---
_id: '7453'
abstract:
- lang: eng
text: We illustrate the ingredients of the state-of-the-art of model-based approach
for the formal design and verification of cyber-physical systems. To capture the
interaction between a discrete controller and its continuously evolving environment,
we use the formal models of timed and hybrid automata. We explain the steps of
modeling and verification in the tools Uppaal and SpaceEx using a case study based
on a dual-chamber implantable pacemaker monitoring a human heart. We show how
to design a model as a composition of components, how to construct models at varying
levels of detail, how to establish that one model is an abstraction of another,
how to specify correctness requirements using temporal logic, and how to verify
that a model satisfies a logical requirement.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This
research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS,
funded by the Danish National Research Foundation and the National Science Foundation,
China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant
LASSO.
alternative_title:
- Lecture Notes in Computer Science
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- 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: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
- first_name: Marius
full_name: Mikučionis, Marius
last_name: Mikučionis
citation:
ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time
models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing
and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22'
apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis,
M. (2019). Continuous-time models for system design and analysis. In B. Steffen
& G. Woeginger (Eds.), Computing and Software Science (Vol. 10000,
pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22
chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius
Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing
and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77.
LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22.
ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time
models for system design and analysis,” in Computing and Software Science,
vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.
ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time
models for system design and analysis. In: Computing and Software Science. Lecture
Notes in Computer Science, vol. 10000, 452–477.'
mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.”
Computing and Software Science, edited by Bernhard Steffen and Gerhard
Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22.
short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B.
Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature,
2019, pp. 452–477.
date_created: 2020-02-05T10:51:44Z
date_published: 2019-10-05T00:00:00Z
date_updated: 2022-09-06T08:25:52Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-319-91908-9_22
editor:
- first_name: Bernhard
full_name: Steffen, Bernhard
last_name: Steffen
- first_name: Gerhard
full_name: Woeginger, Gerhard
last_name: Woeginger
intvolume: ' 10000'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-319-91908-9_22
month: '10'
oa: 1
oa_version: Published Version
page: 452-477
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Computing and Software Science
publication_identifier:
eisbn:
- '9783319919089'
eissn:
- 0302-9743
isbn:
- '9783319919072'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Continuous-time models for system design and analysis
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10000
year: '2019'
...
---
_id: '7459'
abstract:
- lang: eng
text: We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising
of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the
hydrothermal transformation of TiO2 have both inner and outer surfaces, which
facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The
magnetoelectric coupling was studied by measuring the piezoelectric behavior in
the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage
coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni
and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly
on Ti substrate may lead to efficient fabrication of magnetoelectric devices.
article_processing_charge: No
article_type: original
author:
- first_name: Samba Siva
full_name: Vadla, Samba Siva
last_name: Vadla
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Subish
full_name: John, Subish
last_name: John
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
- first_name: Somnath C.
full_name: Roy, Somnath C.
last_name: Roy
citation:
ama: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric
coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 2019;159:33-36.
doi:10.1016/j.scriptamat.2018.09.003
apa: Vadla, S. S., Costanzo, T., John, S., Caruntu, G., & Roy, S. C. (2019).
Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta
Materialia. Elsevier. https://doi.org/10.1016/j.scriptamat.2018.09.003
chicago: Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and
Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.”
Scripta Materialia. Elsevier, 2019. https://doi.org/10.1016/j.scriptamat.2018.09.003.
ieee: S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing
of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” Scripta Materialia,
vol. 159. Elsevier, pp. 33–36, 2019.
ista: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric
coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36.
mla: Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni
1–3 Composites.” Scripta Materialia, vol. 159, Elsevier, 2019, pp. 33–36,
doi:10.1016/j.scriptamat.2018.09.003.
short: S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia
159 (2019) 33–36.
date_created: 2020-02-05T14:19:17Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-02-23T13:08:31Z
day: '15'
doi: 10.1016/j.scriptamat.2018.09.003
extern: '1'
intvolume: ' 159'
language:
- iso: eng
month: '01'
oa_version: None
page: 33-36
publication: Scripta Materialia
publication_identifier:
issn:
- 1359-6462
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2019'
...
---
_id: '7468'
abstract:
- lang: eng
text: We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference
in structured energy minimization problems. The method optimizes a Lagrangean
relaxation of the original energy minimization problem using a multi plane block-coordinate
Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean
decomposition. We show empirically that our method outperforms state-of-the-art
Lagrangean decomposition based algorithms on some challenging Markov Random Field,
multi-label discrete tomography and graph matching problems.
article_number: 11138-11147
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm.
In: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. Vol 2019-June. IEEE; 2019. doi:10.1109/CVPR.2019.01140'
apa: 'Swoboda, P., & Kolmogorov, V. (2019). Map inference via block-coordinate
Frank-Wolfe algorithm. In Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition (Vol. 2019–June). Long Beach, CA,
United States: IEEE. https://doi.org/10.1109/CVPR.2019.01140'
chicago: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
Frank-Wolfe Algorithm.” In Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, Vol. 2019–June. IEEE, 2019. https://doi.org/10.1109/CVPR.2019.01140.
ieee: P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe
algorithm,” in Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition, Long Beach, CA, United States, 2019, vol.
