---
_id: '32'
abstract:
- lang: eng
text: The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between
neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified
the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in
vivo during the peak of myelination by targeting the GluA2 subunit. Expression
of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered
proliferation of OPCs and reduced their differentiation into oligodendrocytes.
Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit
(C-tail), a modification designed to affect the interaction between GluA2 and
AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs,
decreased the differentiation of OPCs without affecting their proliferation. These
findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs,
as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in
the mouse corpus callosum, are important for balancing the response of OPCs to
proliferation and differentiation cues. In the brain, oligodendrocyte precursor
cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from
neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC
synapses alters proliferation and differentiation of OPCs. This expands the traditional
view of synaptic transmission by suggesting neurons also use synapses to modulate
behavior of glia.
acknowledgement: This work was supported by Deutsche Forschungsgemeinschaft (DFG)
grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience
(CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the
Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the
DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported
by the Tistou & Charlotte Kerstan Foundation.
article_processing_charge: No
author:
- first_name: Ting
full_name: Chen, Ting
last_name: Chen
- first_name: Bartosz
full_name: Kula, Bartosz
last_name: Kula
- first_name: Balint
full_name: Nagy, Balint
id: 30F830CE-02D1-11E9-9BAA-DAF4881429F2
last_name: Nagy
orcid: 0000-0002-4002-4686
- first_name: Ruxandra
full_name: Barzan, Ruxandra
last_name: Barzan
- first_name: Andrea
full_name: Gall, Andrea
last_name: Gall
- first_name: Ingrid
full_name: Ehrlich, Ingrid
last_name: Ehrlich
- first_name: Maria
full_name: Kukley, Maria
last_name: Kukley
citation:
ama: Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor
cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell
Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066
apa: Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley,
M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation
and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2018.09.066
chicago: Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid
Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell
Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell
Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.
ieee: T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell
proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell
Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.
ista: Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo
regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.
mla: Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation
and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports,
vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.
short: T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell
Reports 25 (2018) 852–861.e7.
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-11T14:13:32Z
day: '23'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2018.09.066
external_id:
isi:
- '000448219500005'
file:
- access_level: open_access
checksum: d9f74277fd57176e04732707d575cf08
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:42:57Z
date_updated: 2020-07-14T12:46:03Z
file_id: '5703'
file_name: 2018_CellReports_Chen.pdf
file_size: 4461997
relation: main_file
file_date_updated: 2020-07-14T12:46:03Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 852 - 861.e7
publication: Cell Reports
publication_status: published
publisher: Elsevier
publist_id: '8023'
quality_controlled: '1'
scopus_import: '1'
status: public
title: In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation
by the AMPA-receptor Subunit GluA2
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 25
year: '2018'
...
---
_id: '5672'
abstract:
- lang: eng
text: The release of IgM is the first line of an antibody response and precedes
the generation of high affinity IgG in germinal centers. Once secreted by freshly
activated plasmablasts, IgM is released into the efferent lymph of reactive lymph
nodes as early as 3 d after immunization. As pentameric IgM has an enormous size
of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through
the densely lymphocyte-packed environment of a lymph node parenchyma in order
to reach its exit. In this issue of JEM, Thierry et al. show that, in order to
reach the blood stream, IgM molecules take a specific micro-anatomical route via
lymph node conduits.
article_processing_charge: No
author:
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine.
2018;215(12):2959-2961. doi:10.1084/jem.20181934
apa: Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental
Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934
chicago: Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.
ieee: A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental
Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.
ista: Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine.
215(12), 2959–2961.
mla: Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental
Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61,
doi:10.1084/jem.20181934.
short: A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.
date_created: 2018-12-16T22:59:18Z
date_published: 2018-11-20T00:00:00Z
date_updated: 2023-09-11T14:12:06Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20181934
external_id:
isi:
- '000451920600002'
file:
- access_level: open_access
checksum: 687beea1d64c213f4cb9e3c29ec11a14
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T08:49:52Z
date_updated: 2020-07-14T12:47:09Z
file_id: '5931'
file_name: 2018_JournalExperMed_Reversat.pdf
file_size: 1216437
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 215'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2959-2961
publication: Journal of Experimental Medicine
publication_identifier:
issn:
- '00221007'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: IgM's exit route
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 215
year: '2018'
...
---
_id: '398'
abstract:
- lang: eng
text: 'Objective: To report long-term results after Pipeline Embolization Device
(PED) implantation, characterize complex and standard aneurysms comprehensively,
and introduce a modified flow disruption scale. Methods: We retrospectively reviewed
a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs.
Aneurysm complexity was assessed using our proposed classification. Immediate
angiographic results were analyzed using previously published grading scales and
our novel flow disruption scale. Results: According to our new definition, 46
(78%) aneurysms were classified as complex. Most PED interventions were performed
in the paraophthalmic and cavernous internal carotid artery segments. Excellent
neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients.
