---
_id: '7420'
abstract:
- lang: eng
text: β1-integrins mediate cell–matrix interactions and their trafficking is important
in the dynamic regulation of cell adhesion, migration and malignant processes,
including cancer cell invasion. Here, we employ an RNAi screen to characterize
regulators of integrin traffic and identify the association of Golgi-localized
gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role
in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2
limits active β1-integrin levels in focal adhesions and decreases cancer cell
migration and invasion, which is in agreement with its ability to regulate the
dynamics of active integrins. By using the proximity-dependent biotin identification
(BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10,
as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular
accumulation of active β1-integrin, and reduces integrin activity in focal adhesions
and cell migration similarly to GGA2 depletion, indicating that both facilitate
active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are
important specificity determinants for integrin activity-dependent traffic.
article_number: jcs233387
article_processing_charge: No
article_type: original
author:
- first_name: Pranshu
full_name: Sahgal, Pranshu
last_name: Sahgal
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Jaroslav
full_name: Icha, Jaroslav
last_name: Icha
- first_name: Ilkka
full_name: Paatero, Ilkka
last_name: Paatero
- first_name: Hellyeh
full_name: Hamidi, Hellyeh
last_name: Hamidi
- first_name: Antti
full_name: Arjonen, Antti
last_name: Arjonen
- first_name: Mika
full_name: Pietilä, Mika
last_name: Pietilä
- first_name: Anne
full_name: Rokka, Anne
last_name: Rokka
- first_name: Johanna
full_name: Ivaska, Johanna
last_name: Ivaska
citation:
ama: Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent
β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387
apa: Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A.,
… Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387
chicago: Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh
Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and
RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science.
The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.
ieee: P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin
recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists,
2019.
ista: Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka
A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. 132(11), jcs233387.
mla: Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin
Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company
of Biologists, 2019, doi:10.1242/jcs.233387.
short: P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä,
A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).
date_created: 2020-01-30T10:31:42Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-06T15:01:00Z
day: '07'
department:
- _id: MiSi
doi: 10.1242/jcs.233387
external_id:
isi:
- '000473327900017'
pmid:
- '31076515'
intvolume: ' 132'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.233387
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: GGA2 and RAB13 promote activity-dependent β1-integrin recycling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 132
year: '2019'
...
---
_id: '7421'
abstract:
- lang: eng
text: X and Y chromosomes can diverge when rearrangements block recombination between
them. Here we present the first genomic view of a reciprocal translocation that
causes two physically unconnected pairs of chromosomes to be coinherited as sex
chromosomes. In a population of the common frog (Rana temporaria), both pairs
of X and Y chromosomes show extensive sequence differentiation, but not degeneration
of the Y chromosomes. A new method based on gene trees shows both chromosomes
are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical
topologies, showing they have been coinherited since the reciprocal translocation
occurred. Reciprocal translocations can thus reshape sex linkage on a much greater
scale compared with inversions, the type of rearrangement that is much better
known in sex chromosome evolution, and they can greatly amplify the power of sexually
antagonistic selection to drive genomic rearrangement. Two more populations show
evidence of other rearrangements, suggesting that this species has unprecedented
structural polymorphism in its sex chromosomes.
article_processing_charge: No
article_type: original
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Nicolas
full_name: Rodrigues, Nicolas
last_name: Rodrigues
- first_name: Nicolas
full_name: Perrin, Nicolas
last_name: Perrin
- first_name: Mark
full_name: Kirkpatrick, Mark
last_name: Kirkpatrick
citation:
ama: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology.
2019;28(8):1877-1889. doi:10.1111/mec.14990
apa: Toups, M. A., Rodrigues, N., Perrin, N., & Kirkpatrick, M. (2019). A reciprocal
translocation radically reshapes sex‐linked inheritance in the common frog. Molecular
Ecology. Wiley. https://doi.org/10.1111/mec.14990
chicago: Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick.
“A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common
Frog.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14990.
ieee: M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog,” Molecular Ecology,
vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.
ista: Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation
radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology.