2019–June.
ista: 'Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe
algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition
vol. 2019–June, 11138–11147.'
mla: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
Frank-Wolfe Algorithm.” Proceedings of the IEEE Computer Society Conference
on Computer Vision and Pattern Recognition, vol. 2019–June, 11138–11147, IEEE,
2019, doi:10.1109/CVPR.2019.01140.
short: P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, IEEE, 2019.
conference:
end_date: 2019-06-20
location: Long Beach, CA, United States
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2019-06-15
date_created: 2020-02-09T23:00:52Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T14:54:24Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/CVPR.2019.01140
ec_funded: 1
external_id:
arxiv:
- '1806.05049'
isi:
- '000542649304076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05049
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- '9781728132938'
issn:
- '10636919'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Map inference via block-coordinate Frank-Wolfe algorithm
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-June
year: '2019'
...
---
_id: '7476'
abstract:
- lang: eng
text: The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction
is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent
maintenance remain poorly understood. Here, we apply large-scale quantitative
fate mapping to define the patterns of cell fate behaviour during SG development
and maintenance. We show that the SG develops from a defined number of lineage-restricted
progenitors that undergo a programme of independent and stochastic cell fate decisions.
Following an expansion phase, equipotent progenitors transition into a phase of
homeostatic turnover, which is correlated with changes in the mechanical properties
of the stroma and spatial restrictions on gland size. Expression of the oncogene
KrasG12D results in a release from these constraints and unbridled gland expansion.
Quantitative clonal fate analysis reveals that, during this phase, the primary
effect of the Kras oncogene is to drive a constant fate bias with little effect
on cell division rates. These findings provide insight into the developmental
programme of the SG, as well as the mechanisms that drive tumour progression and
gland dysfunction.
article_processing_charge: No
article_type: original
author:
- first_name: Marianne Stemann
full_name: Andersen, Marianne Stemann
last_name: Andersen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Svetlana
full_name: Ulyanchenko, Svetlana
last_name: Ulyanchenko
- first_name: Soline
full_name: Estrach, Soline
last_name: Estrach
- first_name: Yasuko
full_name: Antoku, Yasuko
last_name: Antoku
- first_name: Sabrina
full_name: Pisano, Sabrina
last_name: Pisano
- first_name: Kim E.
full_name: Boonekamp, Kim E.
last_name: Boonekamp
- first_name: Sarah
full_name: Sendrup, Sarah
last_name: Sendrup
- first_name: Martti
full_name: Maimets, Martti
last_name: Maimets
- first_name: Marianne Terndrup
full_name: Pedersen, Marianne Terndrup
last_name: Pedersen
- first_name: Jens V.
full_name: Johansen, Jens V.
last_name: Johansen
- first_name: Ditte L.
full_name: Clement, Ditte L.
last_name: Clement
- first_name: Chloe C.
full_name: Feral, Chloe C.
last_name: Feral
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Kim B.
full_name: Jensen, Kim B.
last_name: Jensen
citation:
ama: Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics
of sebaceous gland development in normal and perturbed states. Nature Cell
Biology. 2019;21(8):924-932. doi:10.1038/s41556-019-0362-x
apa: Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y.,
Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous
gland development in normal and perturbed states. Nature Cell Biology.
Springer Nature. https://doi.org/10.1038/s41556-019-0362-x
chicago: Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline
Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the
Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.”
Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0362-x.
ieee: M. S. Andersen et al., “Tracing the cellular dynamics of sebaceous
gland development in normal and perturbed states,” Nature Cell Biology,
vol. 21, no. 8. Springer Nature, pp. 924–932, 2019.
ista: Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp
KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons
BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development
in normal and perturbed states. Nature Cell Biology. 21(8), 924–932.
mla: Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous
Gland Development in Normal and Perturbed States.” Nature Cell Biology,
vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:10.1038/s41556-019-0362-x.
short: M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano,
K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement,
C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932.
date_created: 2020-02-11T08:43:49Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:47Z
day: '01'
doi: 10.1038/s41556-019-0362-x
extern: '1'
external_id:
pmid:
- '31358966'
intvolume: ' 21'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/
month: '08'
oa: 1
oa_version: Submitted Version
page: 924-932
pmid: 1
publication: Nature Cell Biology
publication_identifier:
issn:
- 1465-7392
- 1476-4679
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Tracing the cellular dynamics of sebaceous gland development in normal and
perturbed states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2019'
...
---
_id: '7479'
abstract:
- lang: eng
text: "Multi-exit architectures, in which a stack of processing layers is interleaved
with early output layers, allow the processing of a test example to stop early
and thus save computation time and/or energy. In this work, we propose a new
training procedure for multi-exit architectures based on the principle of knowledge
distillation. The method encourage searly exits to mimic later, more accurate
exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and
\ ImageNet show that distillation-based training significantly improves the
accuracy of early exits while maintaining state-of-the-art accuracy for late
\ ones. The method is particularly beneficial when training data is limited
\ and it allows a straightforward extension to semi-supervised learning,i.e.
making use of unlabeled data at training time. Moreover, it takes only afew lines
to implement and incurs almost no computational overhead at training time, and
none at all at test time."
