2018;9(1).
doi:10.1038/s41467-018-04342-1
apa: Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J.,
Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class
A orphan G-protein-coupled receptors. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-018-04342-1
chicago: Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy,
Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald
L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled
Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1.
ieee: M. Morri et al., “Optical functionalization of human class A orphan
G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1. Springer
Nature, 2018.
ista: Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P,
Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan
G-protein-coupled receptors. Nature Communications. 9(1), 1950.
mla: Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan
G-Protein-Coupled Receptors.” Nature Communications, vol. 9, no. 1, 1950,
Springer Nature, 2018, doi:10.1038/s41467-018-04342-1.
short: M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld,
J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).
date_created: 2019-02-14T10:50:24Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-19T14:29:32Z
day: '01'
ddc:
- '570'
department:
- _id: HaJa
- _id: CaGu
- _id: MiSi
doi: 10.1038/s41467-018-04342-1
ec_funded: 1
external_id:
isi:
- '000432280000006'
file:
- access_level: open_access
checksum: 8325fcc194264af4749e662a73bf66b5
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T10:58:29Z
date_updated: 2020-07-14T12:47:14Z
file_id: '5985'
file_name: 2018_Springer_Morri.pdf
file_size: 1349914
relation: main_file
file_date_updated: 2020-07-14T12:47:14Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
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: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optical functionalization of human class A orphan G-protein-coupled receptors
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: 9
year: '2018'
...
---
_id: '5976'
abstract:
- lang: eng
text: We propose FlexMaps, a novel framework for fabricating smooth shapes out of
flat, flexible panels with tailored mechanical properties. We start by mapping
the 3D surface onto a 2D domain as in traditional UV mapping to design a set of
deformable flat panels called FlexMaps. For these panels, we design and obtain
specific mechanical properties such that, once they are assembled, the static
equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated
from an almost rigid material, such as wood or plastic, and are made flexible
in a controlled way by using computationally designed spiraling microstructures.
article_number: '241'
article_processing_charge: No
article_type: original
author:
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Jesus
full_name: Perez Rodriguez, Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Emmanuel
full_name: Iarussi, Emmanuel
id: 33F19F16-F248-11E8-B48F-1D18A9856A87
last_name: Iarussi
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Eder
full_name: Miguel, Eder
last_name: Miguel
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Malomo L, Perez Rodriguez J, Iarussi E, et al. FlexMaps: Computational design
of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics.
2018;37(6). doi:10.1145/3272127.3275076'
apa: 'Malomo, L., Perez Rodriguez, J., Iarussi, E., Pietroni, N., Miguel, E., Cignoni,
P., & Bickel, B. (2018). FlexMaps: Computational design of flat flexible shells
for shaping 3D objects. ACM Transactions on Graphics. Association for Computing
Machinery (ACM). https://doi.org/10.1145/3272127.3275076'
chicago: 'Malomo, Luigi, Jesus Perez Rodriguez, Emmanuel Iarussi, Nico Pietroni,
Eder Miguel, Paolo Cignoni, and Bernd Bickel. “FlexMaps: Computational Design
of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics.
Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3272127.3275076.'
ieee: 'L. Malomo et al., “FlexMaps: Computational design of flat flexible
shells for shaping 3D objects,” ACM Transactions on Graphics, vol. 37,
no. 6. Association for Computing Machinery (ACM), 2018.'
ista: 'Malomo L, Perez Rodriguez J, Iarussi E, Pietroni N, Miguel E, Cignoni P,
Bickel B. 2018. FlexMaps: Computational design of flat flexible shells for shaping
3D objects. ACM Transactions on Graphics. 37(6), 241.'
mla: 'Malomo, Luigi, et al. “FlexMaps: Computational Design of Flat Flexible Shells
for Shaping 3D Objects.” ACM Transactions on Graphics, vol. 37, no. 6,
241, Association for Computing Machinery (ACM), 2018, doi:10.1145/3272127.3275076.'
short: L. Malomo, J. Perez Rodriguez, E. Iarussi, N. Pietroni, E. Miguel, P. Cignoni,
B. Bickel, ACM Transactions on Graphics 37 (2018).
date_created: 2019-02-13T13:12:53Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-09-19T14:25:30Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3272127.3275076
ec_funded: 1
external_id:
isi:
- '000455953100064'
file:
- access_level: open_access
checksum: d0529a41c78b37ab8840685579fb33b4
content_type: application/pdf
creator: bbickel
date_created: 2019-09-23T12:48:52Z
date_updated: 2020-07-14T12:47:14Z
file_id: '6901'
file_name: flexmaps_author_version.pdf
file_size: 100109811
relation: main_file
file_date_updated: 2020-07-14T12:47:14Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery (ACM)
pubrep_id: '1068'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FlexMaps: Computational design of flat flexible shells for shaping 3D objects'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '5983'
abstract:
- lang: eng
text: We study a quantum impurity possessing both translational and internal rotational
degrees of freedom interacting with a bosonic bath. Such a system corresponds
to a “rotating polaron,” which can be used to model, e.g., a rotating molecule
immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian
of the rotating polaron and study its spectrum in the weak- and strong-coupling
regimes using a combination of variational, diagrammatic, and mean-field approaches.
We reveal how the coupling between linear and angular momenta affects stable quasiparticle
states, and demonstrate that internal rotation leads to an enhanced self-localization
in the translational degrees of freedom.
article_number: '224506'
article_processing_charge: No
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: 'Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. Theory of the rotating
polaron: Spectrum and self-localization. Physical Review B. 2018;98(22).
doi:10.1103/physrevb.98.224506'
apa: 'Yakaboylu, E., Midya, B., Deuchert, A., Leopold, N. K., & Lemeshko, M.
(2018). Theory of the rotating polaron: Spectrum and self-localization. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.98.224506'
chicago: 'Yakaboylu, Enderalp, Bikashkali Midya, Andreas Deuchert, Nikolai K Leopold,
and Mikhail Lemeshko. “Theory of the Rotating Polaron: Spectrum and Self-Localization.”
Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.98.224506.'
ieee: 'E. Yakaboylu, B. Midya, A. Deuchert, N. K. Leopold, and M. Lemeshko, “Theory
of the rotating polaron: Spectrum and self-localization,” Physical Review B,
vol. 98, no. 22. American Physical Society, 2018.'
ista: 'Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. 2018. Theory of
the rotating polaron: Spectrum and self-localization. Physical Review B. 98(22),
224506.'
mla: 'Yakaboylu, Enderalp, et al. “Theory of the Rotating Polaron: Spectrum and
Self-Localization.” Physical Review B, vol. 98, no. 22, 224506, American
Physical Society, 2018, doi:10.1103/physrevb.98.224506.'
short: E. Yakaboylu, B. Midya, A. Deuchert, N.K. Leopold, M. Lemeshko, Physical
Review B 98 (2018).
date_created: 2019-02-14T10:37:09Z
date_published: 2018-12-12T00:00:00Z
date_updated: 2023-09-19T14:29:03Z
day: '12'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/physrevb.98.224506
ec_funded: 1
external_id:
arxiv:
- '1809.01204'
isi:
- '000452992700008'
intvolume: ' 98'
isi: 1
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.01204
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theory of the rotating polaron: Spectrum and self-localization'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '5982'
abstract:
- lang: eng
text: In the present work, we detail a fast and simple solution-based method to
synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically
textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be
used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown
through a screw dislocation-driven mechanism. This mechanism typically results
in pyramidal structures, but we demonstrate here that the growth from multiple
dislocations results in flower-like structures. Crystallographically textured
SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures
display highly anisotropic charge and heat transport properties and thermoelectric
(TE) figures of merit limited by relatively low electrical conductivities. To
improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles.