Our data showed low permanent procedure-related mortality (0%) and morbidity (3%)
rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total
obliteration in a further 14%. Complete obliteration after deployment of a single
PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale
was an independent predictor of aneurysm occlusion in a multivariable analysis.
All aneurysms with a high flow disruption grade showed complete occlusion at follow-up
regardless of PED number or aneurysm complexity. Conclusions: Treatment with the
PED should be recognized as a primary management strategy for a highly selected
cohort with predominantly complex intracranial aneurysms. We further show that
a priori assessment of aneurysm complexity and our new postinterventional angiographic
flow disruption scale predict occlusion probability and may help to determine
the adequate number of per-aneurysm devices.'
article_processing_charge: No
author:
- first_name: Philippe
full_name: Dodier, Philippe
last_name: Dodier
- first_name: Josa
full_name: Frischer, Josa
last_name: Frischer
- first_name: Wei
full_name: Wang, Wei
last_name: Wang
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Ammar
full_name: Mallouhi, Ammar
last_name: Mallouhi
- first_name: Wolfgang
full_name: Serles, Wolfgang
last_name: Serles
- first_name: Andreas
full_name: Gruber, Andreas
last_name: Gruber
- first_name: Engelbert
full_name: Knosp, Engelbert
last_name: Knosp
- first_name: Gerhard
full_name: Bavinzski, Gerhard
last_name: Bavinzski
citation:
ama: Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic
factor after flow diverter treatment long term experience with the pipeline embolization
device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096
apa: Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W.,
… Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096
chicago: Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi,
Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate
Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term
Experience with the Pipeline Embolization Device.” World Neurosurgery.
Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.
ieee: P. Dodier et al., “Immediate flow disruption as a prognostic factor
after flow diverter treatment long term experience with the pipeline embolization
device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.
ista: Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A,
Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after
flow diverter treatment long term experience with the pipeline embolization device.
World Neurosurgery. 13, e568–e578.
mla: Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor
after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization
Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.
short: P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A.
Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:12:33Z
day: '01'
department:
- _id: BeBi
doi: 10.1016/j.wneu.2018.02.096
external_id:
isi:
- '000432942700070'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: e568-e578
publication: World Neurosurgery
publication_status: published
publisher: Elsevier
publist_id: '7431'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Immediate flow disruption as a prognostic factor after flow diverter treatment
long term experience with the pipeline embolization device
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '458'
abstract:
- lang: eng
text: We consider congruences of straight lines in a plane with the combinatorics
of the square grid, with all elementary quadrilaterals possessing an incircle.
It is shown that all the vertices of such nets (we call them incircular or IC-nets)
lie on confocal conics. Our main new results are on checkerboard IC-nets in the
plane. These are congruences of straight lines in the plane with the combinatorics
of the square grid, combinatorially colored as a checkerboard, such that all black
coordinate quadrilaterals possess inscribed circles. We show how this larger class
of IC-nets appears quite naturally in Laguerre geometry of oriented planes and
spheres and leads to new remarkable incidence theorems. Most of our results are
valid in hyperbolic and spherical geometries as well. We present also generalizations
in spaces of higher dimension, called checkerboard IS-nets. The construction of
these nets is based on a new 9 inspheres incidence theorem.
acknowledgement: DFG Collaborative Research Center TRR 109 “Discretization in Geometry
and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexander
full_name: Bobenko, Alexander
last_name: Bobenko
citation:
ama: Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292
apa: Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/7292
chicago: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal
Conics.” Transactions of the American Mathematical Society. American Mathematical
Society, 2018. https://doi.org/10.1090/tran/7292.
ieee: A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions
of the American Mathematical Society, vol. 370, no. 4. American Mathematical
Society, pp. 2825–2854, 2018.
ista: Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions
of the American Mathematical Society. 370(4), 2825–2854.
mla: Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.”
Transactions of the American Mathematical Society, vol. 370, no. 4, American
Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292.
short: A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society
370 (2018) 2825–2854.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-11T14:19:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/7292
ec_funded: 1
external_id:
isi:
- '000423197800019'
intvolume: ' 370'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.04637
month: '04'
oa: 1
oa_version: Preprint
page: 2825 - 2854
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '7363'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Incircular nets and confocal conics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 370
year: '2018'
...
---
_id: '426'
abstract:
- lang: eng
text: Sperm cells are the most morphologically diverse cells across animal taxa.
Within species, sperm and ejaculate traits have been suggested to vary with the
male's competitive environment, e.g., level of sperm competition, female mating
status and quality, and also with male age, body mass, physiological condition,
and resource availability. Most previous studies have based their conclusions
on the analysis of only one or a few ejaculates per male without investigating
differences among the ejaculates of the same individual. This masks potential
ejaculate-specific traits. Here, we provide data on the length, quantity, and
viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior.
