---
_id: '1024'
abstract:
- lang: eng
text: The history of auxin and cytokinin biology including the initial discoveries
by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt
(1919) is a beautiful demonstration of unceasing continuity of research. Novel
findings are integrated into existing hypotheses and models and deepen our understanding
of biological principles. At the same time new questions are triggered and hand
to hand with this new methodologies are developed to address these new challenges.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Benková E. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1
apa: Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin
biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1
chicago: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.
ieee: A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,”
Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29,
2017.
ista: Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 1569, 1–29.
mla: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer,
2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.
short: A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017)
1–29.
corr_author: '1'
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2026-10-20T22:31:07Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2019-10-15T07:47:05Z
file_id: '5068'
file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
file_size: 840646
relation: main_file
file_date_updated: 2019-10-15T07:47:05Z
fulldoi: https://doi.org/10.1007/978-1-4939-6831-2_1
has_accepted_license: '1'
intvolume: ' 1569'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 29
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Auxins and Cytokinins in Plant Biology
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6369'
pubrep_id: '1019'
quality_controlled: '1'
related_material:
record:
- id: '539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Methodological advances in auxin and cytokinin biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1569
year: '2017'
...
---
_id: '1028'
abstract:
- lang: eng
text: Optogenetics and photopharmacology provide spatiotemporally precise control
over protein interactions and protein function in cells and animals. Optogenetic
methods that are sensitive to green light and can be used to break protein complexes
are not broadly available but would enable multichromatic experiments with previously
inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12)
binding domains of bacterial CarH transcription factors for green-light-induced
receptor dissociation. In cultured cells, we observed oligomerization-induced
cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding
domains in the dark that was rapidly eliminated upon illumination. In zebrafish
embryos expressing fusion receptors, green light endowed control over aberrant
fibroblast growth factor signaling during development. Green-light-induced domain
dissociation and light-inactivated receptors will critically expand the optogenetic
toolbox for control of biological processes.
acknowledgement: "This work was supported by a grant from the European Union\U0010FC1Ds
Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program
MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship
(Austrian Research Promotion Agency, 3580812)"
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
orcid: 0000-0002-6709-2195
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- 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: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced
inactivation of receptor signaling using cobalamin-binding domains. Angewandte
Chemie International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition.
Wiley, 2017. https://doi.org/10.1002/anie.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains,” Angewandte Chemie International Edition, vol. 56, no. 16. Wiley,
pp. 4608–4611, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie International Edition. 56(16), 4608–4611.
mla: Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition,
vol. 56, no. 16, Wiley, 2017, pp. 4608–11, doi:10.1002/anie.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie International Edition 56 (2017) 4608–4611.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2026-10-20T22:31:08Z
day: '20'
ddc:
- '540'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/anie.201611998
ec_funded: 1
external_id:
isi:
- '000398154000038'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:39:55Z
date_updated: 2019-01-18T09:39:55Z
file_id: '5845'
file_name: 2017_communications_Kainrath.pdf
file_size: 2614942
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:39:55Z
fulldoi: https://doi.org/10.1002/anie.201611998
has_accepted_license: '1'
intvolume: ' 56'
isi: 1
issue: '16'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 4608-4611
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
publist_id: '6362'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
- id: '7680'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '1082'
abstract:
- lang: eng
text: In many applications, it is desirable to extract only the relevant aspects
of data. A principled way to do this is the information bottleneck (IB) method,
where one seeks a code that maximises information about a relevance variable,
Y, while constraining the information encoded about the original data, X. Unfortunately
however, the IB method is computationally demanding when data are high-dimensional
and/or non-gaussian. Here we propose an approximate variational scheme for maximising
a lower bound on the IB objective, analogous to variational EM. Using this method,
we derive an IB algorithm to recover features that are both relevant and sparse.
Finally, we demonstrate how kernelised versions of the algorithm can be used to
address a broad range of problems with non-linear relation between X and Y.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
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. Relevant sparse codes with variational information
bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.'
apa: 'Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with
variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the
NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information
Processing Systems Foundation.'
chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes
with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing
Systems Foundation, 2016.
ieee: 'M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational
information bottleneck,” presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.'
ista: 'Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational
information bottleneck. NIPS: Neural Information Processing Systems, Advances
in Neural Information Processing Systems, vol. 29, 1965–1973.'
mla: Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information
Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016,
pp. 1965–73.
short: M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems
Foundation, 2016, pp. 1965–1973.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:03Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-06-03T11:33:51Z
day: '01'
department:
- _id: GaTk
external_id:
arxiv:
- '1605.07332'
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.07332
month: '12'
oa: 1
oa_version: Preprint
page: 1965-1973
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6298'
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck
scopus_import: '1'
status: public
title: Relevant sparse codes with variational information bottleneck
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1083'
abstract:
- lang: eng
text: ' Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent
inhibition in cortical circuits and themselves receive strong GABAergic input.
However, it remains unclear to what extent GABABreceptors (GABABRs) contribute
to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs
in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary
proteins, whereas postsynaptic effector Kir3 channels were present at lower levels.
Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic
currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs
in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable,
suggesting that the expression of Kir3 channels is the limiting factor for the
GABABR currents in these INs. Morphological analysis showed that CCK-INs were
diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting
(DT) interneurons, including a previously undescribed DT type. GABABR-mediated
IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged
activation, GABABR-mediated currents displayed strong desensitization, which was
absent in KCTD12-deficient mice. This study highlights that GABABRs differentially
control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated
currents are modulated by KCTD12 proteins. '
acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft (DFG
SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann
Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation
(3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland
(I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions
to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider,
Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus
transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi
in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus
provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided
by Dr G.V. Ohning, CURE Center, UCLA, CA. "
article_processing_charge: No
author:
- first_name: Sam
full_name: Booker, Sam
last_name: Booker
- first_name: Daniel
full_name: Althof, Daniel
last_name: Althof
- first_name: Anna
full_name: Gross, Anna
last_name: Gross
- first_name: Desiree
full_name: Loreth, Desiree
last_name: Loreth
- first_name: Johanna
full_name: Müller, Johanna
last_name: Müller
- first_name: Andreas
full_name: Unger, Andreas
last_name: Unger
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
- first_name: Andrea
full_name: Varro, Andrea
last_name: Varro
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
citation:
ama: Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics
of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons.
Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090
apa: Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik,
Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated
inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex.
Oxford University Press. https://doi.org/10.1093/cercor/bhw090
chicago: Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller,
Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics
of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.”
Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090.
ieee: S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB
receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral
Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.
ista: Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro
A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12
auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in
Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.
mla: Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated
Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex,
vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.
short: S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler,
A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik,
Cerebral Cortex 27 (2016) 2318–2334.
date_created: 2018-12-11T11:50:03Z
date_published: 2016-04-12T00:00:00Z
date_updated: 2025-09-22T14:19:11Z
day: '12'
department:
- _id: RySh
doi: 10.1093/cercor/bhw090
external_id:
isi:
- '000397636600048'
fulldoi: https://doi.org/10.1093/cercor/bhw090
intvolume: ' 27'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
page: 2318 - 2334
publication: Cerebral Cortex
publication_status: published
publisher: Oxford University Press
publist_id: '6297'
quality_controlled: '1'
scopus_import: '1'
status: public
title: KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition
in Cholecystokinin-containing interneurons
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2016'
...
---
_id: '1088'
abstract:
- lang: eng
text: Cell geometry is tightly coupled to gene expression patterns within the tissue
microenvironment. This perspective synthesizes evidence that the 3D organization
of chromosomes is a critical intermediate for geometric control of genomic programs.
Using a combination of experiments and modeling we outline approaches to decipher
the mechano-genomic code that governs cellular homeostasis and reprogramming.
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: G V
full_name: Shivashankar, G V
last_name: Shivashankar
citation:
ama: Uhler C, Shivashankar GV. Geometric control and modeling of genome reprogramming.
BioArchitecture. 2016;6(4):76-84. doi:10.1080/19490992.2016.1201620
apa: Uhler, C., & Shivashankar, G. V. (2016). Geometric control and modeling
of genome reprogramming. BioArchitecture. Taylor & Francis. https://doi.org/10.1080/19490992.2016.1201620
chicago: Uhler, Caroline, and G V Shivashankar. “Geometric Control and Modeling
of Genome Reprogramming.” BioArchitecture. Taylor & Francis, 2016.
https://doi.org/10.1080/19490992.2016.1201620.
ieee: C. Uhler and G. V. Shivashankar, “Geometric control and modeling of genome
reprogramming,” BioArchitecture, vol. 6, no. 4. Taylor & Francis, pp.
76–84, 2016.
ista: Uhler C, Shivashankar GV. 2016. Geometric control and modeling of genome reprogramming.
BioArchitecture. 6(4), 76–84.
mla: Uhler, Caroline, and G. V. Shivashankar. “Geometric Control and Modeling of
Genome Reprogramming.” BioArchitecture, vol. 6, no. 4, Taylor & Francis,
2016, pp. 76–84, doi:10.1080/19490992.2016.1201620.
short: C. Uhler, G.V. Shivashankar, BioArchitecture 6 (2016) 76–84.
date_created: 2018-12-11T11:50:05Z
date_published: 2016-07-27T00:00:00Z
date_updated: 2021-01-12T06:48:11Z
day: '27'
doi: 10.1080/19490992.2016.1201620
extern: '1'
fulldoi: https://doi.org/10.1080/19490992.2016.1201620
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
page: 76 - 84
publication: BioArchitecture
publication_status: published
publisher: Taylor & Francis
publist_id: '6289'
quality_controlled: '1'
status: public
title: Geometric control and modeling of genome reprogramming
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1090'
abstract:
- lang: eng
text: ' While weighted automata provide a natural framework to express quantitative
properties, many basic properties like average response time cannot be expressed
with weighted automata. Nested weighted automata extend weighted automata and
consist of a master automaton and a set of slave automata that are invoked by
the master automaton. Nested weighted automata are strictly more expressive than
weighted automata (e.g., average response time can be expressed with nested weighted
automata), but the basic decision questions have higher complexity (e.g., for
deterministic automata, the emptiness question for nested weighted automata is
PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME).