The electrical conductivities of the blends are significantly improved with respect
to bare SnSe2 NPLs, what translates into a three-fold increase of the TE Figure
of merit, reaching unprecedented ZT values up to 0.65.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Yu
full_name: Liu, Yu
last_name: Liu
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Ting
full_name: Zhang, Ting
last_name: Zhang
- first_name: Pengyi
full_name: Tang, Pengyi
last_name: Tang
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Ka Ming
full_name: Ng, Ka Ming
last_name: Ng
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Pablo
full_name: Guardia, Pablo
last_name: Guardia
- first_name: Mirko
full_name: Prato, Mirko
last_name: Prato
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Zhang Y, Liu Y, Lim KH, et al. Tin diselenide molecular precursor for solution-processable
thermoelectric materials. Angewandte Chemie International Edition. 2018;57(52):17063-17068.
doi:10.1002/anie.201809847
apa: Zhang, Y., Liu, Y., Lim, K. H., Xing, C., Li, M., Zhang, T., … Cabot, A. (2018).
Tin diselenide molecular precursor for solution-processable thermoelectric materials.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201809847
chicago: Zhang, Yu, Yu Liu, Khak Ho Lim, Congcong Xing, Mengyao Li, Ting Zhang,
Pengyi Tang, et al. “Tin Diselenide Molecular Precursor for Solution-Processable
Thermoelectric Materials.” Angewandte Chemie International Edition. Wiley,
2018. https://doi.org/10.1002/anie.201809847.
ieee: Y. Zhang et al., “Tin diselenide molecular precursor for solution-processable
thermoelectric materials,” Angewandte Chemie International Edition, vol.
57, no. 52. Wiley, pp. 17063–17068, 2018.
ista: Zhang Y, Liu Y, Lim KH, Xing C, Li M, Zhang T, Tang P, Arbiol J, Llorca J,
Ng KM, Ibáñez M, Guardia P, Prato M, Cadavid D, Cabot A. 2018. Tin diselenide
molecular precursor for solution-processable thermoelectric materials. Angewandte
Chemie International Edition. 57(52), 17063–17068.
mla: Zhang, Yu, et al. “Tin Diselenide Molecular Precursor for Solution-Processable
Thermoelectric Materials.” Angewandte Chemie International Edition, vol.
57, no. 52, Wiley, 2018, pp. 17063–68, doi:10.1002/anie.201809847.
short: Y. Zhang, Y. Liu, K.H. Lim, C. Xing, M. Li, T. Zhang, P. Tang, J. Arbiol,
J. Llorca, K.M. Ng, M. Ibáñez, P. Guardia, M. Prato, D. Cadavid, A. Cabot, Angewandte
Chemie International Edition 57 (2018) 17063–17068.
date_created: 2019-02-14T10:23:27Z
date_published: 2018-12-21T00:00:00Z
date_updated: 2023-09-19T14:28:31Z
day: '21'
department:
- _id: MaIb
doi: 10.1002/anie.201809847
external_id:
isi:
- '000454575500020'
intvolume: ' 57'
isi: 1
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://upcommons.upc.edu/bitstream/2117/130444/1/Zhang%20preprint.pdf
month: '12'
oa: 1
oa_version: Submitted Version
page: 17063-17068
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tin diselenide molecular precursor for solution-processable thermoelectric
materials
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 57
year: '2018'
...
---
_id: '5978'
abstract:
- lang: eng
text: 'We consider the MAP-inference problem for graphical models,which is a valued
constraint satisfaction problem defined onreal numbers with a natural summation
operation. We proposea family of relaxations (different from the famous Sherali-Adams
hierarchy), which naturally define lower bounds for itsoptimum. This family always
contains a tight relaxation andwe give an algorithm able to find it and therefore,
solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose
the original probleminto two non-overlapping parts: an easy LP-tight part and
adifficult one. For the latter part a combinatorial solver must beused. As we
show in our experiments, in a number of applica-tions the second, difficult part
constitutes only a small fractionof the whole problem. This property allows to
significantlyreduce the computational time of the combinatorial solver andtherefore
solve problems which were out of reach before.'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Haller, Stefan
last_name: Haller
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Bogdan
full_name: Savchynskyy, Bogdan
last_name: Savchynskyy
citation:
ama: 'Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial
search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial
Intelligence. AAAI Press; 2018:6581-6588.'
apa: 'Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference
by confining combinatorial search with LP relaxation. In Proceedings of the
32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans,
LU, United States: AAAI Press.'
chicago: Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference
by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the
32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018.
ieee: S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining
combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference
on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588.
ista: 'Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining
combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference
on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.'
mla: Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search
with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial
Intelligence, AAAI Press, 2018, pp. 6581–88.
short: S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI
Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588.
conference:
end_date: 2018-02-07
location: New Orleans, LU, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2018-02-02
date_created: 2019-02-13T13:32:48Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-19T14:26:52Z
day: '01'
department:
- _id: VlKo
external_id:
arxiv:
- '2004.06370'
isi:
- '000485488906082'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.06370
month: '02'
oa: 1
oa_version: Preprint
page: 6581-6588
publication: Proceedings of the 32st AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exact MAP-inference by confining combinatorial search with LP relaxation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5990'
abstract:
- lang: eng
text: 'A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor
with highly transparent contacts to superconducting leads. By changing the electric
field, access to two distinct regimes, not combined before in a single device,
is gained: in the accumulation mode the device is highly transparent and the supercurrent
is carried by multiple subbands, while near depletion, the supercurrent is carried
by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole
regime. These results establish Ge–Si nanowires as an important platform for hybrid
superconductor–semiconductor physics and Majorana fermions.'
article_number: '1802257'
article_processing_charge: No
author:
- first_name: Joost
full_name: Ridderbos, Joost
last_name: Ridderbos
- first_name: Matthias
full_name: Brauns, Matthias
id: 33F94E3C-F248-11E8-B48F-1D18A9856A87
last_name: Brauns
- first_name: Jie
full_name: Shen, Jie
last_name: Shen
- first_name: Folkert K.
full_name: de Vries, Folkert K.
last_name: de Vries
- first_name: Ang
full_name: Li, Ang
last_name: Li
- first_name: Erik P. A. M.
full_name: Bakkers, Erik P. A. M.
last_name: Bakkers
- first_name: Alexander
full_name: Brinkman, Alexander
last_name: Brinkman
- first_name: Floris A.
full_name: Zwanenburg, Floris A.
last_name: Zwanenburg
citation:
ama: Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum
dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257
apa: Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P.
A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot.
Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257
chicago: Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li,
Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson
Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257.
ieee: J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,”
Advanced Materials, vol. 30, no. 44. Wiley, 2018.
ista: Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A,
Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials.
30(44), 1802257.
mla: Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced
Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257.
short: J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers,
A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018).
date_created: 2019-02-14T12:14:26Z
date_published: 2018-11-02T00:00:00Z
date_updated: 2023-09-19T14:29:58Z
day: '02'
department:
- _id: GeKa
doi: 10.1002/adma.201802257
external_id:
arxiv:
- '1809.08487'
isi:
- '000450232800015'
intvolume: ' 30'
isi: 1
issue: '44'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.08487
month: '11'
oa: 1
oa_version: Preprint
publication: Advanced Materials
publication_identifier:
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Josephson effect in a few-hole quantum dot
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2018'
...