Males of this ant species are relatively long-lived and can mate with large numbers
of female sexuals throughout their lives. We analyzed all ejaculates across the
individuals' lifespan and manipulated the availability of mating partners. Our
study shows that both the number and size of sperm cells transferred during copulations
differ among individuals and also among ejaculates of the same male. Sperm quality
does not decrease with male age, but the variation in sperm number between ejaculates
indicates that males need considerable time to replenish their sperm supplies.
Producing many ejaculates in a short time appears to be traded-off against male
longevity rather than sperm quality.
acknowledgement: "Research with C. obscurior from Brazil was permitted by Instituto
Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no.
20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1
), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice
concerning graphs. One referee made helpful comments on the manuscript.\r\n"
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits
in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003
apa: Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003
chicago: Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and
Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology.
Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.
ieee: S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific
sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier,
pp. 284–290, 2018.
ista: Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.
mla: Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant
Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90,
doi:10.1016/j.jinsphys.2017.12.003.
short: S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018)
284–290.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-12T07:43:26Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.jinsphys.2017.12.003
external_id:
isi:
- '000434751100034'
intvolume: ' 107'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 284-290
publication: Journal of Insect Physiology
publication_status: published
publisher: Elsevier
publist_id: '7397'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Individual- and ejaculate-specific sperm traits in ant males
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 107
year: '2018'
...
---
_id: '5788'
abstract:
- lang: eng
text: In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner or payoff of the game. Such
games are central in formal verification since they model the interaction between
a non-terminating system and its environment. We study bidding games in which
the players bid for the right to move the token. Two bidding rules have been defined.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the “bank” rather than the
other player. While poorman reachability games have been studied before, we present,
for the first time, results on infinite-duration poorman games. A central quantity
in these games is the ratio between the two players’ initial budgets. The questions
we study concern a necessary and sufficient ratio with which a player can achieve
a goal. For reachability objectives, such threshold ratios are known to exist
for both bidding rules. We show that the properties of poorman reachability games
extend to complex qualitative objectives such as parity, similarly to the Richman
case. Our most interesting results concern quantitative poorman games, namely
poorman mean-payoff games, where we construct optimal strategies depending on
the initial ratio, by showing a connection with random-turn based games. The connection
in itself is interesting, because it does not hold for reachability poorman games.
We also solve the complexity problems that arise in poorman bidding games.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games.
In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2'
apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration
poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International
Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2'
chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration
Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.
ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding
games,” presented at the 14th International Conference on Web and Internet Economics,
WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.
ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding
games. 14th International Conference on Web and Internet Economics, WINE, LNCS,
vol. 11316, 21–36.
mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316,
Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.
conference:
end_date: 2018-12-17
location: Oxford, UK
name: 14th International Conference on Web and Internet Economics, WINE
start_date: 2018-12-15
date_created: 2018-12-30T22:59:14Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-12T07:44:01Z
day: '21'
department:
- _id: ToHe
doi: 10.1007/978-3-030-04612-5_2
external_id:
arxiv:
- '1804.04372'
isi:
- '000865933000002'
intvolume: ' 11316'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04372
month: '11'
oa: 1
oa_version: Preprint
page: 21-36
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
isbn:
- '9783030046118'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infinite-duration poorman-bidding games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11316
year: '2018'
...
---
_id: '150'
abstract:
- lang: eng
text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1,
has a critical role during the formation of the HIV-1 virus particle. During virus
assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle,
which holds together the Gag hexamer and facilitates the formation of a curved
immature hexagonal lattice underneath the viral membrane2,3. Upon completion of
assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in
which the immature lattice is broken down; the liberated CA domain of Gag then
re-assembles into the mature conical capsid that encloses the viral genome and
associated enzymes. Folding and proteolysis of the six-helix bundle are crucial
rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle
is an established target of HIV-1 inhibitors4,5. Here, using a combination of
structural and functional analyses, we show that inositol hexakisphosphate (InsP6,
also known as IP6) facilitates the formation of the six-helix bundle and assembly
of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of
lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks
an alternative binding site, where IP6 interaction promotes the assembly of the
mature capsid lattice. These studies identify IP6 as a naturally occurring small
molecule that promotes both assembly and maturation of HIV-1.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Kaneil K
full_name: Zadrozny, Kaneil K
last_name: Zadrozny
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Terri D
full_name: Lyddon, Terri D
last_name: Lyddon
- first_name: Clifton L
full_name: Ricana, Clifton L
last_name: Ricana
- first_name: Jonathan M
full_name: Wagner, Jonathan M
last_name: Wagner
- first_name: Juan R
full_name: Perilla, Juan R
last_name: Perilla
- first_name: Pornillos Barbie K
full_name: Ganser, Pornillos Barbie K
last_name: Ganser
- first_name: Marc C
full_name: Johnson, Marc C
last_name: Johnson
- first_name: Owen
full_name: Pornillos, Owen
last_name: Pornillos
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
citation:
ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors
for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4
apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C.