We consider a natural subclass of nested weighted automata where at any point
at most a bounded number k of slave automata can be active. We focus on automata
whose master value function is the limit average. We show that these nested weighted
automata with bounded width are strictly more expressive than weighted automata
(e.g., average response time with no overlapping requests can be expressed with
bound k=1, but not with non-nested weighted automata). We show that the complexity
of the basic decision problems (i.e., emptiness and universality) for the subclass
with k constant matches the complexity for weighted automata. Moreover, when k
is part of the input given in unary we establish PSPACE-completeness.'
acknowledgement: "This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award),
ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF)
through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under
grant 2014/15/D/ST6/04543."
alternative_title:
- LIPIcs
article_number: '24'
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata
of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2016. doi:10.4230/LIPIcs.MFCS.2016.24'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average
automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations
of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2016.24'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.
ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average
automata of bounded width,” presented at the MFCS: Mathematical Foundations of
Computer Science, Krakow; Poland, 2016, vol. 58.'
ista: 'Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata
of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs,
vol. 58, 24.'
mla: Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of
Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016, doi:10.4230/LIPIcs.MFCS.2016.24.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Krakow; Poland
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2016-08-22
date_created: 2018-12-11T11:50:05Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-07-10T11:50:02Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2016.24
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:31Z
date_updated: 2018-12-12T10:17:31Z
file_id: '5286'
file_name: IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf
file_size: 564560
relation: main_file
file_date_updated: 2018-12-12T10:17:31Z
fulldoi: https://doi.org/10.4230/LIPIcs.MFCS.2016.24
has_accepted_license: '1'
intvolume: ' 58'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
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: Formal methods for the design and analysis of complex systems
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6286'
pubrep_id: '795'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nested weighted limit-average automata of bounded width
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2016'
...
---
_id: '1093'
abstract:
- lang: eng
text: 'We introduce a general class of distances (metrics) between Markov chains,
which are based on linear behaviour. This class encompasses distances given topologically
(such as the total variation distance or trace distance) as well as by temporal
logics or automata. We investigate which of the distances can be approximated
by observing the systems, i.e. by black-box testing or simulation, and we provide
both negative and positive results. '
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF)
under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award),
by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced
Postdoc. Mobility Fellowship – grant number P300P2_161067."
alternative_title:
- LIPIcs
article_number: '20'
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- 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: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov
chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20'
apa: 'Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear
distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency
Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2016.20'
chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov.
“Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.
ieee: 'P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances
between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City;
Canada, 2016, vol. 59.'
ista: 'Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between
Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.'
mla: Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol.
59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.
short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
- _id: CaGu
doi: 10.4230/LIPIcs.CONCUR.2016.20
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:39Z
date_updated: 2018-12-12T10:11:39Z
file_id: '4895'
file_name: IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf
file_size: 501827
relation: main_file
file_date_updated: 2018-12-12T10:11:39Z
fulldoi: https://doi.org/10.4230/LIPIcs.CONCUR.2016.20
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6283'
pubrep_id: '794'
quality_controlled: '1'
related_material:
record:
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Linear distances between Markov chains
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1094'
abstract:
- lang: eng
text: Immunogold labeling of freeze-fracture replicas has recently been used for
high-resolution visualization of protein localization in electron microscopy.
This method has higher labeling efficiency than conventional immunogold methods
for membrane molecules allowing precise quantitative measurements. However, one
of the limitations of freeze-fracture replica immunolabeling is difficulty in
keeping structural orientation and identifying labeled profiles in complex tissues
like brain. The difficulty is partly due to fragmentation of freeze-fracture replica
preparations during labeling procedures and limited morphological clues on the
replica surface. To overcome these issues, we introduce here a grid-glued replica
method combined with SEM observation. This method allows histological staining
before dissolving the tissue and easy handling of replicas during immunogold labeling,
and keeps the whole replica surface intact without fragmentation. The procedure
described here is also useful for matched double-replica analysis allowing further
identification of labeled profiles in corresponding P-face and E-face.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body
used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron
microscope imaging. This work was supported by the European Union (HBP—Project Ref.
604102). '
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture
replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer;
2016:203-216. doi:10.1007/978-1-4939-6352-2_12'
apa: Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on
grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular
Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12
chicago: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization
on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular
Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.
ieee: H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued
freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–216.
ista: 'Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued
freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods
in Molecular Biology, vol. 1474, 203–216.'
mla: Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on
Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins,
vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.
short: H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins,
Springer, 2016, pp. 203–216.
date_created: 2018-12-11T11:50:06Z
date_published: 2016-08-12T00:00:00Z
date_updated: 2025-04-15T07:12:21Z
day: '12'
department:
- _id: RySh
doi: 10.1007/978-1-4939-6352-2_12
ec_funded: 1
fulldoi: https://doi.org/10.1007/978-1-4939-6352-2_12
intvolume: ' 1474'
language:
- iso: eng
month: '08'
oa_version: None
page: 203 - 216
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
publication: High-Resolution Imaging of Cellular Proteins
publication_identifier:
eissn:
- 1611-3349
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6281'
quality_controlled: '1'
status: public
title: Immunogold protein localization on grid-glued freeze-fracture replicas
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1474
year: '2016'
...