---
_id: '5980'
abstract:
- lang: eng
text: The problem of private set-intersection (PSI) has been traditionally treated
as an instance of the more general problem of multi-party computation (MPC). Consequently,
in order to argue security, or compose these protocols one has to rely on the
general theory that was developed for the purpose of MPC. The pursuit of efficient
protocols, however, has resulted in designs that exploit properties pertaining
to PSI. In almost all practical applications where a PSI protocol is deployed,
it is expected to be executed multiple times, possibly on related inputs. In this
work we initiate a dedicated study of PSI in the multi-interaction (MI) setting.
In this model a server sets up the common system parameters and executes set-intersection
multiple times with potentially different clients. We discuss a few attacks that
arise when protocols are naïvely composed in this manner and, accordingly, craft
security definitions for the MI setting and study their inter-relation. Finally,
we suggest a set of protocols that are MI-secure, at the same time almost as efficient
as their parent, stand-alone, protocols.
article_processing_charge: No
author:
- first_name: Sanjit
full_name: Chatterjee, Sanjit
last_name: Chatterjee
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Vikas
full_name: Kumar, Vikas
last_name: Kumar
citation:
ama: Chatterjee S, Kamath Hosdurg C, Kumar V. Private set-intersection with common
set-up. American Institute of Mathematical Sciences. 2018;12(1):17-47.
doi:10.3934/amc.2018002
apa: Chatterjee, S., Kamath Hosdurg, C., & Kumar, V. (2018). Private set-intersection
with common set-up. American Institute of Mathematical Sciences. AIMS.
https://doi.org/10.3934/amc.2018002
chicago: Chatterjee, Sanjit, Chethan Kamath Hosdurg, and Vikas Kumar. “Private Set-Intersection
with Common Set-Up.” American Institute of Mathematical Sciences. AIMS,
2018. https://doi.org/10.3934/amc.2018002.
ieee: S. Chatterjee, C. Kamath Hosdurg, and V. Kumar, “Private set-intersection
with common set-up,” American Institute of Mathematical Sciences, vol.
12, no. 1. AIMS, pp. 17–47, 2018.
ista: Chatterjee S, Kamath Hosdurg C, Kumar V. 2018. Private set-intersection with
common set-up. American Institute of Mathematical Sciences. 12(1), 17–47.
mla: Chatterjee, Sanjit, et al. “Private Set-Intersection with Common Set-Up.” American
Institute of Mathematical Sciences, vol. 12, no. 1, AIMS, 2018, pp. 17–47,
doi:10.3934/amc.2018002.
short: S. Chatterjee, C. Kamath Hosdurg, V. Kumar, American Institute of Mathematical
Sciences 12 (2018) 17–47.
date_created: 2019-02-13T13:49:41Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-19T14:27:59Z
day: '01'
department:
- _id: KrPi
doi: 10.3934/amc.2018002
external_id:
isi:
- '000430950400002'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 17-47
publication: American Institute of Mathematical Sciences
publication_status: published
publisher: AIMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Private set-intersection with common set-up
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2018'
...
---
_id: '5998'
abstract:
- lang: eng
text: Genome amplification and cellular senescence are commonly associated with
pathological processes. While physiological roles for polyploidization and senescence
have been described in mouse development, controversy exists over their significance
in humans. Here, we describe tetraploidization and senescence as phenomena of
normal human placenta development. During pregnancy, placental extravillous trophoblasts
(EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted
microenvironment required for the developing embryo. This process is critically
dependent on continuous cell proliferation and differentiation, which is thought
to follow the classical model of cell cycle arrest prior to terminal differentiation.
Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied
with a genome-wide polyploidization, independent of mitotic cycles. DNA replication
in these cells was analysed by a fluorescent cell-cycle indicator reporter system,
cell cycle marker expression and EdU incorporation. Upon invasion into the decidua,
EVTs widely lose their replicative potential and enter a senescent state characterized
by high senescence-associated (SA) β-galactosidase activity, induction of a SA
secretory phenotype as well as typical metabolic alterations. Furthermore, we
show that the shift from endocycle-dependent genome amplification to growth arrest
is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy
disorder associated with increased risk of developing choriocarinoma. Senescence
is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy.
We propose induction of cellular senescence as a ploidy-limiting mechanism during
normal human placentation and unravel a link between excessive polyploidization
and reduced senescence in CHM.
article_number: e1007698
article_processing_charge: No
author:
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Gudrun
full_name: Meinhardt, Gudrun
last_name: Meinhardt
- first_name: Kerstin
full_name: Plessl, Kerstin
last_name: Plessl
- first_name: Sigrid
full_name: Vondra, Sigrid
last_name: Vondra
- first_name: Tamara
full_name: Weiss, Tamara
last_name: Weiss
- first_name: Peter
full_name: Haslinger, Peter
last_name: Haslinger
- first_name: Thomas
full_name: Lendl, Thomas
last_name: Lendl
- first_name: Karin
full_name: Aumayr, Karin
last_name: Aumayr
- first_name: Mario
full_name: Mairhofer, Mario
last_name: Mairhofer
- first_name: Xiaowei
full_name: Zhu, Xiaowei
last_name: Zhu
- first_name: Birgit
full_name: Schütz, Birgit
last_name: Schütz
- first_name: Roberta L.
full_name: Hannibal, Roberta L.
last_name: Hannibal
- first_name: Robert
full_name: Lindau, Robert
last_name: Lindau
- first_name: Beatrix
full_name: Weil, Beatrix
last_name: Weil
- first_name: Jan
full_name: Ernerudh, Jan
last_name: Ernerudh
- first_name: Jürgen
full_name: Neesen, Jürgen
last_name: Neesen
- first_name: Gerda
full_name: Egger, Gerda
last_name: Egger
- first_name: Mario
full_name: Mikula, Mario
last_name: Mikula
- first_name: Clemens
full_name: Röhrl, Clemens
last_name: Röhrl
- first_name: Alexander E.
full_name: Urban, Alexander E.
last_name: Urban
- first_name: Julie
full_name: Baker, Julie
last_name: Baker
- first_name: Martin
full_name: Knöfler, Martin
last_name: Knöfler
- first_name: Jürgen
full_name: Pollheimer, Jürgen
last_name: Pollheimer
citation:
ama: Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular
senescence are hallmarks of human placenta development. PLOS Genetics.
2018;14(10). doi:10.1371/journal.pgen.1007698
apa: Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P.,
… Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks
of human placenta development. PLOS Genetics. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007698
chicago: Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara
Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular
Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.
ieee: P. Velicky et al., “Genome amplification and cellular senescence are
hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10.
Public Library of Science, 2018.
ista: Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T,
Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh
J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer
J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta
development. PLOS Genetics. 14(10), e1007698.
mla: Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are
Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10,
e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698.
short: P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T.
Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B.
Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker,
M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).
date_created: 2019-02-14T13:07:45Z
date_published: 2018-10-12T00:00:00Z
date_updated: 2023-09-19T14:31:43Z
day: '12'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1371/journal.pgen.1007698
external_id:
isi:
- '000449328500025'
file:
- access_level: open_access
checksum: 34aa9a5972f61889c19f18be8ee787a0
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T13:14:35Z
date_updated: 2020-07-14T12:47:15Z
file_id: '6000'
file_name: 2018_PLOS_Velicky.pdf
file_size: 4592947
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome amplification and cellular senescence are hallmarks of human placenta
development
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: 14
year: '2018'
...