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Phuong M, Lampert C. Distillation-based training for multi-exit architectures.
In: IEEE International Conference on Computer Vision. Vol 2019-October.
IEEE; 2019:1355-1364. doi:10.1109/ICCV.2019.00144'
apa: 'Phuong, M., & Lampert, C. (2019). Distillation-based training for multi-exit
architectures. In IEEE International Conference on Computer Vision (Vol.
2019–October, pp. 1355–1364). Seoul, Korea: IEEE. https://doi.org/10.1109/ICCV.2019.00144'
chicago: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit
Architectures.” In IEEE International Conference on Computer Vision, 2019–October:1355–64.
IEEE, 2019. https://doi.org/10.1109/ICCV.2019.00144.
ieee: M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,”
in IEEE International Conference on Computer Vision, Seoul, Korea, 2019,
vol. 2019–October, pp. 1355–1364.
ista: 'Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures.
IEEE International Conference on Computer Vision. ICCV: International Conference
on Computer Vision vol. 2019–October, 1355–1364.'
mla: Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit
Architectures.” IEEE International Conference on Computer Vision, vol.
2019–October, IEEE, 2019, pp. 1355–64, doi:10.1109/ICCV.2019.00144.
short: M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision,
IEEE, 2019, pp. 1355–1364.
conference:
end_date: 2019-11-02
location: Seoul, Korea
name: 'ICCV: International Conference on Computer Vision'
start_date: 2019-10-27
date_created: 2020-02-11T09:06:57Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:11:12Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1109/ICCV.2019.00144
ec_funded: 1
external_id:
isi:
- '000531438101047'
file:
- access_level: open_access
checksum: 7b77fb5c2d27c4c37a7612ba46a66117
content_type: application/pdf
creator: bphuong
date_created: 2020-02-11T09:06:39Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7480'
file_name: main.pdf
file_size: 735768
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 1355-1364
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: IEEE International Conference on Computer Vision
publication_identifier:
isbn:
- '9781728148038'
issn:
- '15505499'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '9418'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Distillation-based training for multi-exit architectures
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-October
year: '2019'
...
---
_id: '7513'
abstract:
- lang: eng
text: 'Social insects (i.e., ants, termites and the social bees and wasps) protect
their colonies from disease using a combination of individual immunity and collectively
performed defenses, termed social immunity. The first line of social immune defense
is sanitary care, which is performed by colony members to protect their pathogen-exposed
nestmates from developing an infection. If sanitary care fails and an infection
becomes established, a second line of social immune defense is deployed to stop
disease transmission within the colony and to protect the valuable queens, which
together with the males are the reproductive individuals of the colony. Insect
colonies are separated into these reproductive individuals and the sterile worker
force, forming a superorganismal reproductive unit reminiscent of the differentiated
germline and soma in a multicellular organism. Ultimately, the social immune response
preserves the germline of the superorganism insect colony and increases overall
fitness of the colony in case of disease. '
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
citation:
ama: 'Cremer S, Kutzer M. Social immunity. In: Choe J, ed. Encyclopedia of Animal
Behavior. 2nd ed. Elsevier; 2019:747-755. doi:10.1016/B978-0-12-809633-8.90721-0'
apa: Cremer, S., & Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), Encyclopedia
of Animal Behavior (2nd ed., pp. 747–755). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.90721-0
chicago: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In Encyclopedia
of Animal Behavior, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.90721-0.
ieee: S. Cremer and M. Kutzer, “Social immunity,” in Encyclopedia of Animal Behavior,
2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.
ista: 'Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior.
, 747–755.'
mla: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” Encyclopedia of Animal
Behavior, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:10.1016/B978-0-12-809633-8.90721-0.
short: S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior,
2nd ed., Elsevier, 2019, pp. 747–755.
date_created: 2020-02-23T23:00:36Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-09-08T11:12:04Z
day: '06'
department:
- _id: SyCr
doi: 10.1016/B978-0-12-809633-8.90721-0
edition: '2'
editor:
- first_name: Jae
full_name: Choe, Jae
last_name: Choe
external_id:
isi:
- '000248989500026'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 747-755
publication: Encyclopedia of Animal Behavior
publication_identifier:
eisbn:
- '9780128132524'
isbn:
- '9780128132517'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social immunity
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7524'
abstract:
- lang: eng
text: "We prove a lower bound for the free energy (per unit volume) of the two-dimensional
Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$
and inverse temperature $\\beta$ differs from the one of the non-interacting system
by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$.
Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ =
\\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless
critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho
\\ll 1$ and if $\\beta \\rho \\gtrsim 1$."
article_processing_charge: No
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
Bose gas. I. Lower bound. arXiv:191003372.
apa: Deuchert, A., Mayer, S., & Seiringer, R. (n.d.). The free energy of the
two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372. ArXiv.
chicago: Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy
of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372.