---
_id: '1095'
abstract:
- lang: eng
text: ' The semantics of concurrent data structures is usually given by a sequential
specification and a consistency condition. Linearizability is the most popular
consistency condition due to its simplicity and general applicability. Nevertheless,
for applications that do not require all guarantees offered by linearizability,
recent research has focused on improving performance and scalability of concurrent
data structures by relaxing their semantics. In this paper, we present local linearizability,
a relaxed consistency condition that is applicable to container-type concurrent
data structures like pools, queues, and stacks. While linearizability requires
that the effect of each operation is observed by all threads at the same time,
local linearizability only requires that for each thread T, the effects of its
local insertion operations and the effects of those removal operations that remove
values inserted by T are observed by all threads at the same time. We investigate
theoretical and practical properties of local linearizability and its relationship
to many existing consistency conditions. We present a generic implementation method
for locally linearizable data structures that uses existing linearizable data
structures as building blocks. Our implementations show performance and scalability
improvements over the original building blocks and outperform the fastest existing
container-type implementations. '
acknowledgement: "This work has been supported by the National Research Network RiSE
on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23,
S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship
(Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1,
the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European
Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award)."
alternative_title:
- LIPIcs
article_number: '6'
author:
- first_name: Andreas
full_name: Haas, Andreas
last_name: Haas
- 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: Andreas
full_name: Holzer, Andreas
last_name: Holzer
- first_name: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Michael
full_name: Lippautz, Michael
last_name: Lippautz
- first_name: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
citation:
ama: 'Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent
container-type data structures. In: Leibniz International Proceedings in Informatics.
Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6'
apa: 'Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H.,
… Veith, H. (2016). Local linearizability for concurrent container-type data structures.
In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City;
Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6'
chicago: Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael
Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability
for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings
in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.
ieee: A. Haas et al., “Local linearizability for concurrent container-type
data structures,” in Leibniz International Proceedings in Informatics,
Quebec City; Canada, 2016, vol. 59.
ista: 'Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A,
Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type
data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency
Theory, LIPIcs, vol. 59, 6.'
mla: Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type
Data Structures.” Leibniz International Proceedings in Informatics, vol.
59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6.
short: A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A.
Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.
conference:
end_date: 2016-08-26
location: Quebec City; Canada
name: 'CONCUR: Concurrency Theory'
start_date: 2016-08-23
date_created: 2018-12-11T11:50:07Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-04-15T06:25:58Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2016.6
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:10Z
date_updated: 2018-12-12T10:10:10Z
file_id: '4795'
file_name: IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf
file_size: 589747
relation: main_file
file_date_updated: 2018-12-12T10:10:10Z
fulldoi: https://doi.org/10.4230/LIPIcs.CONCUR.2016.6
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Leibniz International Proceedings in Informatics
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6280'
pubrep_id: '793'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local linearizability for concurrent container-type data structures
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2016'
...
---
_id: '1096'
article_processing_charge: No
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings
of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024
apa: Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P.
J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024
chicago: Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and
Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024.
ieee: C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg,
“Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press,
pp. 493–506, 2016.
ista: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin
rings of power. Developmental Cell. 37(6), 493–506.
mla: Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell,
vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.
short: C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental
Cell 37 (2016) 493–506.
date_created: 2018-12-11T11:50:07Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2026-04-08T13:55:28Z
day: '20'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2016.05.024
external_id:
isi:
- '000378204200005'
fulldoi: https://doi.org/10.1016/j.devcel.2016.05.024
intvolume: ' 37'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 493 - 506
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6279'
quality_controlled: '1'
related_material:
record:
- id: '7186'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Actin rings of power
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2016'
...
---
_id: '1097'
abstract:
- lang: eng
text: We present an interactive system for computational design, optimization, and
fabrication of multicopters. Our computational approach allows non-experts to
design, explore, and evaluate a wide range of different multicopters. We provide
users with an intuitive interface for assembling a multicopter from a collection
of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm
interactively optimizes shape and controller parameters of the current design
to ensure its proper operation. In addition, we allow incorporating a variety
of other metrics (such as payload, battery usage, size, and cost) into the design
process and exploring tradeoffs between them. We show the efficacy of our method
and system by designing, optimizing, fabricating, and operating multicopters with
complex geometries and propeller configurations. We also demonstrate the ability
of our optimization algorithm to improve the multicopter performance under different
metrics.
acknowledgement: "We thank Nobuyuki Umetani for his insightful suggestions in our
discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter
and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard
Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing
mechanical parts and providing 3D printing technical support; Charles Blouin from
RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition
UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael
Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis
work was partially supported by Air Force Research Laboratory’s sponsorship of Julia:
A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2-
0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967,
MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors.
This project has also received funding from the European Union’s Horizon 2020 research
and innovation program under grant agreement No 645599. "
alternative_title:
- ACM Transactions on Graphics
article_number: '227'
article_processing_charge: No
author:
- first_name: Tao
full_name: Du, Tao
last_name: Du
- first_name: Adriana
full_name: Schulz, Adriana
last_name: Schulz
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
citation:
ama: 'Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design.
In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427'
apa: 'Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational
multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition
on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427'
chicago: Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational
Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.
ieee: 'T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter
design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer
Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no.