---
_id: '5995'
abstract:
- lang: eng
text: "Motivation\r\nComputational prediction of the effect of mutations on protein
stability is used by researchers in many fields. The utility of the prediction
methods is affected by their accuracy and bias. Bias, a systematic shift of the
predicted change of stability, has been noted as an issue for several methods,
but has not been investigated systematically. Presence of the bias may lead to
misleading results especially when exploring the effects of combination of different
mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function
of the number of introduced mutations. It is based on a self-consistency test
of the reciprocity the effect of a mutation. An advantage of the used approach
is that it relies solely on crystal structures without experimentally measured
stability values. We applied the protocol to four popular algorithms predicting
change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant,
and found an inherent bias. For one program, FoldX, we manage to substantially
reduce the bias using additional relaxation by Modeller. Authors using algorithms
for predicting effects of mutations should be aware of the bias described here."
article_processing_charge: No
author:
- first_name: Dinara R
full_name: Usmanova, Dinara R
last_name: Usmanova
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Joan
full_name: Ariño Bernad, Joan
last_name: Ariño Bernad
- first_name: Aleksandra A
full_name: Eremina, Aleksandra A
last_name: Eremina
- first_name: Anastasiya A
full_name: Gorshkova, Anastasiya A
last_name: Gorshkova
- first_name: German M
full_name: Kanevskiy, German M
last_name: Kanevskiy
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Alexander V
full_name: Meister, Alexander V
last_name: Meister
- first_name: Alisa G
full_name: Yakupova, Alisa G
last_name: Yakupova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
citation:
ama: Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals
systematic bias in programs for prediction change of stability upon mutation.
Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340
apa: Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova,
A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic
bias in programs for prediction change of stability upon mutation. Bioinformatics.
Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340
chicago: Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra
A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al.
“Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change
of Stability upon Mutation.” Bioinformatics. Oxford University Press ,
2018. https://doi.org/10.1093/bioinformatics/bty340.
ieee: D. R. Usmanova et al., “Self-consistency test reveals systematic bias
in programs for prediction change of stability upon mutation,” Bioinformatics,
vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.
ista: Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy
GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency
test reveals systematic bias in programs for prediction change of stability upon
mutation. Bioinformatics. 34(21), 3653–3658.
mla: Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias
in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics,
vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.
short: D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova,
G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D.
Ivankov, Bioinformatics 34 (2018) 3653–3658.
date_created: 2019-02-14T12:48:00Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-09-19T14:31:13Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/bty340
ec_funded: 1
external_id:
isi:
- '000450038900008'
pmid:
- '29722803'
file:
- access_level: open_access
checksum: 7e0495153f44211479674601d7f6ee03
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T13:00:55Z
date_updated: 2020-07-14T12:47:15Z
file_id: '5997'
file_name: 2018_Oxford_Usmanova.pdf
file_size: 291969
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '21'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 3653-3658
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-consistency test reveals systematic bias in programs for prediction change
of stability upon mutation
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: 34
year: '2018'
...
---
_id: '5992'
abstract:
- lang: eng
text: Lamellipodia are flat membrane protrusions formed during mesenchymal motion.
Polymerization at the leading edge assembles the actin filament network and generates
protrusion force. How this force is supported by the network and how the assembly
rate is shared between protrusion and network retrograde flow determines the protrusion
rate. We use mathematical modeling to understand experiments changing the F-actin
density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex
activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction
of density with a decrease of protrusion velocity, an increase in the ratio of
force to filament number, but constant network assembly rate. The relation between
protrusion force and tension gradient in the F-actin network and the density dependency
of friction, elasticity, and viscosity of the network explain the experimental
observations. The formins act as filament nucleators and elongators with differential
rates. Modulation of their activity suggests an effect on network assembly rate.
Contrary to these expectations, the effect of changes in elongator composition
is much weaker than the consequences of the density change. We conclude that the
force acting on the leading edge membrane is the force required to drive F-actin
network retrograde flow.
article_processing_charge: No
author:
- first_name: Setareh
full_name: Dolati, Setareh
last_name: Dolati
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Jan
full_name: Mueller, Jan
last_name: Mueller
- first_name: Mathias
full_name: Müsken, Mathias
last_name: Müsken
- first_name: Marieluise
full_name: Kirchner, Marieluise
last_name: Kirchner
- first_name: Gunnar
full_name: Dittmar, Gunnar
last_name: Dittmar
- 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: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
citation:
ama: Dolati S, Kage F, Mueller J, et al. On the relation between filament density,
force generation, and protrusion rate in mesenchymal cell motility. Molecular
Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082
apa: Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., …
Falcke, M. (2018). On the relation between filament density, force generation,
and protrusion rate in mesenchymal cell motility. Molecular Biology of the
Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082
chicago: Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner,
Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation
between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal
Cell Motility.” Molecular Biology of the Cell. American Society for Cell
Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.
ieee: S. Dolati et al., “On the relation between filament density, force
generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology
of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686,
2018.
ista: Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner
K, Falcke M. 2018. On the relation between filament density, force generation,
and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell.
29(22), 2674–2686.
mla: Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation,
and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the
Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86,
doi:10.1091/mbc.e18-02-0082.
short: S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K.
Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.
date_created: 2019-02-14T12:25:47Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-09-19T14:30:23Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1091/mbc.e18-02-0082
external_id:
isi:
- '000455641000011'
pmid:
- '30156465'
file:
- access_level: open_access
checksum: e98465b4416b3e804c47f40086932af2
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T12:34:29Z
date_updated: 2020-07-14T12:47:15Z
file_id: '5994'
file_name: 2018_ASCB_Dolati.pdf
file_size: 6668971
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '22'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2674-2686
pmid: 1
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
publication_status: published
publisher: 'American Society for Cell Biology '
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the relation between filament density, force generation, and protrusion
rate in mesenchymal cell motility
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: 29
year: '2018'
...
---
_id: '6010'
abstract:
- lang: eng
text: The optic tectum (TeO), or superior colliculus, is a multisensory midbrain
center that organizes spatially orienting responses to relevant stimuli. To define
the stimulus with the highest priority at each moment, a network of reciprocal
connections between the TeO and the isthmi promotes competition between concurrent
tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression
of tectal inputs are located in separate isthmic nuclei, facilitating the analysis
of the neural processes that mediate competition. A specific subset of radial
neurons in the intermediate tectal layers relay retinal inputs to the isthmi,
but at present it is unclear whether separate neurons innervate individual nuclei
or a single neural type sends a common input to several of them. In this study,
we used in vitro neural tracing and cell-filling experiments in chickens to show
that single neurons innervate, via axon collaterals, the three nuclei that comprise
the isthmotectal network. This demonstrates that the input signals representing
the strength of the incoming stimuli are simultaneously relayed to the mechanisms
promoting both enhancement and suppression of the input signals. By performing
in vivo recordings in anesthetized chicks, we also show that this common input
generates synchrony between both antagonistic mechanisms, demonstrating that activity
enhancement and suppression are closely coordinated. From a computational point
of view, these results suggest that these tectal neurons constitute integrative
nodes that combine inputs from different sources to drive in parallel several
concurrent neural processes, each performing complementary functions within the
network through different firing patterns and connectivity.