L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1.
Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4
chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon,
Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly
Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.
ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,”
Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.
ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla
JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are
assembly co-factors for HIV-1. Nature. 560(7719), 509–512.
mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.”
Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512,
doi:10.1038/s41586-018-0396-4.
short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M.
Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature
560 (2018) 509–512.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-08-29T00:00:00Z
date_updated: 2023-09-12T07:44:37Z
day: '29'
department:
- _id: FlSc
doi: 10.1038/s41586-018-0396-4
external_id:
isi:
- '000442483400046'
pmid:
- '30158708'
intvolume: ' 560'
isi: 1
issue: '7719'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/
month: '08'
oa: 1
oa_version: Submitted Version
page: 509–512
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-018-0505-4
scopus_import: '1'
status: public
title: Inositol phosphates are assembly co-factors for HIV-1
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 560
year: '2018'
...
---
_id: '303'
abstract:
- lang: eng
text: The theory of tropical series, that we develop here, firstly appeared in the
study of the growth of pluriharmonic functions. Motivated by waves in sandpile
models we introduce a dynamic on the set of tropical series, and it is experimentally
observed that this dynamic obeys a power law. So, this paper serves as a compilation
of results we need for other articles and also introduces several objects interesting
by themselves.
acknowledgement: The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility
grant 168647. Support from the Basic Research Program of the National Research University
Higher School of Economics is gratefully acknowledged. The second author, Mikhail
Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science
Foundation as well as by the National Center of Competence in Research SwissMAP
of the Swiss National Science Foundation.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on
them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849.
doi:10.3934/dcds.2018120
apa: Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and
wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A.
AIMS. https://doi.org/10.3934/dcds.2018120
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series
and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series
A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.
ieee: N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic
on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38,
no. 6. AIMS, pp. 2827–2849, 2018.
ista: Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic
on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and
Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A,
vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.
short: N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series
A 38 (2018) 2827–2849.
date_created: 2018-12-11T11:45:43Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-12T07:45:37Z
day: '01'
department:
- _id: TaHa
doi: 10.3934/dcds.2018120
external_id:
arxiv:
- '1706.03062'
isi:
- '000438818400007'
intvolume: ' 38'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.03062
month: '06'
oa: 1
oa_version: Submitted Version
page: 2827 - 2849
publication: Discrete and Continuous Dynamical Systems- Series A
publication_status: published
publisher: AIMS
publist_id: '7576'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to tropical series and wave dynamic on them
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2018'
...
---
_id: '14202'
abstract:
- lang: eng
text: "Approximating a probability density in a tractable manner is a central task\r\nin
Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves
tractability by choosing a relatively simple variational family.\r\nBorrowing
ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost}
VI by replacing the selection of a single density with a\r\ngreedily constructed
mixture of densities. In order to guarantee convergence,\r\nprevious works impose
stringent assumptions that require significant effort for\r\npractitioners. Specifically,
they require a custom implementation of the greedy\r\nstep (called the LMO) for
every probabilistic model with respect to an\r\nunnatural variational family of
truncated distributions. Our work fixes these\r\nissues with novel theoretical
and algorithmic insights. On the theoretical\r\nside, we show that boosting VI
satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence
of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the
LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces
the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow
for black box implementation of the boosting\r\nsubroutine. Finally, we present
a stopping criterion drawn from the duality gap\r\nin the classic FW analyses
and exhaustive experiments to illustrate the\r\nusefulness of our theoretical
and algorithmic contributions."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gideon
full_name: Dresdner, Gideon
last_name: Dresdner
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Isabel
full_name: Valera, Isabel
last_name: Valera
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box
variational inference. In: Advances in Neural Information Processing Systems.
Vol 31. Neural Information Processing Systems Foundation; 2018.'
apa: 'Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018).
Boosting black box variational inference. In Advances in Neural Information
Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing
Systems Foundation.'
chicago: Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and
Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural
Information Processing Systems, Vol. 31. Neural Information Processing Systems
Foundation, 2018.
ieee: F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting
black box variational inference,” in Advances in Neural Information Processing
Systems, Montreal, Canada, 2018, vol. 31.
ista: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black
box variational inference. Advances in Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 31.'
mla: Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances
in Neural Information Processing Systems, vol. 31, Neural Information Processing
Systems Foundation, 2018.
short: F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances
in Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2018.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2018-12-03
date_created: 2023-08-22T14:15:40Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T07:38:24Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02185'
intvolume: ' 31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02185
month: '06'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
isbn:
- '9781510884472'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boosting black box variational inference
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '14201'
abstract:
- lang: eng
text: "Variational inference is a popular technique to approximate a possibly\r\nintractable
Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational
inference has been proposed as a new paradigm to approximate the\r\nposterior
by a mixture of densities by greedily adding components to the\r\nmixture. However,
as is the case with many other variational inference\r\nalgorithms, its theoretical
properties have not been studied. In the present\r\nwork, we study the convergence
properties of this approach from a modern\r\noptimization viewpoint by establishing
connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel
theoretical insights regarding the\r\nsufficient conditions for convergence, explicit
rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works
for variational\r\ninference has been on tractability, our work is especially
important as a much\r\nneeded attempt to bridge the gap between probabilistic
models and their\r\ncorresponding theoretical properties."