ArXiv, n.d.
ieee: A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional
dilute Bose gas. I. Lower bound,” arXiv:1910.03372. ArXiv.
ista: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
Bose gas. I. Lower bound. arXiv:1910.03372, .
mla: Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose
Gas. I. Lower Bound.” ArXiv:1910.03372, ArXiv.
short: A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).
date_created: 2020-02-26T08:46:40Z
date_published: 2019-10-08T00:00:00Z
date_updated: 2023-09-07T13:12:41Z
day: '08'
department:
- _id: RoSe
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.03372
month: '10'
oa: 1
oa_version: Preprint
page: '61'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: arXiv:1910.03372
publication_status: draft
publisher: ArXiv
related_material:
record:
- id: '7790'
relation: later_version
status: public
- id: '7514'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: The free energy of the two-dimensional dilute Bose gas. I. Lower bound
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7542'
abstract:
- lang: eng
text: We present a novel class of convolutional neural networks (CNNs) for set functions,i.e.,
data indexed with the powerset of a finite set. The convolutions are derivedas
linear, shift-equivariant functions for various notions of shifts on set functions.The
framework is fundamentally different from graph convolutions based on theLaplacian,
as it provides not one but several basic shifts, one for each element inthe ground
set. Prototypical experiments with several set function classificationtasks on
synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate
the potential of our new powerset CNNs.
article_processing_charge: No
arxiv: 1
author:
- first_name: Chris
full_name: Wendler, Chris
last_name: Wendler
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Püschel, Markus
last_name: Püschel
citation:
ama: 'Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks.
In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.'
apa: 'Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional
neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural
Information Processing Systems, Vancouver, Canada: Neural Information Processing
Systems Foundation.'
chicago: Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional
Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation,
2019.
ieee: 'C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural
networks,” presented at the NIPS: Conference on Neural Information Processing
Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.'
ista: 'Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks.
NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.'
mla: Wendler, Chris, et al. Powerset Convolutional Neural Networks. Vol.
32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.
short: C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing
Systems Foundation, 2019, pp. 927–938.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NIPS: Conference on Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2020-02-28T10:03:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-08T11:13:52Z
day: '01'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '1909.02253'
isi:
- '000534424300084'
intvolume: ' 32'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks
month: '12'
oa: 1
oa_version: Published Version
page: 927-938
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Powerset convolutional neural networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2019'
...
---
_id: '7547'
abstract:
- lang: eng
text: The BH3-only family of proteins is key for initiating apoptosis in a variety
of contexts, and may also contribute to non-apoptotic cellular processes. Historically,
the nematode Caenorhabditis elegans has provided a powerful system for studying
and identifying conserved regulators of BH3-only proteins. In C. elegans, the
BH3-only protein egl-1 is expressed during development to cell-autonomously trigger
most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed
after development in the sensory neuron pair URX without inducing apoptosis. We
used genetic screening and epistasis analysis to determine that its transcription
is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein
Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family
proteins are also expressed in the adult nervous system of mammals, we suggest
that studying egl-1 expression in URX may shed light on mechanisms that regulate
conserved family members in higher organisms.
article_processing_charge: No
article_type: original
author:
- first_name: Jesse
full_name: Cohn, Jesse
last_name: Cohn
- first_name: Vivek
full_name: Dwivedi, Vivek
last_name: Dwivedi
- first_name: Giulio
full_name: Valperga, Giulio
last_name: Valperga
- first_name: Nicole
full_name: Zarate, Nicole
last_name: Zarate
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: H. Robert
full_name: Horvitz, H. Robert
last_name: Horvitz
- first_name: Jonathan T.
full_name: Pierce, Jonathan T.
last_name: Pierce
citation:
ama: 'Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the
proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans.
G3: Genes, Genomes, Genetics. 2019;9(11):3703-3714. doi:10.1534/g3.119.400654'
apa: 'Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H.
R., & Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic
BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3:
Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.119.400654'
chicago: 'Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono,
H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the
Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.”
G3: Genes, Genomes, Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/g3.119.400654.'
ieee: 'J. Cohn et al., “Activity-dependent regulation of the proapoptotic
BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” G3:
Genes, Genomes, Genetics, vol. 9, no. 11. Genetics Society of America, pp.
3703–3714, 2019.'
ista: 'Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT.
2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in
a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics.
9(11), 3703–3714.'
mla: 'Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only
Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes,
Genetics, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14,
doi:10.1534/g3.119.400654.'
short: 'J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T.
Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.'
date_created: 2020-02-28T10:44:27Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2021-01-12T08:14:07Z
day: '01'
doi: 10.1534/g3.119.400654
extern: '1'
external_id:
pmid:
- '31519744'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: Published Version
page: 3703-3714
pmid: 1
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
- 2160-1836
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a
living neuron pair in Caenorhabditis elegans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2019'
...
---
_id: '7548'
abstract:
- lang: eng
text: Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils
is a well-established hallmark of Alzheimer’s disease, the complex mechanisms
linking this process to neurodegeneration are still incompletely understood. The
nematode worm C. elegans is a valuable model organism through which to study these
mechanisms because of its simple nervous system and its relatively short lifespan.
Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study
the toxic effects of the overexpression of Aβ in the muscle or nervous systems.