article_processing_charge: No
author:
- first_name: Florencia
full_name: Garrido-Charad, Florencia
last_name: Garrido-Charad
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Cristián
full_name: Gutiérrez-Ibáñez, Cristián
last_name: Gutiérrez-Ibáñez
- first_name: Pedro
full_name: Fernandez, Pedro
last_name: Fernandez
- first_name: Luciana
full_name: López-Jury, Luciana
last_name: López-Jury
- first_name: Cristian
full_name: González-Cabrera, Cristian
last_name: González-Cabrera
- first_name: Harvey J.
full_name: Karten, Harvey J.
last_name: Karten
- first_name: Harald
full_name: Luksch, Harald
last_name: Luksch
- first_name: Gonzalo J.
full_name: Marín, Gonzalo J.
last_name: Marín
citation:
ama: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of
Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115
apa: Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P.,
López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of
Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115
chicago: Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez,
Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten,
Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize
the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1804517115.
ieee: F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize
the enhancing and suppressive mechanisms of the midbrain stimulus selection network,”
Proceedings of the National Academy of Sciences, vol. 115, no. 32. National
Academy of Sciences, pp. E7615–E7623, 2018.
ista: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury
L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of Sciences.
115(32), E7615–E7623.
mla: Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize
the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.”
Proceedings of the National Academy of Sciences, vol. 115, no. 32, National
Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.
short: F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L.
López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings
of the National Academy of Sciences 115 (2018) E7615–E7623.
date_created: 2019-02-14T14:33:34Z
date_published: 2018-08-07T00:00:00Z
date_updated: 2023-09-19T14:35:36Z
day: '07'
department:
- _id: MaJö
doi: 10.1073/pnas.1804517115
external_id:
isi:
- '000440982000020'
pmid:
- '30026198'
intvolume: ' 115'
isi: 1
issue: '32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30026198
month: '08'
oa: 1
oa_version: Submitted Version
page: E7615-E7623
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive
mechanisms of the midbrain stimulus selection network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '6003'
abstract:
- lang: eng
text: Digital fabrication devices are powerful tools for creating tangible reproductions
of 3D digital models. Most available printing technologies aim at producing an
accurate copy of a tridimensional shape. However, fabrication technologies can
also be used to create a stylistic representation of a digital shape. We refer
to this class of methods as ‘stylized fabrication methods’. These methods abstract
geometric and physical features of a given shape to create an unconventional representation,
to produce an optical illusion or to devise a particular interaction with the
fabricated model. In this state‐of‐the‐art report, we classify and overview this
broad and emerging class of approaches and also propose possible directions for
future research.
article_processing_charge: No
author:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication.
Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327
apa: Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the
art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327
chicago: Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of
the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018.
https://doi.org/10.1111/cgf.13327.
ieee: B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized
fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342,
2018.
ista: Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized
fabrication. Computer Graphics Forum. 37(6), 325–342.
mla: Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer
Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327.
short: B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37
(2018) 325–342.
date_created: 2019-02-14T13:52:25Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T14:33:40Z
day: '01'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1111/cgf.13327
ec_funded: 1
external_id:
isi:
- '000437272800019'
file:
- access_level: open_access
checksum: d2bbe5c658d8159fbe9016a4f5e82b19
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T14:09:28Z
date_updated: 2020-07-14T12:47:15Z
file_id: '6004'
file_name: StylizedFabricationSTAR-Personal.pdf
file_size: 6209349
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 325-342
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics Forum
publication_identifier:
issn:
- 0167-7055
publication_status: published
publisher: Wiley
pubrep_id: '1051'
quality_controlled: '1'
scopus_import: '1'
status: public
title: State of the art on stylized fabrication
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '6002'
abstract:
- lang: eng
text: The Bogoliubov free energy functional is analysed. The functional serves as
a model of a translation-invariant Bose gas at positive temperature. We prove
the existence of minimizers in the case of repulsive interactions given by a sufficiently
regular two-body potential. Furthermore, we prove the existence of a phase transition
in this model and provide its phase diagram.
article_processing_charge: No
author:
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Robin
full_name: Reuvers, Robin
last_name: Reuvers
- first_name: Jan Philip
full_name: Solovej, Jan Philip
last_name: Solovej
citation:
ama: 'Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional
I: Existence of minimizers and phase diagram. Archive for Rational Mechanics
and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6'
apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov
free energy functional I: Existence of minimizers and phase diagram. Archive
for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6'
chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov
Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive
for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6.'
ieee: 'M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy
functional I: Existence of minimizers and phase diagram,” Archive for Rational
Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.'
ista: 'Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy
functional I: Existence of minimizers and phase diagram. Archive for Rational
Mechanics and Analysis. 229(3), 1037–1090.'
mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I:
Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics
and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6.'
short: M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics
and Analysis 229 (2018) 1037–1090.
date_created: 2019-02-14T13:40:53Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T14:33:12Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00205-018-1232-6
external_id:
arxiv:
- '1511.05935'
isi:
- '000435367300003'
intvolume: ' 229'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.05935
month: '09'
oa: 1
oa_version: Preprint
page: 1037-1090
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Bogoliubov free energy functional I: Existence of minimizers and phase
diagram'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 229
year: '2018'
...
---
_id: '5996'
abstract:
- lang: eng
text: 'In pipes, turbulence sets in despite the linear stability of the laminar
Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears
in a given experiment – the ‘natural transition point’ – depends on imperfections
of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations.
At onset, turbulence typically only occupies a certain fraction of the flow, and
this fraction equally is found to differ from experiment to experiment. Despite
these findings, Reynolds proposed that after sufficiently long times, flows may
settle to steady conditions: below a critical velocity, flows should (regardless
of initial conditions) always return to laminar, while above this velocity, eddying
motion should persist. As will be shown, even in pipes several thousand diameters
long, the spatio-temporal intermittent flow patterns observed at the end of the
pipe strongly depend on the initial conditions, and there is no indication that
different flow patterns would eventually settle to a (statistical) steady state.
Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless),
we continuously recreate the puff sequence exiting the pipe at the pipe entrance,
and in doing so introduce periodic boundary conditions for the puff pattern. This
procedure allows us to study the evolution of the flow patterns for arbitrary
long times, and we find that after times in excess of advective time units, indeed
a statistical steady state is reached. Although the resulting flows remain spatio-temporally
intermittent, puff splitting and decay rates eventually reach a balance, so that
the turbulent fraction fluctuates around a well-defined level which only depends
on . In accordance with Reynolds’ proposition, we find that at lower (here 2020),
flows eventually always resume to laminar, while for higher ( ), turbulence persists.
The critical point for pipe flow hence falls in the interval of $2020 , which
is in very good agreement with the recently proposed value of . The latter estimate
was based on single-puff statistics and entirely neglected puff interactions.
Unlike in typical contact processes where such interactions strongly affect the
percolation threshold, in pipe flow, the critical point is only marginally influenced.