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Joydeep
full_name: Ghosh, Joydeep
last_name: Ghosh
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference:
An optimization perspective. In: Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.'
apa: 'Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational
inference: An optimization perspective. In Proceedings of the 21st International
Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472).
Playa Blanca, Lanzarote: ML Research Press.'
chicago: 'Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch.
“Boosting Variational Inference: An Optimization Perspective.” In Proceedings
of the 21st International Conference on Artificial Intelligence and Statistics,
84:464–72. ML Research Press, 2018.'
ieee: 'F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference:
An optimization perspective,” in Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018,
vol. 84, pp. 464–472.'
ista: 'Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference:
An optimization perspective. Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence
and Statistics, PMLR, vol. 84, 464–472.'
mla: 'Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization
Perspective.” Proceedings of the 21st International Conference on Artificial
Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.'
short: F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st
International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2018, pp. 464–472.
conference:
end_date: 2018-04-11
location: Playa Blanca, Lanzarote
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2018-04-09
date_created: 2023-08-22T14:15:20Z
date_published: 2018-04-15T00:00:00Z
date_updated: 2023-09-13T07:52:40Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1708.01733'
intvolume: ' 84'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01733
month: '04'
oa: 1
oa_version: Preprint
page: 464-472
publication: Proceedings of the 21st International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Boosting variational inference: An optimization perspective'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...
---
_id: '14198'
abstract:
- lang: eng
text: "High-dimensional time series are common in many domains. Since human\r\ncognition
is not optimized to work well in high-dimensional spaces, these areas\r\ncould
benefit from interpretable low-dimensional representations. However, most\r\nrepresentation
learning algorithms for time series data are difficult to\r\ninterpret. This is
due to non-intuitive mappings from data features to salient\r\nproperties of the
representation and non-smoothness over time. To address this\r\nproblem, we propose
a new representation learning framework building on ideas\r\nfrom interpretable
discrete dimensionality reduction and deep generative\r\nmodeling. This framework
allows us to learn discrete representations of time\r\nseries, which give rise
to smooth and interpretable embeddings with superior\r\nclustering performance.
We introduce a new way to overcome the\r\nnon-differentiability in discrete representation
learning and present a\r\ngradient-based version of the traditional self-organizing
map algorithm that is\r\nmore performant than the original. Furthermore, to allow
for a probabilistic\r\ninterpretation of our method, we integrate a Markov model
in the representation\r\nspace. This model uncovers the temporal transition structure,
improves\r\nclustering performance even further and provides additional explanatory\r\ninsights
as well as a natural representation of uncertainty. We evaluate our\r\nmodel in
terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST
data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic
Lorenz attractor system with two macro states, as well as on\r\na challenging
real world medical time series application on the eICU data set.\r\nOur learned
representations compare favorably with competitor methods and\r\nfacilitate downstream
tasks on the real world data."
article_processing_charge: No
author:
- first_name: Vincent
full_name: Fortuin, Vincent
last_name: Fortuin
- first_name: Matthias
full_name: Hüser, Matthias
last_name: Hüser
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Heiko
full_name: Strathmann, Heiko
last_name: Strathmann
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable
discrete representation learning on time series. In: International Conference
on Learning Representations. ; 2018.'
apa: 'Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018).
SOM-VAE: Interpretable discrete representation learning on time series. In International
Conference on Learning Representations. New Orleans, LA, United States.'
chicago: 'Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann,
and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on
Time Series.” In International Conference on Learning Representations,
2018.'
ieee: 'V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE:
Interpretable discrete representation learning on time series,” in International
Conference on Learning Representations, New Orleans, LA, United States, 2018.'
ista: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable
discrete representation learning on time series. International Conference on Learning
Representations. ICLR: International Conference on Learning Representations.'
mla: 'Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning
on Time Series.” International Conference on Learning Representations,
2018.'
short: V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International
Conference on Learning Representations, 2018.
conference:
end_date: 2019-05-09
location: New Orleans, LA, United States
name: 'ICLR: International Conference on Learning Representations'
start_date: 2019-05-06
date_created: 2023-08-22T14:12:48Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T06:35:12Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02199'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02199
month: '06'
oa: 1
oa_version: Preprint
publication: International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: 'SOM-VAE: Interpretable discrete representation learning on time series'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '14203'
abstract:
- lang: eng
text: We propose a conditional gradient framework for a composite convex minimization
template with broad applications. Our approach combines smoothing and homotopy
techniques under the CGM framework, and provably achieves the optimal O(1/k−−√)
convergence rate. We demonstrate that the same rate holds if the linear subproblems
are solved approximately with additive or multiplicative error. In contrast with
the relevant work, we are able to characterize the convergence when the non-smooth
term is an indicator function. Specific applications of our framework include
the non-smooth minimization, semidefinite programming, and minimization with linear
inclusion constraints over a compact domain. Numerical evidence demonstrates the
benefits of our framework.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
- first_name: Olivier
full_name: Fercoq, Olivier
last_name: Fercoq
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework
for composite convex minimization with applications to semidefinite programming.