However, the wide variety of effects associated with the tissue-level overexpression
of Aβ makes it difficult to single out and study specific cellular mechanisms
related to the onset of Alzheimer’s disease. Here, to better understand how to
investigate the early events affecting neuronal signalling, we created a C. elegans
model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion
in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural
assays, we found that the Aβ42-expressing animals displayed a subtle modulation
of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG
neurons in young Aβ42-expressing nematodes were activated more strongly than in
control animals, and that neuronal activation remained intact until old age. Taken
together, our results suggest that Aβ42-expression in this very subtle model of
AD is sufficient to modulate the behavioural response but not strong enough to
generate significant neurotoxicity, suggesting that slightly more aggressive perturbations
will enable effectively studies of the links between the modulation of a physiological
response and its associated neurotoxicity.
article_number: e0217746
article_processing_charge: No
article_type: original
author:
- first_name: Tessa
full_name: Sinnige, Tessa
last_name: Sinnige
- first_name: Prashanth
full_name: Ciryam, Prashanth
last_name: Ciryam
- first_name: Samuel
full_name: Casford, Samuel
last_name: Casford
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
citation:
ama: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression
of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates
the associated behavioural response. PLOS ONE. 2019;14(5). doi:10.1371/journal.pone.0217746
apa: Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., & Vendruscolo,
M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans
sensory neurons modulates the associated behavioural response. PLOS ONE.
Public Library of Science. https://doi.org/10.1371/journal.pone.0217746
chicago: Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson,
Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in
a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural
Response.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0217746.
ieee: T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo,
“Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
modulates the associated behavioural response,” PLOS ONE, vol. 14, no.
5. Public Library of Science, 2019.
ista: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019.
Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.
mla: Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair
of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.”
PLOS ONE, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:10.1371/journal.pone.0217746.
short: T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo,
PLOS ONE 14 (2019).
date_created: 2020-02-28T10:45:13Z
date_published: 2019-05-31T00:00:00Z
date_updated: 2021-01-12T08:14:08Z
day: '31'
doi: 10.1371/journal.pone.0217746
extern: '1'
intvolume: ' 14'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: Published Version
publication: PLOS ONE
publication_identifier:
issn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Expression of the amyloid-β peptide in a single pair of C. elegans sensory
neurons modulates the associated behavioural response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2019'
...
---
_id: '7550'
abstract:
- lang: eng
text: 'We consider an optimal control problem for an abstract nonlinear dissipative
evolution equation. The differential constraint is penalized by augmenting the
target functional by a nonnegative global-in-time functional which is null-minimized
in the evolution equation is satisfied. Different variational settings are presented,
leading to the convergence of the penalization method for gradient flows, noncyclic
and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. '
acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF)
through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and
I 2375.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
- first_name: Ulisse
full_name: Stefanelli, Ulisse
last_name: Stefanelli
citation:
ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
2019;28(2):425-447.
apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals
of optimal-control problems for dissipative evolution. Advances in Mathematical
Sciences and Applications. Gakko Tosho.
chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications. Gakko Tosho, 2019.
ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control
problems for dissipative evolution,” Advances in Mathematical Sciences and
Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.
ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
28(2), 425–447.
mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.
short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications
28 (2019) 425–447.
date_created: 2020-02-28T10:54:41Z
date_published: 2019-10-22T00:00:00Z
date_updated: 2022-06-17T07:52:41Z
day: '22'
department:
- _id: JaMa
external_id:
arxiv:
- '1910.10050'
intvolume: ' 28'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1910.10050'
month: '10'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Advances in Mathematical Sciences and Applications
publication_identifier:
issn:
- 1343-4373
publication_status: published
publisher: Gakko Tosho
quality_controlled: '1'
status: public
title: Penalization via global functionals of optimal-control problems for dissipative
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2019'
...
---
_id: '7552'
abstract:
- lang: eng
text: 'There is increasing evidence that protein binding to specific sites along
DNA can activate the reading out of genetic information without coming into direct
physical contact with the gene. There also is evidence that these distant but
interacting sites are embedded in a liquid droplet of proteins which condenses
out of the surrounding solution. We argue that droplet-mediated interactions can
account for crucial features of gene regulation only if the droplet is poised
at a non-generic point in its phase diagram. We explore a minimal model that embodies
this idea, show that this model has a natural mechanism for self-tuning, and suggest
direct experimental tests. '
article_processing_charge: No
arxiv: 1
author:
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:191208579.
apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional
regulation. arXiv:1912.08579. ArXiv.
chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance
in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional
regulation,” arXiv:1912.08579. ArXiv.
ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:1912.08579, .
mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.”
ArXiv:1912.08579, ArXiv.
short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
date_created: 2020-02-28T10:57:08Z
date_published: 2019-12-18T00:00:00Z
date_updated: 2021-01-12T08:14:09Z
day: '18'
department:
- _id: GaTk
external_id:
arxiv:
- '1912.08579'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08579
month: '12'
oa: 1
oa_version: Preprint
page: '5'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: arXiv:1912.08579
publication_status: submitted
publisher: ArXiv
status: public
title: Action at a distance in transcriptional regulation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7576'
abstract:
- lang: eng
text: We present the results of a friendly competition for formal verification of
continuous and hybrid systems with nonlinear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex,
Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are
applied to solve reachability analysis problems on four benchmark problems, one
of them with hybrid dynamics. We do not rank the tools based on the results, but
show the current status and discover the potential advantages of different tools.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Immler, Fabian
last_name: Immler
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Luis
full_name: Benet, Luis
last_name: Benet
- first_name: Alexandre
full_name: Chapoutot, Alexandre
last_name: Chapoutot
- first_name: Xin
full_name: Chen, Xin
last_name: Chen
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Luca
full_name: Geretti, Luca
last_name: Geretti
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: David P.
full_name: Sanders, David P.
last_name: Sanders
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b'
apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., …
Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems
with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61).
Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b'
chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin
Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian
Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear
Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications,
2019. https://doi.org/10.29007/m75b.'
ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal,
Canada, 2019, vol. 61, pp. 41–61.'
ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper
N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and
hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International
Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.'
mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair
Publications, 2019, pp. 41–61, doi:10.29007/m75b.'
short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti,
N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair
Publications, 2019, pp. 41–61.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-03-08T23:00:49Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:14:17Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/m75b
file:
- access_level: open_access
checksum: 9138977a06fcd6a95976eb4bca875f0c
content_type: application/pdf
creator: dernst
date_created: 2020-03-24T07:36:36Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7617'
file_name: 2019_ARCH19_Immler.pdf
file_size: 1934830
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 61'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 41-61
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair Publications
quality_controlled: '1'
scopus_import: 1
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '7606'
abstract:
- lang: eng
text: We derive a tight lower bound on equivocation (conditional entropy), or equivalently
a tight upper bound on mutual information between a signal variable and channel
outputs. The bound is in terms of the joint distribution of the signals and maximum
a posteriori decodes (most probable signals given channel output). As part of
our derivation, we describe the key properties of the distribution of signals,
channel outputs and decodes, that minimizes equivocation and maximizes mutual
information. This work addresses a problem in data analysis, where mutual information
between signals and decodes is sometimes used to lower bound the mutual information
between signals and channel outputs. Our result provides a corresponding upper
bound.
article_number: '8989292'
article_processing_charge: No
arxiv: 1
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information.
In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292'
apa: 'Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound
on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby,
Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292'
chicago: Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper
Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019.
IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.
ieee: M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual
information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden,
2019.
ista: Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information.
IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.
mla: Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE
Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.
short: M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop,
ITW 2019, IEEE, 2019.
conference:
end_date: 2019-08-28
location: Visby, Sweden
name: Information Theory Workshop
start_date: 2019-08-25
date_created: 2020-03-22T23:00:47Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2025-06-30T13:21:05Z
day: '01'
department:
- _id: GaTk
doi: 10.1109/ITW44776.2019.8989292
ec_funded: 1
external_id:
arxiv:
- '1812.01475'
isi:
- '000540384500015'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.01475
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: IEEE Information Theory Workshop, ITW 2019
publication_identifier:
isbn:
- '9781538669006'
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A tight upper bound on mutual information
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7627'
abstract:
- lang: eng
text: 'Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2
batteries and determines rate, capacity, and reversibility. Current understanding states that the
partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film,
leading to low capacity even at low rates, or in solution, leading to particles
and high capacities. Here we show that Li2O2 forms to the widest extent as particles
via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the
whole range of electrolytes. Deciding for particle morphology, achievable rate
and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration
distribution of associated LiO2 in solution. Provided that species mobilities
and surface are high, high, capacities are possible even with low-donor-number
electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic
voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering
(SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving
rich quantitative information from complex multi-phase systems. On a wider perspective,
this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and
beyond. '
article_processing_charge: No
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Aleksej
full_name: Samojlov, Aleksej
last_name: Samojlov
- first_name: Manfred
full_name: Nachtnebel, Manfred
last_name: Nachtnebel
- first_name: Manfred
full_name: Kriechbaum, Manfred
last_name: Kriechbaum
- first_name: Heinz
full_name: Amenitsch, Heinz
last_name: Amenitsch
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger
SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering.
apa: Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., &
Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as
revealed by in situ small angle X-ray scattering. ChemRxiv.
chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum,
Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model
in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv,
n.d.
ieee: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S.
A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by
in situ small angle X-ray scattering.” ChemRxiv.
ista: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger
SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering.
mla: Prehal, Christian, et al. A Revised O2 Reduction Model in Li-O2 Batteries
as Revealed by in Situ Small Angle X-Ray Scattering. ChemRxiv.
short: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A.
Freunberger, (n.d.).
date_created: 2020-04-01T10:10:21Z
date_published: 2019-12-26T00:00:00Z
date_updated: 2020-04-06T10:36:21Z
day: '26'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv.11447775.v1
month: '12'
oa: 1
oa_version: Preprint
page: '50'
publication_status: submitted
publisher: ChemRxiv
status: public
title: A revised O2 reduction model in Li-O2 batteries as revealed by in situ small
angle X-ray scattering
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7639'
abstract:
- lang: eng
text: Deep neural networks (DNNs) have become increasingly important due to their
excellent empirical performance on a wide range of problems. However, regularization
is generally achieved by indirect means, largely due to the complex set of functions
defined by a network and the difficulty in measuring function complexity. There
exists no method in the literature for additive regularization based on a norm
of the function, as is classically considered in statistical learning theory.