28(8), 1877–1889.
mla: Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked
Inheritance in the Common Frog.” Molecular Ecology, vol. 28, no. 8, Wiley,
2019, pp. 1877–89, doi:10.1111/mec.14990.
short: M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28
(2019) 1877–1889.
date_created: 2020-01-30T10:33:05Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-09-06T15:00:13Z
day: '01'
department:
- _id: BeVi
doi: 10.1111/mec.14990
external_id:
isi:
- '000468200800004'
pmid:
- '30576024'
intvolume: ' 28'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: 1877-1889
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: A reciprocal translocation radically reshapes sex‐linked inheritance in the
common frog
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2019'
...
---
_id: '7422'
abstract:
- lang: eng
text: Biochemical reactions often occur at low copy numbers but at once in crowded
and diverse environments. Space and stochasticity therefore play an essential
role in biochemical networks. Spatial-stochastic simulations have become a prominent
tool for understanding how stochasticity at the microscopic level influences the
macroscopic behavior of such systems. While particle-based models guarantee the
level of detail necessary to accurately describe the microscopic dynamics at very
low copy numbers, the algorithms used to simulate them typically imply trade-offs
between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s
Function Reaction Dynamics) is an exact algorithm that evades such trade-offs
by partitioning the N-particle system into M ≤ N analytically tractable one- and
two-particle systems; the analytical solutions (Green’s functions) then are used
to implement an event-driven particle-based scheme that allows particles to make
large jumps in time and space while retaining access to their state variables
at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that
implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based
simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on
2D planes representing membranes, and on 1D elongated cylinders representative
of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion
used to model active transport. We find that, for low particle densities, eGFRD2
is up to 6 orders of magnitude faster than conventional Brownian dynamics. We
exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1
gradient formation, which involves 3D diffusion, active transport on microtubules,
and autophosphorylation on the membrane, confirming recent experimental and theoretical
results on this system to hold under genuinely stochastic conditions.
article_number: '054108'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- 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: Joris
full_name: Paijmans, Joris
last_name: Paijmans
- first_name: Laurens
full_name: Bossen, Laurens
last_name: Bossen
- first_name: Thomas
full_name: Miedema, Thomas
last_name: Miedema
- first_name: Martijn
full_name: Wehrens, Martijn
last_name: Wehrens
- first_name: Nils B.
full_name: Becker, Nils B.
last_name: Becker
- first_name: Kazunari
full_name: Kaizu, Kazunari
last_name: Kaizu
- first_name: Koichi
full_name: Takahashi, Koichi
last_name: Takahashi
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: Pieter Rein
full_name: ten Wolde, Pieter Rein
last_name: ten Wolde
citation:
ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The
Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker,
N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn
Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom,
and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal
of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu
K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal
of Chemical Physics. 150(5), 054108.
mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of
Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker,
K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics
150 (2019).
date_created: 2020-01-30T10:34:36Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-09-06T14:59:28Z
day: '07'
department:
- _id: GaTk
doi: 10.1063/1.5064867
external_id:
arxiv:
- '1708.09364'
isi:
- '000458109300009'
intvolume: ' 150'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.09364
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: eGFRD in all dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2019'
...
---
_id: '7423'
abstract:
- lang: eng
text: 'We compare finite rank perturbations of the following three ensembles of
complex rectangular random matrices: First, a generalised Wishart ensemble with
one random and two fixed correlation matrices introduced by Borodin and Péché,
second, the product of two independent random matrices where one has correlated
entries, and third, the case when the two random matrices become also coupled
through a fixed matrix. The singular value statistics of all three ensembles is
shown to be determinantal and we derive double contour integral representations
for their respective kernels. Three different kernels are found in the limit of
infinite matrix dimension at the origin of the spectrum. They depend on finite
rank perturbations of the correlation and coupling matrices and are shown to be
integrable. The first kernel (I) is found for two independent matrices from the
second, and two weakly coupled matrices from the third ensemble. It generalises
the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel
(III) is obtained for the generalised Wishart ensemble and for two strongly coupled
matrices. It further generalises the perturbed Bessel kernel of Desrosiers and
Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices,
provides an interpolation between the kernels (I) and (III), generalising previous
findings of part of the authors.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gernot
full_name: Akemann, Gernot
last_name: Akemann
- first_name: Tomasz
full_name: Checinski, Tomasz
last_name: Checinski
- first_name: Dangzheng
full_name: Liu, Dangzheng
id: 2F947E34-F248-11E8-B48F-1D18A9856A87
last_name: Liu
- first_name: Eugene
full_name: Strahov, Eugene
last_name: Strahov
citation:
ama: 'Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products
of coupled random matrices: From one correlated to two Wishart ensembles. Annales
de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479.