Interactions, on the other hand, are responsible for the approach to the statistical
steady state. As shown, they strongly affect the resulting flow patterns, where
they cause ‘puff clustering’, and these regions of large puff densities are observed
to travel across the puff pattern in a wave-like fashion.'
acknowledgement: ' We also thank Philipp Maier and the IST Austria workshop for theirdedicated
technical support'
article_processing_charge: No
article_type: original
author:
- first_name: Mukund
full_name: Vasudevan, Mukund
id: 3C5A959A-F248-11E8-B48F-1D18A9856A87
last_name: Vasudevan
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe
flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923
apa: Vasudevan, M., & Hof, B. (2018). The critical point of the transition to
turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University
Press. https://doi.org/10.1017/jfm.2017.923
chicago: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition
to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University
Press, 2018. https://doi.org/10.1017/jfm.2017.923.
ieee: M. Vasudevan and B. Hof, “The critical point of the transition to turbulence
in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University
Press, pp. 76–94, 2018.
ista: Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence
in pipe flow. Journal of Fluid Mechanics. 839, 76–94.
mla: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to
Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge
University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923.
short: M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94.
date_created: 2019-02-14T12:50:50Z
date_published: 2018-03-25T00:00:00Z
date_updated: 2023-09-19T14:37:49Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.923
ec_funded: 1
external_id:
arxiv:
- '1709.06372'
isi:
- '000437858300003'
intvolume: ' 839'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.06372
month: '03'
oa: 1
oa_version: Preprint
page: 76-94
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The critical point of the transition to turbulence in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 839
year: '2018'
...
---
_id: '5993'
abstract:
- lang: eng
text: 'In this article, we consider the termination problem of probabilistic programs
with real-valued variables. Thequestions concerned are: 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);
andquantitative ones that ask (i) to approximate the expected termination time
(expectation problem) and (ii) tocompute a boundBsuch that the probability not
to terminate afterBsteps decreases exponentially (con-centration problem). To
solve these questions, we utilize the notion of ranking supermartingales, which
isa powerful approach for proving termination of probabilistic programs. In detail,
we focus on algorithmicsynthesis of linear ranking-supermartingales over affine
probabilistic programs (Apps) with both angelic anddemonic non-determinism. An
important subclass of Apps is LRApp which is defined as the class of all Appsover
which a linear ranking-supermartingale exists.Our main contributions are as follows.
Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial
time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor
Apps with angelic non-determinism. Moreover, theNP-hardness result holds already
for Appswithout probability and demonic non-determinism. Secondly, we show that
the concentration problem overLRApp can be solved in the same complexity as for
the membership problem of LRApp. Finally, we show thatthe expectation problem
over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability
and non-determinism (i.e., deterministic programs). Our experimental results demonstrate
theeffectiveness of our approach to answer the qualitative and quantitative questions
over Apps with at mostdemonic non-determinism.'
article_number: '7'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- 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. ACM
Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800
apa: Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic
analysis of qualitative and quantitative termination problems for affine probabilistic
programs. ACM Transactions on Programming Languages and Systems. Association
for Computing Machinery (ACM). https://doi.org/10.1145/3174800
chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad.
“Algorithmic Analysis of Qualitative and Quantitative Termination Problems for
Affine Probabilistic Programs.” ACM Transactions on Programming Languages and
Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.
ieee: K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs,” ACM Transactions on Programming Languages and Systems, vol.
40, no. 2. Association for Computing Machinery (ACM), 2018.
ista: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.
mla: Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative
Termination Problems for Affine Probabilistic Programs.” ACM Transactions on
Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing
Machinery (ACM), 2018, doi:10.1145/3174800.
short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming
Languages and Systems 40 (2018).
date_created: 2019-02-14T12:29:10Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T14:38:42Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3174800
ec_funded: 1
external_id:
arxiv:
- '1510.08517'
isi:
- '000434634500003'
intvolume: ' 40'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08517
month: '06'
oa: 1
oa_version: Submitted Version
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: ACM Transactions on Programming Languages and Systems
publication_identifier:
issn:
- 0164-0925
publication_status: published
publisher: Association for Computing Machinery (ACM)
quality_controlled: '1'
related_material:
record:
- id: '1438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Algorithmic analysis of qualitative and quantitative termination problems for
affine probabilistic programs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '5999'
abstract:
- lang: eng
text: "We introduce for each quiver Q and each algebraic oriented cohomology theory
A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli
of representations of the preprojective algebra of Q. This generalizes the K-theoretic
Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is
the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's
reformulated conjecture on modular representations of algebraic groups.\r\nWe
construct an action of the preprojective CoHA on the A-homology of Nakajima quiver
varieties. We compare this with the action of the Borel subalgebra of Yangian
when A is the intersection theory. We also give a shuffle algebra description
of this CoHA in terms of the underlying formal group law of A. As applications,
we obtain a shuffle description of the Yangian. "
article_processing_charge: No
author:
- first_name: Yaping
full_name: Yang, Yaping
last_name: Yang
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
citation:
ama: Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra.
Proceedings of the London Mathematical Society. 2018;116(5):1029-1074.
doi:10.1112/plms.12111
apa: Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective
algebra. Proceedings of the London Mathematical Society. Oxford University
Press. https://doi.org/10.1112/plms.12111
chicago: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective
Algebra.” Proceedings of the London Mathematical Society. Oxford University
Press, 2018. https://doi.org/10.1112/plms.12111.
ieee: Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,”
Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford
University Press, pp. 1029–1074, 2018.
ista: Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra.
Proceedings of the London Mathematical Society. 116(5), 1029–1074.
mla: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective
Algebra.” Proceedings of the London Mathematical Society, vol. 116, no.
5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111.
short: Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018)
1029–1074.
date_created: 2019-02-14T13:14:22Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-19T14:37:19Z
day: '01'
department:
- _id: TaHa
doi: 10.1112/plms.12111
external_id:
arxiv:
- '1407.7994'
isi:
- '000431506400001'
intvolume: ' 116'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1407.7994
month: '05'
oa: 1
oa_version: Preprint
page: 1029-1074
publication: Proceedings of the London Mathematical Society
publication_identifier:
issn:
- 0024-6115
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cohomological Hall algebra of a preprojective algebra
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2018'
...
---
_id: '5989'
abstract:
- lang: eng
text: Schistosomes are the causative agents of schistosomiasis, a neglected tropical
disease affecting over 230 million people worldwide.Additionally to their major
impact on human health, they are also models of choice in evolutionary biology.
These parasitic flatwormsare unique among the common hermaphroditic trematodes
as they have separate sexes. This so-called “evolutionary scandal”displays a female
heterogametic genetic sex-determination system (ZZ males and ZW females), as well
as a pronounced adult sexualdimorphism. These phenotypic differences are determined
by a shared set of genes in both sexes, potentially leading to intralocussexual
conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms
such as sex-biased gene expression couldoccur, but parent-of-origin gene expression
also provides an alternative. In this work we investigated the latter mechanism,
that is,genes expressed preferentially from either the maternal or the paternal
allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and
female hybrid adults obtained by strain crosses were sequenced. Strain-specific
single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental
origin, while reciprocal crosses helped to differentiate parentalexpression from
strain-specific expression. We identified genes containing SNPs expressed in a
parent-of-origin manner consistentwith paternal and maternal imprints. Although
the majority of the SNPs was identified in mitochondrial and Z-specific loci,
theremaining SNPs found in male and female transcriptomes were situated in genes
that have the potential to explain sexual differencesin schistosome parasites.