In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:5727-5736.'
apa: 'Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional
gradient framework for composite convex minimization with applications to semidefinite
programming. In Proceedings of the 35th International Conference on Machine
Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.'
chicago: Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher.
“A Conditional Gradient Framework for Composite Convex Minimization with Applications
to Semidefinite Programming.” In Proceedings of the 35th International Conference
on Machine Learning, 80:5727–36. ML Research Press, 2018.
ieee: A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming,” in Proceedings of the 35th International Conference on Machine
Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.
ista: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming. Proceedings of the 35th International Conference on Machine Learning.
ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.'
mla: Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex
Minimization with Applications to Semidefinite Programming.” Proceedings of
the 35th International Conference on Machine Learning, vol. 80, ML Research
Press, 2018, pp. 5727–36.
short: A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the
35th International Conference on Machine Learning, ML Research Press, 2018, pp.
5727–5736.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2023-08-22T14:16:01Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-13T08:13:39Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1804.08544'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.08544
month: '07'
oa: 1
oa_version: Preprint
page: 5727-5736
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A conditional gradient framework for composite convex minimization with applications
to semidefinite programming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '282'
abstract:
- lang: eng
text: Adaptive introgression is common in nature and can be driven by selection
acting on multiple, linked genes. We explore the effects of polygenic selection
on introgression under the infinitesimal model with linkage. This model assumes
that the introgressing block has an effectively infinite number of genes, each
with an infinitesimal effect on the trait under selection. The block is assumed
to introgress under directional selection within a native population that is genetically
homogeneous. We use individual-based simulations and a branching process approximation
to compute various statistics of the introgressing block, and explore how these
depend on parameters such as the map length and initial trait value associated
with the introgressing block, the genetic variability along the block, and the
strength of selection. Our results show that the introgression dynamics of a block
under infinitesimal selection is qualitatively different from the dynamics of
neutral introgression. We also find that in the long run, surviving descendant
blocks are likely to have intermediate lengths, and clarify how the length is
shaped by the interplay between linkage and infinitesimal selection. Our results
suggest that it may be difficult to distinguish introgression of single loci from
that of genomic blocks with multiple, tightly linked and weakly selected loci.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal
selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018
apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome
under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018
chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301018.
ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal
selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp.
1279–1303, 2018.
ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal
selection. Genetics. 209(4), 1279–1303.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society
of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.
short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T08:22:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301018
external_id:
isi:
- '000440014100020'
intvolume: ' 209'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/11/30/227082
month: '08'
oa: 1
oa_version: Submitted Version
page: 1279 - 1303
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7617'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introgression of a block of genome under infinitesimal selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '14204'
abstract:
- lang: eng
text: Two popular examples of first-order optimization methods over linear spaces
are coordinate descent and matching pursuit algorithms, with their randomized
variants. While the former targets the optimization by moving along coordinates,
the latter considers a generalized notion of directions. Exploiting the connection
between the two algorithms, we present a unified analysis of both, providing affine
invariant sublinear O(1/t) rates on smooth objectives and linear convergence on
strongly convex objectives. As a byproduct of our affine invariant analysis of
matching pursuit, our rates for steepest coordinate descent are the tightest known.
Furthermore, we show the first accelerated convergence rate O(1/t2) for matching
pursuit and steepest coordinate descent on convex objectives.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Anant
full_name: Raj, Anant
last_name: Raj
- first_name: Sai Praneeth
full_name: Karimireddy, Sai Praneeth
last_name: Karimireddy
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Sebastian U.
full_name: Stich, Sebastian U.
last_name: Stich
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate
descent. In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:3198-3207.'
apa: Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich,
S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In
Proceedings of the 35th International Conference on Machine Learning (Vol.
80, pp. 3198–3207). ML Research Press.
chicago: Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch,
Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit
and Coordinate Descent.” In Proceedings of the 35th International Conference
on Machine Learning, 80:3198–3207. ML Research Press, 2018.
ieee: F. Locatello et al., “On matching pursuit and coordinate descent,”
in Proceedings of the 35th International Conference on Machine Learning,
2018, vol. 80, pp. 3198–3207.
ista: Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi
M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International
Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.
mla: Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.”