6.'
ista: 'Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter
design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.'
mla: Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227,
ACM, 2016, doi:10.1145/2980179.2982427.
short: T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.
conference:
end_date: 2016-12-08
location: Macao, China
name: 'SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:07Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T14:17:29Z
day: '01'
ddc:
- '006'
department:
- _id: BeBi
doi: 10.1145/2980179.2982427
ec_funded: 1
external_id:
isi:
- '000388446200069'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:42Z
date_updated: 2018-12-12T10:17:42Z
file_id: '5298'
file_name: IST-2017-759-v1+1_copter.pdf
file_size: 33114420
relation: main_file
file_date_updated: 2018-12-12T10:17:42Z
fulldoi: https://doi.org/10.1145/2980179.2982427
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
publication_status: published
publisher: ACM
publist_id: '6278'
pubrep_id: '759'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational multicopter design
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2016'
...
---
_id: '1098'
abstract:
- lang: eng
text: Better understanding of the potential benefits of information transfer and
representation learning is an important step towards the goal of building intelligent
systems that are able to persist in the world and learn over time. In this work,
we consider a setting where the learner encounters a stream of tasks but is able
to retain only limited information from each encountered task, such as a learned
predictor. In contrast to most previous works analyzing this scenario, we do not
make any distributional assumptions on the task generating process. Instead, we
formulate a complexity measure that captures the diversity of the observed tasks.
We provide a lifelong learning algorithm with error guarantees for every observed
task (rather than on average). We show sample complexity reductions in comparison
to solving every task in isolation in terms of our task complexity measure. Further,
our algorithmic framework can naturally be viewed as learning a representation
from encountered tasks with a neural network.
acknowledgement: "This work was in parts funded by the European Research Council under
the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement
no 308036.\r\n\r\n"
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Ruth
full_name: Urner, Ruth
last_name: Urner
citation:
ama: 'Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol
29. Neural Information Processing Systems Foundation; 2016:3619-3627.'
apa: 'Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority
votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing
Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.'
chicago: Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority
Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.
ieee: 'A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,”
presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain,
2016, vol. 29, pp. 3619–3627.'
ista: 'Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes.
NIPS: Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 29, 3619–3627.'
mla: Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority
Votes. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp.
3619–27.
short: A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation,
2016, pp. 3619–3627.
conference:
end_date: 2016-12-10
location: Barcelona, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:08Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-06-03T11:35:58Z
day: '01'
ddc:
- '006'
department:
- _id: ChLa
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:42Z
date_updated: 2018-12-12T10:12:42Z
file_id: '4961'
file_name: IST-2017-775-v1+1_main.pdf
file_size: 237111
relation: main_file
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:43Z
date_updated: 2018-12-12T10:12:43Z
file_id: '4962'
file_name: IST-2017-775-v1+2_supplementary.pdf
file_size: 185818
relation: main_file
file_date_updated: 2018-12-12T10:12:43Z
has_accepted_license: '1'
intvolume: ' 29'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 3619-3627
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6277'
pubrep_id: '775'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lifelong learning with weighted majority votes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '1099'
abstract:
- lang: eng
text: We present FlexMolds, a novel computational approach to automatically design
flexible, reusable molds that, once 3D printed, allow us to physically fabricate,
by means of liquid casting, multiple copies of complex shapes with rich surface
details and complex topology. The approach to design such flexible molds is based
on a greedy bottom-up search of possible cuts over an object, evaluating for each
possible cut the feasibility of the resulting mold. We use a dynamic simulation
approach to evaluate candidate molds, providing a heuristic to generate forces
that are able to open, detach, and remove a complex mold from the object it surrounds.
We have tested the approach with a number of objects with nontrivial shapes and
topologies.
acknowledgement: "The armadillo, bunny and dragon models are courtesy of the Stanford
\ 3D Scanning Repository. The bimba, fertility and elephant models are courtesy
of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the
European Union’s Horizon 2020 research and innovation programme under grant
\ agreement\r\nNo. 645599."
alternative_title:
- ACM Transactions on Graphics
article_number: '223'
article_processing_charge: No
author:
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of
flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397'
apa: 'Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds:
Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH
Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques
in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397'
chicago: 'Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds:
Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.'
ieee: 'L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic
design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference
and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao,
China, 2016, vol. 35, no. 6.'
ista: 'Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design
of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer
Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol.
35, 223.'
mla: 'Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for
Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397.'
short: L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.
conference:
end_date: 2016-12-08
location: Macao, China
name: 'SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive
Techniques in Asia'
start_date: 2016-12-05
date_created: 2018-12-11T11:50:08Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-22T14:16:02Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: BeBi
doi: 10.1145/2980179.2982397
ec_funded: 1
external_id:
isi:
- '000388446200065'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2018-12-12T10:12:01Z
file_id: '4918'
file_name: IST-2017-760-v1+1_flexmolds.pdf
file_size: 11122029
relation: main_file
file_date_updated: 2018-12-12T10:12:01Z
fulldoi: https://doi.org/10.1145/2980179.2982397
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 25082902-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '645599'
name: Soft-bodied intelligence for Manipulation
publication_status: published
publisher: ACM
publist_id: '6276'
pubrep_id: '760'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FlexMolds: Automatic design of flexible shells for molding'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2016'
...