In this work, we study the tractability of function norms for deep neural networks
with ReLU activations. We provide, to the best of our knowledge, the first proof
in the literature of the NP-hardness of computing function norms of DNNs of 3
or more layers. We also highlight a fundamental difference between shallow and
deep networks. In the light on these results, we propose a new regularization
strategy based on approximate function norms, and show its efficiency on a segmentation
task with a DNN.
article_number: 748-752
article_processing_charge: No
author:
- first_name: Amal
full_name: Rannen-Triki, Amal
last_name: Rannen-Triki
- first_name: Maxim
full_name: Berman, Maxim
last_name: Berman
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Matthew B.
full_name: Blaschko, Matthew B.
last_name: Blaschko
citation:
ama: 'Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural
networks. In: Proceedings of the 2019 International Conference on Computer
Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00097'
apa: 'Rannen-Triki, A., Berman, M., Kolmogorov, V., & Blaschko, M. B. (2019).
Function norms for neural networks. In Proceedings of the 2019 International
Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00097'
chicago: Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko.
“Function Norms for Neural Networks.” In Proceedings of the 2019 International
Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00097.
ieee: A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms
for neural networks,” in Proceedings of the 2019 International Conference on
Computer Vision Workshop, Seoul, South Korea, 2019.
ista: 'Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms
for neural networks. Proceedings of the 2019 International Conference on Computer
Vision Workshop. ICCVW: International Conference on Computer Vision Workshop,
748–752.'
mla: Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” Proceedings
of the 2019 International Conference on Computer Vision Workshop, 748–752,
IEEE, 2019, doi:10.1109/ICCVW.2019.00097.
short: A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings
of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.
conference:
end_date: 2019-10-28
location: Seoul, South Korea
name: 'ICCVW: International Conference on Computer Vision Workshop'
start_date: 2019-10-27
date_created: 2020-04-05T22:00:50Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:19:12Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/ICCVW.2019.00097
external_id:
isi:
- '000554591600090'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
publication: Proceedings of the 2019 International Conference on Computer Vision Workshop
publication_identifier:
isbn:
- '9781728150239'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Function norms for neural networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7640'
abstract:
- lang: eng
text: We propose a new model for detecting visual relationships, such as "person
riding motorcycle" or "bottle on table". This task is an important step towards
comprehensive structured mage understanding, going beyond detecting individual
objects. Our main novelty is a Box Attention mechanism that allows to model pairwise
interactions between objects using standard object detection pipelines. The resulting
model is conceptually clean, expressive and relies on well-justified training
and prediction procedures. Moreover, unlike previously proposed approaches, our
model does not introduce any additional complex components or hyperparameters
on top of those already required by the underlying detection model. We conduct
an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating
strong quantitative and qualitative results.
article_number: 1749-1753
article_processing_charge: No
arxiv: 1
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Alina
full_name: Kuznetsova, Alina
last_name: Kuznetsova
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Vittorio
full_name: Ferrari, Vittorio
last_name: Ferrari
citation:
ama: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships
using box attention. In: Proceedings of the 2019 International Conference on
Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217'
apa: 'Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting
visual relationships using box attention. In Proceedings of the 2019 International
Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217'
chicago: Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio
Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings
of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019.
https://doi.org/10.1109/ICCVW.2019.00217.
ieee: A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual
relationships using box attention,” in Proceedings of the 2019 International
Conference on Computer Vision Workshop, Seoul, South Korea, 2019.
ista: 'Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual
relationships using box attention. Proceedings of the 2019 International Conference
on Computer Vision Workshop. ICCVW: International Conference on Computer Vision
Workshop, 1749–1753.'
mla: Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.”
Proceedings of the 2019 International Conference on Computer Vision Workshop,
1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217.
short: A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of
the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.
conference:
end_date: 2019-10-28
location: Seoul, South Korea
name: 'ICCVW: International Conference on Computer Vision Workshop'
start_date: 2019-10-27
date_created: 2020-04-05T22:00:51Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-08T11:18:37Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/ICCVW.2019.00217
ec_funded: 1
external_id:
arxiv:
- '1807.02136'
isi:
- '000554591601098'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.02136
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Proceedings of the 2019 International Conference on Computer Vision Workshop
publication_identifier:
isbn:
- '9781728150239'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Detecting visual relationships using box attention
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7710'
abstract:
- lang: eng
text: 'The number of human genomes being genotyped or sequenced increases exponentially
and efficient haplotype estimation methods able to handle this amount of data
are now required. Here we present a method, SHAPEIT4, which substantially improves
upon other methods to process large genotype and high coverage sequencing datasets.