Proceedings of the 35th International Conference on Machine Learning, vol.
80, ML Research Press, 2018, pp. 3198–207.
short: F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich,
M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning,
ML Research Press, 2018, pp. 3198–3207.
date_created: 2023-08-22T14:16:25Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-13T08:19:05Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1803.09539'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.09539
month: '07'
oa: 1
oa_version: Preprint
page: 3198-3207
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On matching pursuit and coordinate descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '160'
abstract:
- lang: eng
text: We present layered concurrent programs, a compact and expressive notation
for specifying refinement proofs of concurrent programs. A layered concurrent
program specifies a sequence of connected concurrent programs, from most concrete
to most abstract, such that common parts of different programs are written exactly
once. These programs are expressed in the ordinary syntax of imperative concurrent
programs using gated atomic actions, sequencing, choice, and (recursive) procedure
calls. Each concurrent program is automatically extracted from the layered program.
We reduce refinement to the safety of a sequence of concurrent checker programs,
one each to justify the connection between every two consecutive concurrent programs.
These checker programs are also automatically extracted from the layered program.
Layered concurrent programs have been implemented in the CIVL verifier which has
been successfully used for the verification of several complex concurrent programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: 'Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102.
doi:10.1007/978-3-319-96145-3_5'
apa: 'Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981,
pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer.
https://doi.org/10.1007/978-3-319-96145-3_5'
chicago: Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102.
Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.
ieee: 'B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV:
Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.'
ista: 'Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided
Verification, LNCS, vol. 10981, 79–102.'
mla: Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol.
10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.
short: B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.
conference:
end_date: 2018-07-17
location: Oxford, UK
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-13T08:45:09Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_5
external_id:
isi:
- '000491481600005'
file:
- access_level: open_access
checksum: c64fff560fe5a7532ec10626ad1c215e
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:52:12Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5705'
file_name: 2018_LNCS_Kragl.pdf
file_size: 1603844
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 102
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '7761'
quality_controlled: '1'
related_material:
record:
- id: '8332'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Layered Concurrent Programs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '280'
abstract:
- lang: eng
text: Flowers have a species-specific functional life span that determines the time
window in which pollination, fertilization and seed set can occur. The stigma
tissue plays a key role in flower receptivity by intercepting pollen and initiating
pollen tube growth toward the ovary. In this article, we show that a developmentally
controlled cell death programme terminates the functional life span of stigma
cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also
known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074)
as partially redundant transcription factors that modulate stigma longevity by
controlling the expression of programmed cell death-associated genes. KIRA1 expression
is sufficient to induce cell death and terminate floral receptivity, whereas lack
of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly,
the extension of stigma longevity is accompanied by only a moderate extension
of flower receptivity, suggesting that additional processes participate in the
control of the flower's receptive life span.
acknowledgement: We gratefully acknowledge funding from the Chinese Scholarship Council
(CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek
(FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the
Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation
by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.),
the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH
(project number 639234 to M.K.N.).
article_processing_charge: No
author:
- first_name: Zhen
full_name: Gao, Zhen
last_name: Gao
- first_name: Anna
full_name: Daneva, Anna
last_name: Daneva
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Zongcheng
full_name: Lin, Zongcheng
last_name: Lin
- first_name: Freya
full_name: De Winter, Freya
last_name: De Winter
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Jan
full_name: Van De Velde, Jan
last_name: Van De Velde
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Davy
full_name: Van De Walle, Davy
last_name: Van De Walle
- first_name: Koen
full_name: Dewettinck, Koen
last_name: Dewettinck
- first_name: Bart
full_name: Lambrecht, Bart
last_name: Lambrecht
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375.
doi:10.1038/s41477-018-0160-7
apa: Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., …
Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting
cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing
Group. https://doi.org/10.1038/s41477-018-0160-7
chicago: Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans,
Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity
by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.
ieee: Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by
promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol.
4, no. 6. Nature Publishing Group, pp. 365–375, 2018.
ista: Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F,
Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck
K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.
mla: Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting
Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6,
Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.
short: Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De
Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle,
K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-28T00:00:00Z
date_updated: 2023-09-13T08:24:17Z
day: '28'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0160-7
external_id:
isi:
- '000435571000017'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 365 - 375
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7619'
quality_controlled: '1'
scopus_import: '1'
status: public
title: KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in
the stigma of Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '503'
abstract:
- lang: eng
text: Buffers are essential for diluting bacterial cultures for flow cytometry analysis
in order to study bacterial physiology and gene expression parameters based on
fluorescence signals. Using a variety of constitutively expressed fluorescent
proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes
in fluorescence levels after dilution into the commonly used flow cytometry buffer
phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9
salts. These changes appeared very rapidly after dilution, and were linked to
increased membrane permeability and loss in cell viability. We observed buffer-related
effects in several different E. coli strains, K-12, C and W, but not E. coli B,
which can be partially explained by differences in lipopolysaccharide (LPS) and
outer membrane composition. Supplementing the buffers with divalent cations responsible
for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane
integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane
is essential for precise and unbiased measurements of fluorescence parameters
using flow cytometry.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1
and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all
members of the Guet lab for critically reading the manuscript. We also thank the
Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n"
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers
affect fluorescence signals by reducing membrane stability and viability of Escherichia
coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008
apa: Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow
cytometry buffers affect fluorescence signals by reducing membrane stability and
viability of Escherichia coli strains. Journal of Biotechnology. Elsevier.