Furthermore, we identified and validated four new Z-specific scaffolds.
article_processing_charge: No
author:
- first_name: Julien
full_name: Kincaid-Smith, Julien
last_name: Kincaid-Smith
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Céline
full_name: Cosseau, Céline
last_name: Cosseau
- first_name: Jérôme
full_name: Boissier, Jérôme
last_name: Boissier
- first_name: Dany
full_name: Severac, Dany
last_name: Severac
- first_name: Christoph
full_name: Grunau, Christoph
last_name: Grunau
- first_name: Eve
full_name: Toulza, Eve
last_name: Toulza
citation:
ama: Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene
Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution.
2018;10(3):840-856. doi:10.1093/gbe/evy037
apa: Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D.,
Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression
in Male and Female Schistosome Parasites. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evy037
chicago: Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier,
Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene
Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution.
Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037.
ieee: J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression
in Male and Female Schistosome Parasites,” Genome Biology and Evolution,
vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018.
ista: Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza
E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome
Parasites. Genome Biology and Evolution. 10(3), 840–856.
mla: Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in
Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol.
10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037.
short: J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C.
Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856.
date_created: 2019-02-14T12:13:52Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-19T14:39:08Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evy037
external_id:
isi:
- '000429483700013'
file:
- access_level: open_access
checksum: 736a459cb77de5824354466bb0331caf
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T12:20:01Z
date_updated: 2020-07-14T12:47:15Z
file_id: '5991'
file_name: 2018_GBE_Kincaid_Smith.pdf
file_size: 529755
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 840-856
publication: Genome Biology and Evolution
publication_identifier:
issn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites
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: 10
year: '2018'
...
---
_id: '6031'
abstract:
- lang: eng
text: We introduce Clover, a new library for efficient computation using low-precision
data, providing mathematical routines required by fundamental methods in optimization
and sparse recovery. Our library faithfully implements variants of stochastic
quantization that guarantee convergence at low precision, and supports data formats
from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular,
we show that 4-bit can be implemented efficiently using Intel AVX despite the
lack of native support for this data format. Experimental results with dot product,
matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard
thresholding (IHT) demonstrate that the attainable speedups are in many cases
close to linear with respect to the reduction of precision due to reduced data
movement. Finally, for GD and IHT, we show examples of absolute speedup achieved
by 4-bit versus 32-bit, by iterating until a given target error is achieved.
article_number: '8598402'
article_processing_charge: No
author:
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler Michael
full_name: Smith, Tyler Michael
last_name: Smith
- 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: Markus
full_name: Puschel, Markus
last_name: Puschel
citation:
ama: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on
x86: Trading compute for data movement. In: 2018 IEEE International Workshop
on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402'
apa: 'Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast
quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE
International Workshop on Signal Processing Systems (Vol. 2018–October). Cape
Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402'
chicago: 'Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel.
“Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018
IEEE International Workshop on Signal Processing Systems, Vol. 2018–October.
IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.'
ieee: 'A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized
arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International
Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol.
2018–October.'
ista: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic
on x86: Trading compute for data movement. 2018 IEEE International Workshop on
Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October,
8598402.'
mla: 'Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute
for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems,
vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.'
short: A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International
Workshop on Signal Processing Systems, IEEE, 2018.
conference:
end_date: 2018-10-24
location: Cape Town, South Africa
name: 'SiPS: Workshop on Signal Processing Systems'
start_date: 2018-10-21
date_created: 2019-02-17T22:59:25Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2023-09-19T14:41:51Z
day: '31'
department:
- _id: DaAl
doi: 10.1109/SiPS.2018.8598402
external_id:
isi:
- '000465106800060'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
publication: 2018 IEEE International Workshop on Signal Processing Systems
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fast quantized arithmetic on x86: Trading compute for data movement'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-October
year: '2018'
...
---
_id: '25'
abstract:
- lang: eng
text: 'Partially observable Markov decision processes (POMDPs) are the standard
models for planning under uncertainty with both finite and infinite horizon. Besides
the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs)
is another classical objective for POMDPs. In this case, given a set of target
states and a positive cost for each transition, the optimization objective is
to minimize the expected total cost until a target state is reached. In the literature,
RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving
Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees,
and HSVI may even fail to terminate its trials. We give the following contributions:
(1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they
prevent the original HSVI from converging. (2) We present a novel algorithm inspired
by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees.
(3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.'
acknowledgement: '∗This work has been supported by Vienna Science and Technology Fund
(WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE),
and ERC Starting grant (279307: Graph Games). This research was sponsored by the
Army Research Laboratory and was accomplished under Cooperative Agreement Number
W911NF-13-2-0045 (ARL Cyber Security CRA). '
article_processing_charge: No
author:
- first_name: Karel
full_name: Horák, Karel
last_name: Horák
- first_name: Branislav
full_name: Bošanský, Branislav
last_name: Bošanský
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration
for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770.
doi:10.24963/ijcai.2018/662'
apa: 'Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic
search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence (Vol. 2018–July,
pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662'
chicago: 'Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI:
Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, 2018–July:4764–70.
IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.'
ieee: 'K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value
iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International
Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol.
2018–July, pp. 4764–4770.'
ista: 'Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value
iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. IJCAI: International Joint Conference on
Artificial Intelligence vol. 2018–July, 4764–4770.'
mla: 'Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.”
Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662.'
short: K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-19T14:44:59Z
day: '01'
department:
- _id: KrCh
doi: 10.24963/ijcai.2018/662
ec_funded: 1
external_id:
isi:
- '000764175404127'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.24963/ijcai.2018/662
month: '07'
oa: 1
oa_version: Published Version
page: 4764 - 4770
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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'
publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence
publication_status: published
publisher: IJCAI
publist_id: '8030'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Goal-HSVI: Heuristic search value iteration for goal-POMDPs'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-July
year: '2018'
...
---
_id: '24'
abstract:
- lang: eng
text: Partially-observable Markov decision processes (POMDPs) with discounted-sum
payoff are a standard framework to model a wide range of problems related to decision
making under uncertainty. Traditionally, the goal has been to obtain policies
that optimize the expectation of the discounted-sum payoff. A key drawback of
the expectation measure is that even low probability events with extreme payoff
can significantly affect the expectation, and thus the obtained policies are not
necessarily risk-averse. An alternate approach is to optimize the probability
that the payoff is above a certain threshold, which allows obtaining risk-averse
policies, but ignores optimization of the expectation. We consider the expectation
optimization with probabilistic guarantee (EOPG) problem, where the goal is to
optimize the expectation ensuring that the payoff is above a given threshold with
at least a specified probability. We present several results on the EOPG problem,
including the first algorithm to solve it.
acknowledgement: "This research was supported by the Vienna Science and Technology
Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and
an ERC Start Grant (279307:Graph Games).\r\n"
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Owen
full_name: Rouillé, Owen
last_name: Rouillé
citation:
ama: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with
probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018.
IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652'
apa: 'Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation
optimization with probabilistic guarantees in POMDPs with discounted-sum objectives
(Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference
on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652'
chicago: Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé.
“Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum
Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652.
ieee: 'K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented
at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm,
Sweden, 2018, vol. 2018, pp. 4692–4699.'
ista: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI:
International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.'
mla: Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic
Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018,
pp. 4692–99, doi:10.24963/ijcai.2018/652.
short: K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp.