doi:10.1214/18-aihp888'
apa: 'Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank
perturbations in products of coupled random matrices: From one correlated to two
Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888'
chicago: 'Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov.
“Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated
to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités
et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.'
ieee: 'G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles,”
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol.
55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.'
ista: 'Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles.
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.'
mla: 'Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled
Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de
l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute
of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.'
short: G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri
Poincaré, Probabilités et Statistiques 55 (2019) 441–479.
date_created: 2020-01-30T10:36:50Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-06T14:58:39Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-aihp888
external_id:
arxiv:
- '1704.05224'
isi:
- '000456070200013'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.05224
month: '02'
oa: 1
oa_version: Preprint
page: 441-479
publication: Annales de l'Institut Henri Poincaré, Probabilités et Statistiques
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: 'Finite rank perturbations in products of coupled random matrices: From one
correlated to two Wishart ensembles'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2019'
...
---
_id: '7436'
abstract:
- lang: eng
text: 'For an ordinary K3 surface over an algebraically closed field of positive
characteristic we show that every automorphism lifts to characteristic zero. Moreover,
we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one
correspondence with the Fourier-Mukai partners of the geometric generic fiber
of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai
partners of the K3 surfaces with Picard rank two and with discriminant equal to
minus of a prime number, in terms of the class number of the prime, holds over
a field of positive characteristic as well. We show that the image of the derived
autoequivalence group of a K3 surface of finite height in the group of isometries
of its crystalline cohomology has index at least two. Moreover, we provide a conditional
upper bound on the kernel of this natural cohomological descent map. Further,
we give an extended remark in the appendix on the possibility of an F-crystal
structure on the crystalline cohomology of a K3 surface over an algebraically
closed field of positive characteristic and show that the naive F-crystal structure
fails in being compatible with inner product. '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177
apa: Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive
characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177
chicago: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive
Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177.
ieee: T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,”
Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.
ista: Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 24, 1135–1177.
mla: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.”
Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.
short: T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.
date_created: 2020-02-02T23:01:06Z
date_published: 2019-05-20T00:00:00Z
date_updated: 2023-10-17T07:42:21Z
day: '20'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.25537/dm.2019v24.1135-1177
external_id:
arxiv:
- '1809.08970'
isi:
- '000517806400019'
file:
- access_level: open_access
checksum: 9a1a64bd49ab03fa4f738fb250fc4f90
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T06:26:12Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7438'
file_name: 2019_DocumMath_Srivastava.pdf
file_size: 469730
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1135-1177
publication: Documenta Mathematica
publication_identifier:
eissn:
- 1431-0643
issn:
- 1431-0635
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On derived equivalences of k3 surfaces in positive characteristic
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: 24
year: '2019'
...
---
_id: '7437'
abstract:
- lang: eng
text: 'Most of today''s distributed machine learning systems assume reliable networks:
whenever two machines exchange information (e.g., gradients or models), the network
should guarantee the delivery of the message. At the same time, recent work exhibits
the impressive tolerance of machine learning algorithms to errors or noise arising
from relaxed communication or synchronization. In this paper, we connect these
two trends, and consider the following question: Can we design machine learning
systems that are tolerant to network unreliability during training? With this
motivation, we focus on a theoretical problem of independent interest-given a
standard distributed parameter server architecture, if every communication between
the worker and the server has a non-zero probability p of being dropped, does
there exist an algorithm that still converges, and at what speed? The technical
contribution of this paper is a novel theoretical analysis proving that distributed
learning over unreliable network can achieve comparable convergence rate to centralized
or distributed learning over reliable networks. Further, we prove that the influence
of the packet drop rate diminishes with the growth of the number of parameter
servers. We map this theoretical result onto a real-world scenario, training deep
neural networks over an unreliable network layer, and conduct network simulation
to validate the system improvement by allowing the networks to be unreliable.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Chen
full_name: Yu, Chen
last_name: Yu
- first_name: Hanlin
full_name: Tang, Hanlin
last_name: Tang
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
- first_name: Simon
full_name: Kassing, Simon
last_name: Kassing
- first_name: Ankit
full_name: Singla, Ankit
last_name: Singla
- 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: Ce
full_name: Zhang, Ce
last_name: Zhang
- first_name: Ji
full_name: Liu, Ji
last_name: Liu
citation:
ama: 'Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks.