https://doi.org/10.1016/j.jbiotec.2018.01.008
chicago: Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations
in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability
and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier,
2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.
ieee: K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry
buffers affect fluorescence signals by reducing membrane stability and viability
of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier,
pp. 40–52, 2018.
ista: Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry
buffers affect fluorescence signals by reducing membrane stability and viability
of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.
mla: Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect
Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia
Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp.
40–52, doi:10.1016/j.jbiotec.2018.01.008.
short: K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018)
40–52.
date_created: 2018-12-11T11:46:50Z
date_published: 2018-02-20T00:00:00Z
date_updated: 2023-09-13T08:24:51Z
day: '20'
department:
- _id: CaGu
doi: 10.1016/j.jbiotec.2018.01.008
external_id:
isi:
- '000425715100006'
intvolume: ' 268'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 40 - 52
publication: Journal of Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '7317'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lack of cations in flow cytometry buffers affect fluorescence signals by reducing
membrane stability and viability of Escherichia coli strains
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 268
year: '2018'
...
---
_id: '82'
abstract:
- lang: eng
text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage,
bacterial cells resistant to the phage commonly emerge and become the dominant
population of bacteria. Following the ascent of resistant mutants, the densities
of bacteria in these simple communities become limited by resources rather than
the phage. Despite the evolution of resistant hosts, upon which the phage cannot
replicate, the lytic phage population is most commonly maintained in an apparently
stable state with the resistant bacteria. Several mechanisms have been put forward
to account for this result. Here we report the results of population dynamic/evolution
experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli
in serial transfer cultures. We show that, following the ascent of λVIR-resistant
bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal
media and in all cases in nutrient-rich broth. Using mathematical models and experiments,
we show that the dominant mechanism responsible for maintenance of λVIRin these
resource-limited populations dominated by resistant E. coli is a high rate of
either phenotypic or genetic transition from resistance to susceptibility—a hitherto
undemonstrated mechanism we term "leaky resistance." We discuss the
implications of leaky resistance to our understanding of the conditions for the
maintenance of phage in populations of bacteria—their “existence conditions.”.
article_number: '2005971'
article_processing_charge: Yes
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for
the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance
and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence
of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of
Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Leaky resistance and the conditions for the existence of lytic
bacteriophage. PLoS Biology. 16(8), 2005971.
mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence
of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public
Library of Science, 2018, doi:10.1371/journal.pbio.2005971.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:44:32Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971
external_id:
isi:
- '000443383300024'
file:
- access_level: open_access
checksum: 527076f78265cd4ea192cd1569851587
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:55:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5706'
file_name: 2018_Plos_Chaudhry.pdf
file_size: 4007095
relation: main_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7972'
quality_controlled: '1'
related_material:
record:
- id: '9810'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Leaky resistance and the conditions for the existence of lytic bacteriophage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '4'
abstract:
- lang: eng
text: We present a data-driven technique to instantly predict how fluid flows around
various three-dimensional objects. Such simulation is useful for computational
fabrication and engineering, but is usually computationally expensive since it
requires solving the Navier-Stokes equation for many time steps. To accelerate
the process, we propose a machine learning framework which predicts aerodynamic
forces and velocity and pressure fields given a threedimensional shape input.
Handling detailed free-form three-dimensional shapes in a data-driven framework
is challenging because machine learning approaches usually require a consistent
parametrization of input and output. We present a novel PolyCube maps-based parametrization
that can be computed for three-dimensional shapes at interactive rates. This allows
us to efficiently learn the nonlinear response of the flow using a Gaussian process
regression. We demonstrate the effectiveness of our approach for the interactive
design and optimization of a car body.
article_number: '89'
article_processing_charge: No
author:
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic
design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325
apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325
chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for
Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.
ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive
aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.
ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. 37(4), 89.
mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive
Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018,
doi:10.1145/3197517.3201325.
short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:06Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:46:15Z
day: '04'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201325
ec_funded: 1
external_id:
isi:
- '000448185000050'
file:
- access_level: open_access
checksum: 7a2243668f215821bc6aecad0320079a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5216'
file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf
file_size: 22803163
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8053'
pubrep_id: '1049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/
scopus_import: '1'
status: public
title: Learning three-dimensional flow for interactive aerodynamic design
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...