---
_id: '1101'
abstract:
- lang: eng
text: Optical sensors based on the phenomenon of Förster resonance energy transfer
(FRET) are powerful tools that have advanced the study of small molecules in biological
systems. However, sensor construction is not trivial and often requires multiple
rounds of engineering or an ability to screen large numbers of variants. A method
that would allow the accurate rational design of FRET sensors would expedite the
production of biologically useful sensors. Here, we present Rangefinder, a computational
algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding
protein for the conjugation of a dye molecule to act as a Förster acceptor for
a fused fluorescent protein. We present three ratiometric fluorescent sensors
designed with Rangefinder, including a maltose sensor with a dynamic range of
>300% and the first sensors for the most abundant sialic acid in human cells,
N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation
that this model will facilitate the design of an optical sensor for any small
molecule of interest.
acknowledgement: "J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate
Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships.
C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator
Award and a Discovery Project and Future\r\nFellowship from the Australian Research
Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153)
and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure."
article_processing_charge: No
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET
sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576'
apa: 'Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L.,
O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor
design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576'
chicago: 'Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger,
Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic
FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society,
2016. https://doi.org/10.1021/acssensors.6b00576.'
ieee: 'J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design
algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp.
1286–1290, 2016.'
ista: 'Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS.
1(11), 1286–1290.'
mla: 'Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design
Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016,
pp. 1286–90, doi:10.1021/acssensors.6b00576.'
short: J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, ACS SENSORS 1 (2016) 1286–1290.
date_created: 2018-12-11T11:50:09Z
date_published: 2016-11-10T00:00:00Z
date_updated: 2025-09-22T14:14:58Z
day: '10'
department:
- _id: HaJa
doi: 10.1021/acssensors.6b00576
external_id:
isi:
- '000388914800003'
fulldoi: https://doi.org/10.1021/acssensors.6b00576
intvolume: ' 1'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1286 - 1290
publication: ACS SENSORS
publication_status: published
publisher: American Chemical Society
publist_id: '6274'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rangefinder: A semisynthetic FRET sensor design algorithm'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1
year: '2016'
...
---
_id: '1102'
abstract:
- lang: eng
text: Weakly-supervised object localization methods tend to fail for object classes
that consistently co-occur with the same background elements, e.g. trains on tracks.
We propose a method to overcome these failures by adding a very small amount of
model-specific additional annotation. The main idea is to cluster a deep network\'s
mid-level representations and assign object or distractor labels to each cluster.
Experiments show substantially improved localization results on the challenging
ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for
semantic segmentation.
acknowledgement: "This work was funded in parts by the European Research Council\r\nunder
the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement
no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe
donation of the GPUs used for this research."
article_processing_charge: No
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. Improving weakly-supervised object localization by
micro-annotation. In: Proceedings of the British Machine Vision Conference
2016. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:10.5244/C.30.92'
apa: 'Kolesnikov, A., & Lampert, C. (2016). Improving weakly-supervised object
localization by micro-annotation. In Proceedings of the British Machine Vision
Conference 2016 (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom:
BMVA Press. https://doi.org/10.5244/C.30.92'
chicago: Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised
Object Localization by Micro-Annotation.” In Proceedings of the British Machine
Vision Conference 2016, 2016–September:92.1-92.12. BMVA Press, 2016. https://doi.org/10.5244/C.30.92.
ieee: A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization
by micro-annotation,” in Proceedings of the British Machine Vision Conference
2016, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.
ista: 'Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization
by micro-annotation. Proceedings of the British Machine Vision Conference 2016.
BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.'
mla: Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised
Object Localization by Micro-Annotation.” Proceedings of the British Machine
Vision Conference 2016, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12,
doi:10.5244/C.30.92.
short: A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision
Conference 2016, BMVA Press, 2016, p. 92.1-92.12.
conference:
end_date: 2016-09-22
location: York, United Kingdom
name: 'BMVC: British Machine Vision Conference'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:09Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2026-06-18T10:46:30Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.5244/C.30.92
ec_funded: 1
fulldoi: https://doi.org/10.5244/C.30.92
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf
month: '09'
oa: 1
oa_version: Published Version
page: 92.1-92.12
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the British Machine Vision Conference 2016
publication_status: published
publisher: BMVA Press
publist_id: '6273'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improving weakly-supervised object localization by micro-annotation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-September
year: '2016'
...
---
_id: '1103'
abstract:
- lang: eng
text: We propose two parallel state-space-exploration algorithms for hybrid automaton
(HA), with the goal of enhancing performance on multi-core shared-memory systems.
The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN
model checker, when traversing the discrete modes of the HA, and enhances it with
a parallel exploration of the continuous states within each mode. We show that
this simple-minded extension of PBFS does not provide the desired load balancing
in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS),
which uses a cheap precomputation of the cost associated with the post operations
(both continuous and discrete) in order to improve load balancing. We illustrate
the TP-BFS and the cost precomputation of the post operators on a support-function-based
algorithm for state-space exploration. The performance comparison of the two algorithms
shows that, in general, TP-BFS provides a better utilization/load-balancing of
the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments
show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect
to SpaceEx LGG scenario. In order to make the comparison fair, we employed an
equal number of post operations in both tools. To the best of our knowledge, this
paper represents the first attempt to provide parallel, reachability-analysis
algorithms for HA.
acknowledgement: This work was supported in part by DST-SERB, GoI under Project No.
YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM)
and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23
(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).
article_number: '7797741'
article_processing_charge: No
arxiv: 1
author:
- first_name: Amit
full_name: Gurung, Amit
last_name: Gurung
- first_name: Arup
full_name: Deka, Arup
last_name: Deka
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
citation:
ama: 'Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability
analysis for hybrid systems. In: IEEE; 2016. doi:10.1109/MEMCOD.2016.7797741'
apa: 'Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R.
(2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE:
Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE.
https://doi.org/10.1109/MEMCOD.2016.7797741'
chicago: Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and
Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016.
https://doi.org/10.1109/MEMCOD.2016.7797741.
ieee: 'A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel
reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference
on Formal Methods and Models for System Design, Kanpur, India , 2016.'
ista: 'Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel
reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods
and Models for System Design, 7797741.'
mla: Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems.
7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741.
short: A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE,
2016.
conference:
end_date: 2016-11-20
location: 'Kanpur, India '
name: 'MEMOCODE: Conference on Formal Methods and Models for System Design'
start_date: 2016-11-18
date_created: 2018-12-11T11:50:09Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2025-06-04T11:52:29Z
day: '27'
department:
- _id: ToHe
doi: 10.1109/MEMCOD.2016.7797741
ec_funded: 1
external_id:
arxiv:
- '1606.05473'
fulldoi: https://doi.org/10.1109/MEMCOD.2016.7797741
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.05473
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: IEEE
publist_id: '6272'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parallel reachability analysis for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1105'
abstract:
- lang: eng
text: Jointly characterizing neural responses in terms of several external variables
promises novel insights into circuit function, but remains computationally prohibitive
in practice. Here we use gaussian process (GP) priors and exploit recent advances
in fast GP inference and learning based on Kronecker methods, to efficiently estimate
multidimensional nonlinear tuning functions. Our estimator require considerably
less data than traditional methods and further provides principled uncertainty
estimates. We apply these tools to hippocampal recordings during open field exploration
and use them to characterize the joint dependence of CA1 responses on the position
of the animal and several other variables, including the animal\'s speed, direction
of motion, and network oscillations.Our results provide an unprecedentedly detailed
quantification of the tuning of hippocampal neurons. The model\'s generality suggests
that our approach can be used to estimate neural response properties in other
brain regions.
acknowledgement: "We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis
work was supported by the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no.
291734."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Savin C, Tkačik G. Estimating nonlinear neural response functions using GP
priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems
Foundation; 2016:3610-3618.'
apa: 'Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions
using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the
NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information
Processing Systems Foundation.'
chicago: Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information
Processing Systems Foundation, 2016.
ieee: 'C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using
GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing
Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.'
ista: 'Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using
GP priors and Kronecker methods. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 3610–3618.'
mla: Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response
Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information
Processing Systems Foundation, 2016, pp. 3610–18.
short: C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation,
2016, pp. 3610–3618.
conference:
end_date: 2016-12-10
location: Barcelona; Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
corr_author: '1'
date_created: 2018-12-11T11:50:10Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2025-06-03T11:36:49Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods
month: '12'
oa: 1
oa_version: None
page: 3610-3618
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '6265'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Estimating nonlinear neural response functions using GP priors and Kronecker
methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '11069'
abstract:
- lang: eng
text: Repeated rounds of nuclear envelope (NE) rupture and repair have been observed
in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization.
Currently, the causes of NE rupture are unclear. Here, we show that NE rupture
in cancer cells relies on the assembly of contractile actin bundles that interact
with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex.
We found that the loss of actin bundles or the LINC complex did not rescue nuclear
lamina defects, a previously identified determinant of nuclear membrane stability,
but did decrease the number and size of chromatin hernias. Finally, NE rupture
inhibition could be rescued in cells treated with actin-depolymerizing drugs by
mechanically constraining nucleus height. These data suggest a model of NE rupture
where weak membrane areas, caused by defects in lamina organization, rupture because
of an increase in intranuclear pressure from actin-based nucleus confinement.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Hetzer M. Nuclear envelope rupture is induced by actin-based nucleus
confinement. Journal of Cell Biology. 2016;215(1):27-36. doi:10.1083/jcb.201603053
apa: Hatch, E. M., & Hetzer, M. (2016). Nuclear envelope rupture is induced
by actin-based nucleus confinement. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.201603053
chicago: Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced
by Actin-Based Nucleus Confinement.” Journal of Cell Biology. Rockefeller
University Press, 2016. https://doi.org/10.1083/jcb.201603053.
ieee: E. M. Hatch and M. Hetzer, “Nuclear envelope rupture is induced by actin-based
nucleus confinement,” Journal of Cell Biology, vol. 215, no. 1. Rockefeller
University Press, pp. 27–36, 2016.
ista: Hatch EM, Hetzer M. 2016. Nuclear envelope rupture is induced by actin-based
nucleus confinement. Journal of Cell Biology. 215(1), 27–36.
mla: Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by
Actin-Based Nucleus Confinement.” Journal of Cell Biology, vol. 215, no.