4692–4699.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-19T14:45:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.24963/ijcai.2018/652
ec_funded: 1
external_id:
arxiv:
- '1804.10601'
isi:
- '000764175404117'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10601
month: '07'
oa: 1
oa_version: Preprint
page: 4692 - 4699
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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'
publication_status: published
publisher: IJCAI
publist_id: '8031'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum
objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '34'
abstract:
- lang: eng
text: Partially observable Markov decision processes (POMDPs) are widely used in
probabilistic planning problems in which an agent interacts with an environment
using noisy and imprecise sensors. We study a setting in which the sensors are
only partially defined and the goal is to synthesize “weakest” additional sensors,
such that in the resulting POMDP, there is a small-memory policy for the agent
that almost-surely (with probability 1) satisfies a reachability objective. We
show that the problem is NP-complete, and present a symbolic algorithm by encoding
the problem into SAT instances. We illustrate trade-offs between the amount of
memory of the policy and the number of additional sensors on a simple example.
We have implemented our approach and consider three classical POMDP examples from
the literature, and show that in all the examples the number of sensors can be
significantly decreased (as compared to the existing solutions in the literature)
without increasing the complexity of the policies.
alternative_title:
- ICAPS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chemlík, Martin
last_name: Chemlík
- first_name: Ufuk
full_name: Topcu, Ufuk
last_name: Topcu
citation:
ama: 'Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability
objectives. In: Vol 2018. AAAI Press; 2018:47-55.'
apa: 'Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for
POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS:
International Conference on Automated Planning and Scheduling, Delft, Netherlands:
AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis
for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.
ieee: 'K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with
reachability objectives,” presented at the ICAPS: International Conference on
Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.'
ista: 'Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with
reachability objectives. ICAPS: International Conference on Automated Planning
and Scheduling, ICAPS, vol. 2018, 47–55.'
mla: Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability
Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.
short: K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.
conference:
end_date: 2018-06-29
location: Delft, Netherlands
name: 'ICAPS: International Conference on Automated Planning and Scheduling'
start_date: 2018-06-24
date_created: 2018-12-11T11:44:16Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T14:44:14Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1710.00675'
isi:
- '000492986200006'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.00675
month: '06'
oa: 1
oa_version: Preprint
page: 47 - 55
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: AAAI Press
publist_id: '8021'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensor synthesis for POMDPs with reachability objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '18'
abstract:
- lang: eng
text: An N-superconcentrator is a directed, acyclic graph with N input nodes and
N output nodes such that every subset of the inputs and every subset of the outputs
of same cardinality can be connected by node-disjoint paths. It is known that
linear-size and bounded-degree superconcentrators exist. We prove the existence
of such superconcentrators with asymptotic density 25.3 (where the density is
the number of edges divided by N). The previously best known densities were 28
[12] and 27.4136 [17].
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria.
2018;141(10):269-304.
apa: Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3.
Ars Combinatoria. Charles Babbage Research Centre.
chicago: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density
25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018.
ieee: V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars
Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304,
2018.
ista: Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria.
141(10), 269–304.
mla: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.”
Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018,
pp. 269–304.
short: V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T14:46:18Z
day: '01'
department:
- _id: VlKo
external_id:
arxiv:
- '1405.7828'
isi:
- '000446809500022'
intvolume: ' 141'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.7828
month: '10'
oa: 1
oa_version: Preprint
page: 269 - 304
publication: Ars Combinatoria
publication_identifier:
issn:
- 0381-7032
publication_status: published
publisher: Charles Babbage Research Centre
publist_id: '8037'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconcentrators of density 25.3
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2018'
...
---
_id: '6355'
abstract:
- lang: eng
text: We prove that any cyclic quadrilateral can be inscribed in any closed convex
C1-curve. The smoothness condition is not required if the quadrilateral is a
rectangle.
article_number: e7
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
citation:
ama: Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed
convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7
apa: Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed
in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge
University Press. https://doi.org/10.1017/fms.2018.7
chicago: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be
Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma.
Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7.
ieee: A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in
any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge
University Press, 2018.
ista: Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in
any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.
mla: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed
in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6,
e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.
short: A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018).
date_created: 2019-04-30T06:09:57Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-19T14:50:12Z
day: '31'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
- _id: JaMa
doi: 10.1017/fms.2018.7
ec_funded: 1
external_id:
arxiv:
- '1712.10205'
isi:
- '000433915500001'
file:
- access_level: open_access
checksum: 5a71b24ba712a3eb2e46165a38fbc30a
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T06:14:58Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6356'
file_name: 2018_ForumMahtematics_Akopyan.pdf
file_size: 249246
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Any cyclic quadrilateral can be inscribed in any closed convex smooth curve
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '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: '6941'
abstract:
- lang: eng
text: "Bitcoin has become the most successful cryptocurrency ever deployed, and
its most distinctive feature is that it is decentralized. Its underlying protocol
(Nakamoto consensus) achieves this by using proof of work, which has the drawback
that it causes the consumption of vast amounts of energy to maintain the ledger.
Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards
addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs
of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather
than computation. We argue that SpaceMint’s design solves or alleviates several
of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also
rewards smaller miners fairly according to their contribution to the network,
thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof
of space to enable its use in cryptocurrency, studies the attacks that can arise
against a Bitcoin-like blockchain that uses proof of space, and proposes a new
blockchain format and transaction types to address these attacks. Our prototype
shows that initializing 1 TB for mining takes about a day (a one-off setup cost),
and miners spend on average just a fraction of a second per block mined. Finally,
we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the
canonical game-theoretic notion for games that take place over time) and show
that this stylized game satisfies a strong equilibrium notion, thereby arguing
for SpaceMint ’s stability and consensus."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sunoo
full_name: Park, Sunoo
last_name: Park
- first_name: Albert
full_name: Kwon, Albert
last_name: Kwon
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A
cryptocurrency based on proofs of space. In: 22nd International Conference
on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499.
doi:10.1007/978-3-662-58387-6_26'
apa: 'Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak,
K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd
International Conference on Financial Cryptography and Data Security (Vol.
10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26'
chicago: 'Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen,
and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
In 22nd International Conference on Financial Cryptography and Data Security,
10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.'
ieee: 'S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak,
“SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International
Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao,
2018, vol. 10957, pp. 480–499.'
ista: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint:
A cryptocurrency based on proofs of space. 22nd International Conference on Financial
Cryptography and Data Security. FC: Financial Cryptography and Data Security,
LNCS, vol. 10957, 480–499.'
mla: 'Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
22nd International Conference on Financial Cryptography and Data Security,
vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26.'
short: S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:,
22nd International Conference on Financial Cryptography and Data Security, Springer
Nature, 2018, pp. 480–499.
conference:
end_date: 2018-03-02
location: Nieuwpoort, Curacao
name: 'FC: Financial Cryptography and Data Security'
start_date: 2018-02-26
date_created: 2019-10-14T06:35:38Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2023-09-19T15:02:13Z
day: '07'
department:
- _id: KrPi
doi: 10.1007/978-3-662-58387-6_26
ec_funded: 1
external_id:
isi:
- '000540656400026'
intvolume: ' 10957'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/528
month: '12'
oa: 1
oa_version: Submitted Version
page: 480-499
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 22nd International Conference on Financial Cryptography and Data Security
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783662583869'
- '9783662583876'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SpaceMint: A cryptocurrency based on proofs of space'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10957
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
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page: 1869–1890
publication: The Journal of Experimental Medicine
publication_identifier:
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issn:
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publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
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title: The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective
CD8+T cells
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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---
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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. 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, 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, 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,
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: 2023-09-19T14:52:32Z
day: '01'
ddc:
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department:
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doi: 10.15252/embr.201845836
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date_updated: 2020-07-14T12:47:32Z
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intvolume: ' 19'
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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
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)
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type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...