It notably exhibits sub-linear running times with sample size, provides highly
accurate haplotypes and allows integrating external phasing information such as
large reference panels of haplotypes, collections of pre-phased variants and long
sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate
its performance in terms of accuracy and running times on two gold standard datasets:
the UK Biobank data and the Genome In A Bottle.'
article_number: '5436'
article_processing_charge: No
article_type: original
author:
- first_name: Olivier
full_name: Delaneau, Olivier
last_name: Delaneau
- first_name: Jean-François
full_name: Zagury, Jean-François
last_name: Zagury
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jonathan L.
full_name: Marchini, Jonathan L.
last_name: Marchini
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
citation:
ama: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate,
scalable and integrative haplotype estimation. Nature Communications. 2019;10.
doi:10.1038/s41467-019-13225-y
apa: Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis,
E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y
chicago: Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan
L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative
Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y.
ieee: O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis,
“Accurate, scalable and integrative haplotype estimation,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate,
scalable and integrative haplotype estimation. Nature Communications. 10, 5436.
mla: Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.”
Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y.
short: O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis,
Nature Communications 10 (2019).
date_created: 2020-04-30T10:40:32Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2021-01-12T08:15:01Z
day: '28'
doi: 10.1038/s41467-019-13225-y
extern: '1'
intvolume: ' 10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-13225-y
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Accurate, scalable and integrative haplotype estimation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '7711'
abstract:
- lang: eng
text: The nature and extent of mitochondrial DNA variation in a population and how
it affects traits is poorly understood. Here we resequence the mitochondrial genomes
of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that
stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear
allelic imbalances, thus implying that mitochondrial haplotypes are reflected
in the nuclear genome. However, no major fitness effects are associated with mitonuclear
imbalance, suggesting that such imbalances reflect population structure at the
mitochondrial level rather than genomic incompatibilities. Although mitochondrial
haplotypes have no direct impact on mitochondrial respiration, some haplotypes
are associated with stress- and metabolism-related phenotypes, including food
intake in males. Finally, through reciprocal swapping of mitochondrial genomes,
we demonstrate that a mitochondrial haplotype associated with high food intake
can rescue a low food intake phenotype. Together, our findings provide new insight
into population structure at the mitochondrial level and point to the importance
of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.
article_processing_charge: No
article_type: original
author:
- first_name: Roel P. J.
full_name: Bevers, Roel P. J.
last_name: Bevers
- first_name: Maria
full_name: Litovchenko, Maria
last_name: Litovchenko
- first_name: Adamandia
full_name: Kapopoulou, Adamandia
last_name: Kapopoulou
- first_name: Virginie S.
full_name: Braman, Virginie S.
last_name: Braman
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Johan
full_name: Auwerx, Johan
last_name: Auwerx
- first_name: Brian
full_name: Hollis, Brian
last_name: Hollis
- first_name: Bart
full_name: Deplancke, Bart
last_name: Deplancke
citation:
ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect
metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism.
2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3
apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson,
M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic
phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism.
Springer Nature. https://doi.org/10.1038/s42255-019-0147-3
chicago: Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S.
Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke.
“Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic
Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3.
ieee: R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic
phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism,
vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.
ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J,
Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes
in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.
mla: Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes
in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1,
no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3.
short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson,
J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.
date_created: 2020-04-30T10:40:56Z
date_published: 2019-12-09T00:00:00Z
date_updated: 2021-01-12T08:15:01Z
day: '09'
doi: 10.1038/s42255-019-0147-3
extern: '1'
intvolume: ' 1'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1226-1242
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-020-0202-0
status: public
title: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic
Reference Panel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2019'
...
---
_id: '5'
abstract:
- lang: eng
text: In this paper, we introduce a quantum version of the wonderful compactification
of a group as a certain noncommutative projective scheme. Our approach stems from
the fact that the wonderful compactification encodes the asymptotics of matrix
coefficients, and from its realization as a GIT quotient of the Vinberg semigroup.
In order to define the wonderful compactification for a quantum group, we adopt
a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key
to our construction is a quantum version of the Vinberg semigroup, which we define
as a q-deformation of a certain Rees algebra, compatible with a standard Poisson
structure. Furthermore, we discuss quantum analogues of the stratification of
the wonderful compactification by orbits for a certain group action, and provide
explicit computations in the case of SL2.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Iordan V
full_name: Ganev, Iordan V
id: 447491B8-F248-11E8-B48F-1D18A9856A87
last_name: Ganev
citation:
ama: Ganev IV. The wonderful compactification for quantum groups. Journal of
the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193
apa: Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal
of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193
chicago: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal
of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193.
ieee: I. V. Ganev, “The wonderful compactification for quantum groups,” Journal
of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.
ista: Ganev IV. 2019. The wonderful compactification for quantum groups. Journal
of the London Mathematical Society. 99(3), 778–806.
mla: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal
of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806,
doi:10.1112/jlms.12193.
short: I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.
date_created: 2018-12-11T11:44:06Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-19T10:13:08Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/jlms.12193
external_id:
isi:
- '000470025900008'
file:
- access_level: open_access
checksum: 1be56239b2cd740a0e9a084f773c22f6
content_type: application/pdf
creator: kschuh
date_created: 2020-01-07T13:31:53Z
date_updated: 2020-07-14T12:46:35Z
file_id: '7238'
file_name: 2019_Wiley_Ganev.pdf
file_size: 431754
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 99'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 778-806
publication: Journal of the London Mathematical Society
publication_status: published
publisher: Wiley
publist_id: '8052'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The wonderful compactification for quantum groups
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: 99
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...