1, Rockefeller University Press, 2016, pp. 27–36, doi:10.1083/jcb.201603053.
short: E.M. Hatch, M. Hetzer, Journal of Cell Biology 215 (2016) 27–36.
date_created: 2022-04-07T07:47:42Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2024-10-14T11:20:38Z
day: '03'
doi: 10.1083/jcb.201603053
extern: '1'
external_id:
pmid:
- '27697922'
fulldoi: https://doi.org/10.1083/jcb.201603053
intvolume: ' 215'
issue: '1'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1083/jcb.201603053
month: '10'
oa: 1
oa_version: Published Version
page: 27-36
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
issn:
- 0021-9525
- 1540-8140
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear envelope rupture is induced by actin-based nucleus confinement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2016'
...
---
_id: '11070'
abstract:
- lang: eng
text: The organization of the genome in the three-dimensional space of the nucleus
is coupled with cell type-specific gene expression. However, how nuclear architecture
influences transcription that governs cell identity remains unknown. Here, we
show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers
(SE), regulatory structures that drive the expression of key genes that specify
cell identity. We found that nucleoporin-associated SEs localize preferentially
to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic
transcriptional changes of SE-associated genes. Our results reveal a crucial role
of NPC components in the regulation of cell type-specifying genes and highlight
nuclear architecture as a regulatory layer of genome functions in cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Swati
full_name: Tyagi, Swati
last_name: Tyagi
- first_name: Jonah
full_name: Cool, Jonah
last_name: Cool
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation
of cell identity genes. Genes & Development. 2016;30(20):2253-2258.
doi:10.1101/gad.287417.116
apa: Ibarra, A., Benner, C., Tyagi, S., Cool, J., & Hetzer, M. (2016). Nucleoporin-mediated
regulation of cell identity genes. Genes & Development. Cold Spring
Harbor Laboratory. https://doi.org/10.1101/gad.287417.116
chicago: Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer.
“Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development.
Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.287417.116.
ieee: A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated
regulation of cell identity genes,” Genes & Development, vol. 30, no.
20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.
ista: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated
regulation of cell identity genes. Genes & Development. 30(20), 2253–2258.
mla: Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.”
Genes & Development, vol. 30, no. 20, Cold Spring Harbor Laboratory,
2016, pp. 2253–58, doi:10.1101/gad.287417.116.
short: A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes & Development
30 (2016) 2253–2258.
date_created: 2022-04-07T07:48:08Z
date_published: 2016-11-02T00:00:00Z
date_updated: 2024-10-14T11:21:07Z
day: '02'
doi: 10.1101/gad.287417.116
extern: '1'
external_id:
pmid:
- '27807035'
fulldoi: https://doi.org/10.1101/gad.287417.116
intvolume: ' 30'
issue: '20'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.287417.116
month: '11'
oa: 1
oa_version: Published Version
page: 2253-2258
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleoporin-mediated regulation of cell identity genes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2016'
...
---
_id: '11071'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic
cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic
transport, recent research suggests that certain NPC proteins have additionally
acquired the role of affecting gene expression at the nuclear periphery and in
the nucleoplasm in metazoans. Here we identify a widely expressed variant of the
transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that
arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks
the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead,
sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified
transcriptional regulator, at gene promoters to control transcription of its target
genes in human cells. Interestingly, sPom121 transcripts appear independently
in several mammalian species, suggesting convergent innovation of Nup-mediated
transcription regulation during mammalian evolution. Our findings implicate alternate
transcription initiation as a mechanism to increase the functional diversity of
NPC components.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Iñigo
full_name: Narvaiza, Iñigo
last_name: Narvaiza
- first_name: Maria C.N.
full_name: Marchetto, Maria C.N.
last_name: Marchetto
- first_name: Janet M.
full_name: Young, Janet M.
last_name: Young
- first_name: Harmit S.
full_name: Malik, Harmit S.
last_name: Malik
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator
from a transmembrane nucleoporin. Genes & Development. 2016;30(10):1155-1171.
doi:10.1101/gad.280941.116
apa: Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M.,
Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from
a transmembrane nucleoporin. Genes & Development. Cold Spring Harbor
Laboratory. https://doi.org/10.1101/gad.280941.116
chicago: Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto,
Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of
a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes &
Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.280941.116.
ieee: T. M. Franks et al., “Evolution of a transcriptional regulator from
a transmembrane nucleoporin,” Genes & Development, vol. 30, no. 10.
Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.
ista: Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH,
Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane
nucleoporin. Genes & Development. 30(10), 1155–1171.
mla: Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a
Transmembrane Nucleoporin.” Genes & Development, vol. 30, no. 10, Cold
Spring Harbor Laboratory, 2016, pp. 1155–71, doi:10.1101/gad.280941.116.
short: T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik,
F.H. Gage, M. Hetzer, Genes & Development 30 (2016) 1155–1171.
date_created: 2022-04-07T07:48:20Z
date_published: 2016-05-19T00:00:00Z
date_updated: 2024-10-14T11:21:48Z
day: '19'
doi: 10.1101/gad.280941.116
extern: '1'
external_id:
pmid:
- '27198230'
fulldoi: https://doi.org/10.1101/gad.280941.116
intvolume: ' 30'
issue: '10'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.280941.116
month: '05'
oa: 1
oa_version: Published Version
page: 1155-1171
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of a transcriptional regulator from a transmembrane nucleoporin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2016'
...