In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June.
IMLS; 2019:12481-12512.'
apa: 'Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., …
Liu, J. (2019). Distributed learning over unreliable networks. In 36th International
Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512).
Long Beach, CA, United States: IMLS.'
chicago: Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian
Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.”
In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512.
IMLS, 2019.
ieee: C. Yu et al., “Distributed learning over unreliable networks,” in 36th
International Conference on Machine Learning, ICML 2019, Long Beach, CA, United
States, 2019, vol. 2019–June, pp. 12481–12512.
ista: 'Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu
J. 2019. Distributed learning over unreliable networks. 36th International Conference
on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning
vol. 2019–June, 12481–12512.'
mla: Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International
Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp.
12481–512.
short: C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang,
J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS,
2019, pp. 12481–12512.
conference:
end_date: 2019-06-15
location: Long Beach, CA, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2019-06-10
date_created: 2020-02-02T23:01:06Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-06T15:21:48Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1810.07766'
isi:
- '000684034307036'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.07766
month: '06'
oa: 1
oa_version: Preprint
page: 12481-12512
publication: 36th International Conference on Machine Learning, ICML 2019
publication_identifier:
isbn:
- '9781510886988'
publication_status: published
publisher: IMLS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed learning over unreliable networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2019-June
year: '2019'
...
---
_id: '7451'
abstract:
- lang: eng
text: We prove that the observable telegraph signal accompanying the bistability
in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings
model is the finite-size precursor of what in the thermodynamic limit is a genuine
first-order phase transition. We construct a finite-size scaling of the system
parameters to a well-defined thermodynamic limit, in which the system remains
the same microscopic system, but the telegraph signal becomes macroscopic both
in its timescale and intensity. The existence of such a finite-size scaling completes
and justifies the classification of the photon-blockade-breakdown effect as a
first-order dissipative quantum phase transition.
article_number: '150'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Vukics, A.
last_name: Vukics
- first_name: A.
full_name: Dombi, A.
last_name: Dombi
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: P.
full_name: Domokos, P.
last_name: Domokos
citation:
ama: Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade
breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150
apa: Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling
of the photon-blockade breakdown dissipative quantum phase transition. Quantum.
Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften.
https://doi.org/10.22331/q-2019-06-03-150
chicago: Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling
of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum.
Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften,
2019. https://doi.org/10.22331/q-2019-06-03-150.
ieee: A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the
photon-blockade breakdown dissipative quantum phase transition,” Quantum,
vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften,
2019.
ista: Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade
breakdown dissipative quantum phase transition. Quantum. 3, 150.
mla: Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative
Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des
Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150.
short: A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).
date_created: 2020-02-05T09:57:57Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-09-07T14:57:39Z
day: '03'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.22331/q-2019-06-03-150
external_id:
arxiv:
- '1809.09737'
isi:
- '000469987500004'
file:
- access_level: open_access
checksum: 26b9ba8f0155d183f1ee55295934a17f
content_type: application/pdf
creator: dernst
date_created: 2020-02-11T09:25:23Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7483'
file_name: 2019_Quantum_Vukics.pdf
file_size: 5805248
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Quantum
publication_identifier:
issn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
status: public
title: Finite-size scaling of the photon-blockade breakdown dissipative quantum phase
transition
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: 3
year: '2019'
...
---
_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'
...